Psyllid ID: psy9277

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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-------18
Protein Sequence
MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQAN
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEccccccHHHHHHHHHHHHcccccccEEEEEEcccHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHcccccEEEcccHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHcccEEEccccccccccHHHccccHHHHHHHHHcccccccccHHHHHHHHHccccEEEEccccHHHHHHHHHHHHHHcccccccccEEEEcccHHHHHHHHHHHHHHcccccccEEEEcccccHHHHHHHHHHccEEEEEccHHHHHHHHHcccEEEEEccc
Coil and Loop (DISEMBL)
maaggsritkkvipedlsnvefetsedvevvstfdnmglREDLLRGIYAygfekpsaiqqrsikpivkgRDVIAqaqsgtgktaTFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDfmnvqchaciggtnlsedlrkldygqhvvsgtpgrVFDMIrssqgrrttnqan
Flexible Loop (DISEMBL)
maaggsritkkvipedlsnvefetsedvevvstfdnmgLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAqsgtgktatFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGqhvvsgtpgrvfdmirssqgrrttnqan
Low Complexity Region (SEG)
MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQAN
Disordered region (IsUnstruct)
*************************EDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD***************
Disordered Region (DISOPRED)
************************SEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR*******
Disordered Region (DISEMBL)
********TKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS**********
Disordered Region (DISPRO)
*******ITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQA*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQAN
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	178	2.2.26 [Sep-21-2011]
Q3B8Q2	411	Eukaryotic initiation fac	yes	N/A	0.932	0.403	0.783	8e-74
A6M931	411	Eukaryotic initiation fac	yes	N/A	0.932	0.403	0.783	8e-74
Q2NL22	411	Eukaryotic initiation fac	yes	N/A	0.932	0.403	0.783	8e-74
P38919	411	Eukaryotic initiation fac	yes	N/A	0.932	0.403	0.783	9e-74
Q91VC3	411	Eukaryotic initiation fac	yes	N/A	0.932	0.403	0.777	1e-73
Q4R3Q1	411	Eukaryotic initiation fac	N/A	N/A	0.932	0.403	0.771	1e-72
Q5ZM36	412	Eukaryotic initiation fac	yes	N/A	0.915	0.395	0.783	2e-72
B5FZY7	410	Eukaryotic initiation fac	yes	N/A	0.882	0.382	0.808	2e-72
Q7ZVA6	406	Eukaryotic initiation fac	yes	N/A	0.960	0.421	0.738	6e-72
Q5U526	415	Eukaryotic initiation fac	N/A	N/A	0.904	0.387	0.774	7e-72

>sp|Q3B8Q2|IF4A3_RAT Eukaryotic initiation factor 4A-III OS=Rattus norvegicus GN=Eif4a3 PE=1 SV=1

 Score =  275 bits (704), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.
Rattus norvegicus (taxid: 10116)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|A6M931|IF4A3_PIG Eukaryotic initiation factor 4A-III OS=Sus scrofa GN=EIF4A3 PE=2 SV=1

 Score =  275 bits (704), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Sus scrofa (taxid: 9823)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2NL22|IF4A3_BOVIN Eukaryotic initiation factor 4A-III OS=Bos taurus GN=EIF4A3 PE=2 SV=3

 Score =  275 bits (704), Expect = 8e-74,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P38919|IF4A3_HUMAN Eukaryotic initiation factor 4A-III OS=Homo sapiens GN=EIF4A3 PE=1 SV=4

 Score =  275 bits (704), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q91VC3|IF4A3_MOUSE Eukaryotic initiation factor 4A-III OS=Mus musculus GN=Eif4a3 PE=2 SV=3

 Score =  275 bits (702), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 129/166 (77%), Positives = 147/166 (88%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFS+S+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q4R3Q1|IF4A3_MACFA Eukaryotic initiation factor 4A-III OS=Macaca fascicularis GN=EIF4A3 PE=2 SV=3

 Score =  272 bits (695), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 128/166 (77%), Positives = 145/166 (87%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+P RELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPARELAVQIQKGL 126

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           L LGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LTLGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH/RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH/RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed.

Macaca fascicularis (taxid: 9541)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5ZM36|IF4A3_CHICK Eukaryotic initiation factor 4A-III OS=Gallus gallus GN=EIF4A3 PE=2 SV=1

 Score =  271 bits (693), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 146/166 (87%), Gaps = 3/166 (1%)

Query: 6   SRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP 65
            RI K+   ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK 
Sbjct: 16  KRIMKE---EDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQ 72

Query: 66  IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD 125
           I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +LALGD
Sbjct: 73  IIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGD 132

Query: 126 FMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
           +MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR    R
Sbjct: 133 YMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLR 178

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|B5FZY7|IF4A3_TAEGU Eukaryotic initiation factor 4A-III OS=Taeniopygia guttata GN=EIF4A3 PE=2 SV=1

 Score =  271 bits (693), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 127/157 (80%), Positives = 142/157 (90%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIA
Sbjct: 20  EDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIA 79

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           Q+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +LALGD+MNVQCHAC
Sbjct: 80  QSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHAC 139

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
           IGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR    R
Sbjct: 140 IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLR 176

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Taeniopygia guttata (taxid: 59729)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q7ZVA6|IF4A3_DANRE Eukaryotic initiation factor 4A-III OS=Danio rerio GN=eif4a3 PE=2 SV=1

 Score =  269 bits (688), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 127/172 (73%), Positives = 148/172 (86%), Gaps = 1/172 (0%)

Query: 1   MAAGGSRITKKVIPE-DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQ 59
           MA     + K+++ E D++ +EFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQ
Sbjct: 1   MATAVVPVRKRILKEEDMTKIEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQ 60

Query: 60  QRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV 119
           QR+IK I+KGRDVIAQ+QSGTGKTATF +S+LQ LD Q+RETQ L L+PTRELA QIQKV
Sbjct: 61  QRAIKQIIKGRDVIAQSQSGTGKTATFCVSVLQCLDIQVRETQALILAPTRELAGQIQKV 120

Query: 120 VLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
           +LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR    R
Sbjct: 121 LLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLR 172

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5U526|I4A3A_XENLA Eukaryotic initiation factor 4A-III-A OS=Xenopus laevis GN=eif4a3-a PE=2 SV=1

 Score =  269 bits (687), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 127/164 (77%), Positives = 146/164 (89%), Gaps = 3/164 (1%)

Query: 3   AGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRS 62
           AG  R+ ++   ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQR+
Sbjct: 16  AGRKRLLRE---EDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRA 72

Query: 63  IKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLA 122
           IK I+KGRDVIAQ+QSGTGKTATF +S+LQ LD Q+RETQ L L+PTRELA QIQKV+LA
Sbjct: 73  IKQIIKGRDVIAQSQSGTGKTATFCVSVLQCLDIQVRETQALILAPTRELAGQIQKVLLA 132

Query: 123 LGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 133 LGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 176

ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. When overexpressed, induces epidermis in dissociated cells that would otherwise adopt a neural fate, a process that requires an active BMP signaling pathway. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions.

Xenopus laevis (taxid: 8355)

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	178
156543906	319	PREDICTED: eukaryotic initiation factor	0.932	0.520	0.873	1e-79
389609093	405	DEAD box ATP-dependent RNA helicase [Pap	0.932	0.409	0.849	1e-78
118783118	400	AGAP003089-PA [Anopheles gambiae str. PE	0.853	0.38	0.921	2e-78
322788219	423	hypothetical protein SINV_14366 [Solenop	0.915	0.385	0.855	2e-78
312377148	400	hypothetical protein AND_11649 [Anophele	0.853	0.38	0.914	2e-78
307169387	402	Eukaryotic initiation factor 4A-III [Cam	0.915	0.405	0.855	3e-78
242024557	407	DEAD box ATP-dependent RNA helicase, put	0.853	0.373	0.921	3e-78
340714648	403	PREDICTED: eukaryotic initiation factor	0.853	0.377	0.914	4e-78
48136057	403	PREDICTED: eukaryotic initiation factor	0.853	0.377	0.914	4e-78
332027726	366	Eukaryotic initiation factor 4A-III [Acr	0.853	0.415	0.914	4e-78

>gi|156543906|ref|XP_001607077.1| PREDICTED: eukaryotic initiation factor 4A-III-like [Nasonia vitripennis]

 Score =  300 bits (769), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 145/166 (87%), Positives = 153/166 (92%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA G SR       EDLSNVEFETSEDVEV+ TFDNMGLR++LLRGIYAYGFEKPSAIQQ
Sbjct: 1   MAEGRSRRVPAAQNEDLSNVEFETSEDVEVIPTFDNMGLRDELLRGIYAYGFEKPSAIQQ 60

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           RSIKPI+KGRDVIAQAQSGTGKTATFSI+ILQSLDTQLRETQVL LSPTRELA QIQKV+
Sbjct: 61  RSIKPIMKGRDVIAQAQSGTGKTATFSIAILQSLDTQLRETQVLVLSPTRELATQIQKVI 120

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGDFMNVQCHACIGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 121 LALGDFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 166

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389609093|dbj|BAM18158.1| DEAD box ATP-dependent RNA helicase [Papilio xuthus] gi|389610941|dbj|BAM19081.1| DEAD box ATP-dependent RNA helicase [Papilio polytes]

 Score =  297 bits (761), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 141/166 (84%), Positives = 152/166 (91%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           M +      +K+I EDLSNVEF+TSEDVEV+ TFD+MGLR++LLRGIY YGFEKPSAIQQ
Sbjct: 1   MTSSEVSFNRKIISEDLSNVEFDTSEDVEVIPTFDSMGLRDELLRGIYTYGFEKPSAIQQ 60

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           RSI+PIVKGRDVIAQAQSGTGKTATFSISILQSLDT LRETQVL LSPTRELA QIQKV+
Sbjct: 61  RSIQPIVKGRDVIAQAQSGTGKTATFSISILQSLDTTLRETQVLVLSPTRELATQIQKVI 120

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGDFMNVQCHACIGGTNL ED+RKLDYGQHVVSGTPGRVFDMIR
Sbjct: 121 LALGDFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIR 166

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|118783118|ref|XP_312776.3| AGAP003089-PA [Anopheles gambiae str. PEST] gi|116129059|gb|EAA08469.4| AGAP003089-PA [Anopheles gambiae str. PEST]

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 140/152 (92%), Positives = 149/152 (98%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           EDLSNVEFETSEDVEV+ TF++MGLRE+LLRGIYAYGFEKPSAIQQRSI+PIVKGRDVIA
Sbjct: 10  EDLSNVEFETSEDVEVLPTFNSMGLREELLRGIYAYGFEKPSAIQQRSIQPIVKGRDVIA 69

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKTATFSISILQS+DT LRETQVLCLSPTRELAVQIQKV+LALGDFMNVQCHAC
Sbjct: 70  QAQSGTGKTATFSISILQSMDTTLRETQVLCLSPTRELAVQIQKVILALGDFMNVQCHAC 129

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           IGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 130 IGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 161

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322788219|gb|EFZ14001.1| hypothetical protein SINV_14366 [Solenopsis invicta]

 Score =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 142/166 (85%), Positives = 153/166 (92%), Gaps = 3/166 (1%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA    R+ +    EDLSNVEFETSEDVEV+ TFDNMGLR++LLRGIYAYGFEKPSAIQQ
Sbjct: 22  MAEKSRRVAQT---EDLSNVEFETSEDVEVIPTFDNMGLRDELLRGIYAYGFEKPSAIQQ 78

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           RSIKPI+KGRDVIAQAQSGTGKTATFSI+ILQSLDTQ+RETQVL LSPTRELA QIQKV+
Sbjct: 79  RSIKPIMKGRDVIAQAQSGTGKTATFSIAILQSLDTQVRETQVLVLSPTRELATQIQKVI 138

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGDFMNVQCHACIGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 139 LALGDFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 184

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312377148|gb|EFR24056.1| hypothetical protein AND_11649 [Anopheles darlingi]

 Score =  296 bits (758), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 139/152 (91%), Positives = 149/152 (98%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           EDLSNVEFETSEDVEV+ TF++MGLRE+LLRGIYAYGFEKPSAIQQRSI+PIVKGRDVIA
Sbjct: 10  EDLSNVEFETSEDVEVLPTFNSMGLREELLRGIYAYGFEKPSAIQQRSIQPIVKGRDVIA 69

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKTATFSISILQS+DT LRETQVLCLSPTRELAVQIQKV+LALGDFMN+QCHAC
Sbjct: 70  QAQSGTGKTATFSISILQSMDTTLRETQVLCLSPTRELAVQIQKVILALGDFMNIQCHAC 129

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           IGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 130 IGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 161

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307169387|gb|EFN62107.1| Eukaryotic initiation factor 4A-III [Camponotus floridanus]

 Score =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 142/166 (85%), Positives = 153/166 (92%), Gaps = 3/166 (1%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA    R+ +    EDLSNVEFETSEDVEV+ TFDNMGLR++LLRGIYAYGFEKPSAIQQ
Sbjct: 1   MADKSRRVAQT---EDLSNVEFETSEDVEVIPTFDNMGLRDELLRGIYAYGFEKPSAIQQ 57

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           RSIKPI+KGRDVIAQAQSGTGKTATFSI+ILQSLDTQ+RETQVL LSPTRELA QIQKV+
Sbjct: 58  RSIKPIMKGRDVIAQAQSGTGKTATFSIAILQSLDTQVRETQVLVLSPTRELATQIQKVI 117

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGDFMNVQCHACIGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 118 LALGDFMNVQCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 163

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242024557|ref|XP_002432694.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis] gi|212518164|gb|EEB19956.1| DEAD box ATP-dependent RNA helicase, putative [Pediculus humanus corporis]

 Score =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 140/152 (92%), Positives = 147/152 (96%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           EDLS VEFETSEDVEV+ TFD MGLRE+LLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA
Sbjct: 17  EDLSLVEFETSEDVEVIPTFDRMGLREELLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 76

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKTATFSISI+QSLDT +RETQVLCLSPTRELAVQIQKV+LALGDFMNVQCHAC
Sbjct: 77  QAQSGTGKTATFSISIIQSLDTTVRETQVLCLSPTRELAVQIQKVILALGDFMNVQCHAC 136

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           IGGTNL ED+RKLDYGQHV+SGTPGRVFDMIR
Sbjct: 137 IGGTNLGEDIRKLDYGQHVISGTPGRVFDMIR 168

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714648|ref|XP_003395838.1| PREDICTED: eukaryotic initiation factor 4A-III-like [Bombus terrestris] gi|350410965|ref|XP_003489194.1| PREDICTED: eukaryotic initiation factor 4A-III-like [Bombus impatiens] gi|383854330|ref|XP_003702674.1| PREDICTED: eukaryotic initiation factor 4A-III-like [Megachile rotundata]

 Score =  295 bits (756), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 139/152 (91%), Positives = 148/152 (97%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           EDLSNVEFETSEDVEV+ TFDNMGLR++LLRGIYAYGFEKPSAIQQRSIKPI+KGRDVIA
Sbjct: 13  EDLSNVEFETSEDVEVIPTFDNMGLRDELLRGIYAYGFEKPSAIQQRSIKPIMKGRDVIA 72

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKTATFSI+ILQSLDTQ+RETQVL LSPTRELA QIQKV+LALGDFMNVQCHAC
Sbjct: 73  QAQSGTGKTATFSIAILQSLDTQVRETQVLVLSPTRELATQIQKVILALGDFMNVQCHAC 132

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           IGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 133 IGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 164

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|48136057|ref|XP_393356.1| PREDICTED: eukaryotic initiation factor 4A-III-like isoform 1 [Apis mellifera] gi|380025932|ref|XP_003696717.1| PREDICTED: eukaryotic initiation factor 4A-III-like [Apis florea]

 Score =  295 bits (756), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 139/152 (91%), Positives = 148/152 (97%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           EDLSNVEFETSEDVEV+ TFDNMGLR++LLRGIYAYGFEKPSAIQQRSIKPI+KGRDVIA
Sbjct: 13  EDLSNVEFETSEDVEVIPTFDNMGLRDELLRGIYAYGFEKPSAIQQRSIKPIMKGRDVIA 72

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKTATFSI+ILQSLDTQ+RETQVL LSPTRELA QIQKV+LALGDFMNVQCHAC
Sbjct: 73  QAQSGTGKTATFSIAILQSLDTQVRETQVLVLSPTRELATQIQKVILALGDFMNVQCHAC 132

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           IGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 133 IGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 164

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027726|gb|EGI67794.1| Eukaryotic initiation factor 4A-III [Acromyrmex echinatior]

 Score =  295 bits (756), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 139/152 (91%), Positives = 148/152 (97%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
           EDLSNVEFETSEDVEV+ TFDNMGLR++LLRGIYAYGFEKPSAIQQRSIKPI+KGRDVIA
Sbjct: 12  EDLSNVEFETSEDVEVIPTFDNMGLRDELLRGIYAYGFEKPSAIQQRSIKPIMKGRDVIA 71

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKTATFSI+ILQSLDTQ+RETQVL LSPTRELA QIQKV+LALGDFMNVQCHAC
Sbjct: 72  QAQSGTGKTATFSIAILQSLDTQVRETQVLVLSPTRELATQIQKVILALGDFMNVQCHAC 131

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           IGGTNL ED+RKLDYGQHVVSGTPGRVFDMI+
Sbjct: 132 IGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIK 163

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

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	178
FB|FBgn0037573	399	eIF4AIII "eIF4AIII" [Drosophil	0.882	0.393	0.872	3.8e-69
WB|WBGene00018007	399	F33D11.10 [Caenorhabditis eleg	0.882	0.393	0.834	1.1e-66
WB|WBGene00022029	399	Y65B4A.6 [Caenorhabditis elega	0.853	0.380	0.848	4.5e-66
UNIPROTKB|Q2NL22	411	EIF4A3 "Eukaryotic initiation	0.932	0.403	0.783	5.8e-66
UNIPROTKB|E2RDZ4	411	EIF4A3 "Uncharacterized protei	0.932	0.403	0.783	5.8e-66
UNIPROTKB|P38919	411	EIF4A3 "Eukaryotic initiation	0.932	0.403	0.783	5.8e-66
UNIPROTKB|A6M931	411	EIF4A3 "Eukaryotic initiation	0.932	0.403	0.783	5.8e-66
RGD|1591139	411	Eif4a3 "eukaryotic translation	0.932	0.403	0.783	5.8e-66
UNIPROTKB|Q5ZM36	412	EIF4A3 "Eukaryotic initiation	0.904	0.390	0.786	5.2e-65
ZFIN|ZDB-GENE-040426-915	406	eif4a3 "eukaryotic translation	0.932	0.408	0.754	1.1e-64

FB|FBgn0037573 eIF4AIII "eIF4AIII" [Drosophila melanogaster (taxid:7227)]

 Score = 701 (251.8 bits), Expect = 3.8e-69, P = 3.8e-69
 Identities = 137/157 (87%), Positives = 145/157 (92%)

Query:    10 KKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG 69
             K    EDLSNVEFETSEDVEV+ TF+ M L+E+LLRGIYAYGFEKPSAIQQRSI PIVKG
Sbjct:     4 KNAQAEDLSNVEFETSEDVEVIPTFNAMNLKEELLRGIYAYGFEKPSAIQQRSITPIVKG 63

Query:    70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV 129
             RDVIAQAQSGTGKTATFSISILQSLDT LRETQVLCLSPTRELAVQIQKV+LALGD MNV
Sbjct:    64 RDVIAQAQSGTGKTATFSISILQSLDTTLRETQVLCLSPTRELAVQIQKVILALGDMMNV 123

Query:   130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             QCH CIGGTNL ED+RKLDYGQH+VSGTPGRVFDMI+
Sbjct:   124 QCHVCIGGTNLGEDIRKLDYGQHIVSGTPGRVFDMIK 160

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

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

GO:0006413 "translational initiation" evidence=ISS

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

GO:0005524 "ATP binding" evidence=IEA

GO:0045495 "pole plasm" evidence=IDA

GO:0045451 "pole plasm oskar mRNA localization" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

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

GO:0006974 "response to DNA damage stimulus" evidence=IMP

GO:0008380 "RNA splicing" evidence=IMP

WB|WBGene00018007 F33D11.10 [Caenorhabditis elegans (taxid:6239)]

 Score = 678 (243.7 bits), Expect = 1.1e-66, P = 1.1e-66
 Identities = 131/157 (83%), Positives = 144/157 (91%)

Query:    10 KKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG 69
             KK   +D++ VEFE+SE+V V+ TFD MGLREDLLRGIYAYGFEKPSAIQQR++  I+K 
Sbjct:     4 KKAEKDDMATVEFESSEEVNVIPTFDKMGLREDLLRGIYAYGFEKPSAIQQRAVPAILKA 63

Query:    70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV 129
             RDVIAQAQSGTGKTATFSIS+LQSLDTQ+RETQ L LSPTRELAVQIQKVVLALGD+MNV
Sbjct:    64 RDVIAQAQSGTGKTATFSISVLQSLDTQVRETQALILSPTRELAVQIQKVVLALGDYMNV 123

Query:   130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             QCHACIGGTNL ED+RKLDYGQHVVSGTPGRVFDMIR
Sbjct:   124 QCHACIGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIR 160

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0001703 "gastrulation with mouth forming first" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0051301 "cell division" evidence=IMP

GO:0000910 "cytokinesis" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

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

WB|WBGene00022029 Y65B4A.6 [Caenorhabditis elegans (taxid:6239)]

 Score = 672 (241.6 bits), Expect = 4.5e-66, P = 4.5e-66
 Identities = 129/152 (84%), Positives = 142/152 (93%)

Query:    15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
             +D++ VEFE+SE+V ++ TFD MGLREDLLRGIYAYGFEKPSAIQQR+I  I+K RDVIA
Sbjct:     9 DDMATVEFESSEEVSIIPTFDKMGLREDLLRGIYAYGFEKPSAIQQRAIPAILKARDVIA 68

Query:    75 QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
             QAQSGTGKTATFSIS+LQSLDTQ+RETQ L LSPTRELAVQIQKVVLALGD+MNVQCHAC
Sbjct:    69 QAQSGTGKTATFSISVLQSLDTQVRETQALILSPTRELAVQIQKVVLALGDYMNVQCHAC 128

Query:   135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             IGGTNL ED+RKLDYGQHVVSGTPGRVFDMIR
Sbjct:   129 IGGTNLGEDIRKLDYGQHVVSGTPGRVFDMIR 160

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0018991 "oviposition" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0018996 "molting cycle, collagen and cuticulin-based cuticle" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0040020 "regulation of meiosis" evidence=IMP

GO:0007281 "germ cell development" evidence=IMP

UNIPROTKB|Q2NL22 EIF4A3 "Eukaryotic initiation factor 4A-III" [Bos taurus (taxid:9913)]

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query:     1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
             MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct:     7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query:    61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
             R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct:    67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query:   121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|E2RDZ4 EIF4A3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query:     1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
             MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct:     7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query:    61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
             R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct:    67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query:   121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|P38919 EIF4A3 "Eukaryotic initiation factor 4A-III" [Homo sapiens (taxid:9606)]

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query:     1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
             MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct:     7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query:    61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
             R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct:    67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query:   121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

GO:0006364 "rRNA processing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IMP

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

GO:0035145 "exon-exon junction complex" evidence=IDA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IMP;TAS

GO:0005515 "protein binding" evidence=IPI

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

GO:0005524 "ATP binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

GO:0017148 "negative regulation of translation" evidence=IDA

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

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

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

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

UNIPROTKB|A6M931 EIF4A3 "Eukaryotic initiation factor 4A-III" [Sus scrofa (taxid:9823)]

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query:     1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
             MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct:     7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query:    61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
             R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct:    67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query:   121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

GO:0016607 "nuclear speck" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

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

RGD|1591139 Eif4a3 "eukaryotic translation initiation factor 4A, isoform 3" [Rattus norvegicus (taxid:10116)]

 Score = 671 (241.3 bits), Expect = 5.8e-66, P = 5.8e-66
 Identities = 130/166 (78%), Positives = 147/166 (88%)

Query:     1 MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
             MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct:     7 MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66

Query:    61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
             R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct:    67 RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126

Query:   121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008143 "poly(A) RNA binding" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

GO:0017148 "negative regulation of translation" evidence=IEA

GO:0035145 "exon-exon junction complex" evidence=IEA

GO:0045727 "positive regulation of translation" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0048026 "positive regulation of mRNA splicing, via spliceosome" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0071013 "catalytic step 2 spliceosome" evidence=IEA

UNIPROTKB|Q5ZM36 EIF4A3 "Eukaryotic initiation factor 4A-III" [Gallus gallus (taxid:9031)]

 Score = 662 (238.1 bits), Expect = 5.2e-65, P = 5.2e-65
 Identities = 129/164 (78%), Positives = 148/164 (90%)

Query:     4 GGSRITKKVIPE-DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRS 62
             G +R  K+++ E D++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQR+
Sbjct:    12 GSAR--KRIMKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRA 69

Query:    63 IKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLA 122
             IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +LA
Sbjct:    70 IKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLA 129

Query:   123 LGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             LGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   130 LGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 173

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

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016607 "nuclear speck" evidence=IEA

ZFIN|ZDB-GENE-040426-915 eif4a3 "eukaryotic translation initiation factor 4A, isoform 3" [Danio rerio (taxid:7955)]

 Score = 659 (237.0 bits), Expect = 1.1e-64, P = 1.1e-64
 Identities = 126/167 (75%), Positives = 147/167 (88%)

Query:     1 MAAGGSRITKKVIPE-DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQ 59
             MA     + K+++ E D++ +EFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQ
Sbjct:     1 MATAVVPVRKRILKEEDMTKIEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQ 60

Query:    60 QRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV 119
             QR+IK I+KGRDVIAQ+QSGTGKTATF +S+LQ LD Q+RETQ L L+PTRELA QIQKV
Sbjct:    61 QRAIKQIIKGRDVIAQSQSGTGKTATFCVSVLQCLDIQVRETQALILAPTRELAGQIQKV 120

Query:   120 VLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             +LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct:   121 LLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 167

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0051028 "mRNA transport" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006417 "regulation of translation" evidence=IEA

GO:0016607 "nuclear speck" 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)
P0CQ72	FAL1_CRYNJ	3, ., 6, ., 4, ., 1, 3	0.7733	0.8426	0.3787	yes	N/A
Q4IAA0	FAL1_GIBZE	3, ., 6, ., 4, ., 1, 3	0.7236	0.8539	0.3790	yes	N/A
A6M931	IF4A3_PIG	3, ., 6, ., 4, ., 1, 3	0.7831	0.9325	0.4038	yes	N/A
B5FZY7	IF4A3_TAEGU	3, ., 6, ., 4, ., 1, 3	0.8089	0.8820	0.3829	yes	N/A
Q55D61	IF4A_DICDI	3, ., 6, ., 4, ., 1, 3	0.7183	0.7977	0.3506	yes	N/A
Q5AUL4	FAL1_EMENI	3, ., 6, ., 4, ., 1, 3	0.7302	0.8539	0.3809	yes	N/A
Q2NL22	IF4A3_BOVIN	3, ., 6, ., 4, ., 1, 3	0.7831	0.9325	0.4038	yes	N/A
Q2UAK1	FAL1_ASPOR	3, ., 6, ., 4, ., 1, 3	0.7302	0.8539	0.3819	yes	N/A
Q91VC3	IF4A3_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7771	0.9325	0.4038	yes	N/A
A5AAE5	FAL1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.7302	0.8539	0.3809	yes	N/A
Q7ZVA6	IF4A3_DANRE	3, ., 6, ., 4, ., 1, 3	0.7383	0.9606	0.4211	yes	N/A
P38919	IF4A3_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7831	0.9325	0.4038	yes	N/A
Q5ZM36	IF4A3_CHICK	3, ., 6, ., 4, ., 1, 3	0.7831	0.9157	0.3956	yes	N/A
B7ZTW1	IF4A3_XENTR	3, ., 6, ., 4, ., 1, 3	0.7757	0.9101	0.3903	yes	N/A
Q6C347	FAL1_YARLI	3, ., 6, ., 4, ., 1, 3	0.7210	0.8258	0.3702	yes	N/A
Q3B8Q2	IF4A3_RAT	3, ., 6, ., 4, ., 1, 3	0.7831	0.9325	0.4038	yes	N/A
Q10I26	RH34_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6708	0.8651	0.3811	yes	N/A
Q5VNM3	RH2_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.6708	0.8651	0.3811	yes	N/A
Q10055	FAL1_SCHPO	3, ., 6, ., 4, ., 1, 3	0.7388	0.8820	0.3984	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.824
3rd Layer	3.6.4	0.766

---

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	178
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	9e-73
cd00268	203	cd00268, DEADc, DEAD-box helicases	4e-68
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	3e-45
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-35
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-30
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	8e-30
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-28
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	2e-26
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-23
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-22
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-22
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	3e-17
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	5e-17
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	3e-16
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-15
COG1205	851	COG1205, COG1205, Distinct helicase family with a	8e-05
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	5e-04
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	0.001
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	0.001

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

 Score =  223 bits (571), Expect = 9e-73
 Identities = 95/152 (62%), Positives = 115/152 (75%), Gaps = 1/152 (0%)

Query: 14  PEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVI 73
            +  S    E++ D E+V +FD + L EDLLRGIY+YGFEKPSAIQQR IKPI+ G D I
Sbjct: 11  EQVASTGTIESNYD-EIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTI 69

Query: 74  AQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA 133
            QAQSGTGKTATF I+ LQ +D  L   Q L L+PTRELA QIQKVVLALGD++ V+CHA
Sbjct: 70  GQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHA 129

Query: 134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
           C+GGT + +D+ KL  G H+V GTPGRV+DMI
Sbjct: 130 CVGGTVVRDDINKLKAGVHMVVGTPGRVYDMI 161

Length = 401

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

 Score =  205 bits (525), Expect = 4e-68
 Identities = 68/135 (50%), Positives = 92/135 (68%), Gaps = 2/135 (1%)

Query: 34  FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
           F+ +GL  +LLRGIYA GFEKP+ IQ R+I P++ GRDVI QAQ+G+GKTA F I IL+ 
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 94  LDTQLR--ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
           LD   +    Q L L+PTRELA+QI +V   LG   N++     GGT++ + +RKL  G 
Sbjct: 61  LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120

Query: 152 HVVSGTPGRVFDMIR 166
           H+V  TPGR+ D++ 
Sbjct: 121 HIVVATPGRLLDLLE 135

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 =  154 bits (392), Expect = 3e-45
 Identities = 53/162 (32%), Positives = 90/162 (55%), Gaps = 3/162 (1%)

Query: 8   ITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV 67
              + +    ++    +  + +    F ++GL  +LL+ +   GFE+P+ IQ  +I  I+
Sbjct: 5   DYDRFVKLKSAHNVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLIL 64

Query: 68  KGRDVIAQAQSGTGKTATFSISILQSLD--TQLRETQVLCLSPTRELAVQIQKVVLALGD 125
            GRDV+ QAQ+GTGKTA F + +LQ +    + +    L L+PTRELAVQI + +  LG 
Sbjct: 65  AGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGK 124

Query: 126 FM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
            +  ++     GG ++ + +  L  G  +V  TPGR+ D+I+
Sbjct: 125 NLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIK 166

Length = 513

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

 Score =  121 bits (305), Expect = 2e-35
 Identities = 46/113 (40%), Positives = 70/113 (61%), Gaps = 1/113 (0%)

Query: 56  SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ 115
           + IQ ++I  I+ G+DV+ QA +G+GKT  F + ILQ+L  +    Q L L+PTRELA Q
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60

Query: 116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRS 167
           I + +  L   + ++     GGT+L E  RKL  G+  ++ GTPGR+ D++R 
Sbjct: 61  IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR 113

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

 Score =  115 bits (289), Expect = 3e-30
 Identities = 60/142 (42%), Positives = 86/142 (60%), Gaps = 7/142 (4%)

Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E  +TF ++GL+  +L  +   G+EKPS IQ   I  ++ GRDV+  AQ+G+GKTA FS+
Sbjct: 3   EFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSL 62

Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDL 144
            +L +LD +L+  Q+L L+PTRELAVQ+ +   A+ DF      V   A  GG      L
Sbjct: 63  PLLHNLDPELKAPQILVLAPTRELAVQVAE---AMTDFSKHMRGVNVVALYGGQRYDVQL 119

Query: 145 RKLDYGQHVVSGTPGRVFDMIR 166
           R L  G  +V GTPGR+ D ++
Sbjct: 120 RALRQGPQIVVGTPGRLLDHLK 141

Length = 629

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

 Score =  107 bits (270), Expect = 8e-30
 Identities = 43/122 (35%), Positives = 69/122 (56%), Gaps = 3/122 (2%)

Query: 47  IYAYGFEKPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLC 105
           I  +GFE     Q+ +I+ ++ G RDVI  A +G+GKT    +  L++L    +  +VL 
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRG-KGGRVLV 59

Query: 106 LSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDM 164
           L PTRELA Q  + +  LG  + ++     GG +  E LRKL+ G+  ++  TPGR+ D+
Sbjct: 60  LVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDL 119

Query: 165 IR 166
           + 
Sbjct: 120 LE 121

Length = 201

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

 Score =  109 bits (276), Expect = 1e-28
 Identities = 52/136 (38%), Positives = 81/136 (59%), Gaps = 1/136 (0%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           + F  + L   LL  +   G+ + + IQ +S+  I+ G+DVIAQA++G+GKTA F + +L
Sbjct: 4   TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL 63

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
           Q LD +    Q L L PTRELA Q+ K +  L  F+ N++     GG  +   +  L++G
Sbjct: 64  QKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG 123

Query: 151 QHVVSGTPGRVFDMIR 166
            H++ GTPGR+ D +R
Sbjct: 124 AHIIVGTPGRILDHLR 139

Length = 460

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

 Score =  103 bits (259), Expect = 2e-26
 Identities = 54/138 (39%), Positives = 88/138 (63%), Gaps = 6/138 (4%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
           +FD++GL  D+LR +   G+ +P+ IQQ++I  +++GRD++A AQ+GTGKTA F++ +LQ
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 93  SLDTQ------LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK 146
            L T+       R  + L L+PTRELA QI + V     ++N++     GG +++  + K
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121

Query: 147 LDYGQHVVSGTPGRVFDM 164
           L  G  V+  TPGR+ D+
Sbjct: 122 LRGGVDVLVATPGRLLDL 139

Length = 456

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

 Score = 89.3 bits (222), Expect = 3e-23
 Identities = 37/100 (37%), Positives = 57/100 (57%), Gaps = 2/100 (2%)

Query: 70  RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV 129
           RDV+  A +G+GKT    + IL+ LD  L+  QVL L+PTRELA Q+ + +  L     +
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLD-SLKGGQVLVLAPTRELANQVAERLKELFGE-GI 58

Query: 130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ 169
           +    IGGT++ +  + L     +V GTPGR+ D +   +
Sbjct: 59  KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLK 98

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

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

 Score = 91.9 bits (229), Expect = 3e-22
 Identities = 48/137 (35%), Positives = 67/137 (48%), Gaps = 4/137 (2%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
           TF  + L E LL  +   G+ +P+AIQ  +I P + GRDV+  A +GTGKTA F +  LQ
Sbjct: 2   TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61

Query: 93  SLDTQLRE----TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
            L    R      ++L L+PTRELA+Q+      L    ++      GG           
Sbjct: 62  HLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFS 121

Query: 149 YGQHVVSGTPGRVFDMI 165
             Q +V  TPGR+   I
Sbjct: 122 ENQDIVVATPGRLLQYI 138

Length = 434

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

 Score = 92.3 bits (229), Expect = 3e-22
 Identities = 53/171 (30%), Positives = 84/171 (49%), Gaps = 10/171 (5%)

Query: 2   AAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQR 61
                R  +K  P  L  +E    E  E  + F +  L  +L+  I+  GF   + IQ +
Sbjct: 57  KKDKPRRERKPKPASLWKLEDFVVEPQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQ 116

Query: 62  SIKPIVKGRDVIAQAQSGTGKTATFSISILQSL-------DTQLRETQVLCLSPTRELAV 114
            +   + G D I +AQ+GTGKTA F ISI+  L       +  + E + L ++PTREL V
Sbjct: 117 VLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVV 176

Query: 115 QIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH--VVSGTPGRVFD 163
           QI K   AL  +  +     +GG +  + L++L+  +   ++  TPGR+ D
Sbjct: 177 QIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLE-ARFCDILVATPGRLLD 226

Length = 475

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

 Score = 77.7 bits (192), Expect = 3e-17
 Identities = 43/144 (29%), Positives = 68/144 (47%), Gaps = 9/144 (6%)

Query: 34  FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
           F +  L   ++  +   GF   + IQ  ++   + GRDV  QAQ+GTGKT  F  +    
Sbjct: 10  FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69

Query: 94  L-------DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK 146
           L       D ++ + + L ++PTRELAVQI      L     ++     GG    + L+ 
Sbjct: 70  LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129

Query: 147 LDYGQHVVSGTPGRVFDMIRSSQG 170
           L+ G  ++ GT GR+ D  +  Q 
Sbjct: 130 LESGVDILIGTTGRLIDYAK--QN 151

Length = 423

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

 Score = 77.3 bits (190), Expect = 5e-17
 Identities = 46/141 (32%), Positives = 74/141 (52%), Gaps = 7/141 (4%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
           TF +  L   LL G+ + GF + + IQ  ++   + G DV  QAQ+GTGKT  F ++++ 
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 93  SL-------DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
            L       D +  + + L L+PTRELA+QI K  +  G  + ++     GG +  +   
Sbjct: 70  RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRE 129

Query: 146 KLDYGQHVVSGTPGRVFDMIR 166
            L  G  V+  TPGR+ D ++
Sbjct: 130 LLQQGVDVIIATPGRLIDYVK 150

Length = 572

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

 Score = 75.2 bits (185), Expect = 3e-16
 Identities = 43/141 (30%), Positives = 74/141 (52%), Gaps = 9/141 (6%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL- 91
           +F + GL   LL  +   G+E P+ IQ ++I   + GR ++  A +G+GKTA+F + I+ 
Sbjct: 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIS 181

Query: 92  -------QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL 144
                       Q R    + L+PTREL VQ++     LG  +  +    +GG  + + L
Sbjct: 182 RCCTIRSGHPSEQ-RNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQL 240

Query: 145 RKLDYGQHVVSGTPGRVFDMI 165
            ++  G  ++ GTPGR+ D++
Sbjct: 241 YRIQQGVELIVGTPGRLIDLL 261

Length = 518

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

 Score = 71.3 bits (175), Expect = 5e-15
 Identities = 42/143 (29%), Positives = 71/143 (49%), Gaps = 5/143 (3%)

Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
           V +F+     + +L+ +   GF +P+ IQ +     + GRD+I  A++G+GKT  F +  
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPA 188

Query: 91  LQSLDTQ--LRETQ---VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
           +  ++ Q  LR      VL L+PTRELA QI++     G    ++     GG      + 
Sbjct: 189 IVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIY 248

Query: 146 KLDYGQHVVSGTPGRVFDMIRSS 168
            L  G  ++   PGR+ D + S+
Sbjct: 249 ALRRGVEILIACPGRLIDFLESN 271

Length = 545

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

 Score = 41.6 bits (98), Expect = 8e-05
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 39  LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
             E L   +   G E+  + Q  +++ I +GR+V+    +G+GKT +F + IL  L  + 
Sbjct: 55  RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL-LRD 113

Query: 99  RETQVLCLSPTRELA 113
              + L L PT  LA
Sbjct: 114 PSARALLLYPTNALA 128

Length = 851

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

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 52  FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKT-ATF--SISILQSLDTQLRETQVLCL-- 106
           F   +  Q+ +I  I  G +V+  A +G+GKT A F   I+ L SL     E  +  L  
Sbjct: 20  FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYI 79

Query: 107 SPTRELAVQIQKVVLALGDFMN 128
           SP + L   I++ +      + 
Sbjct: 80  SPLKALNNDIRRRLEEPLRELG 101

Length = 814

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 1/85 (1%)

Query: 40  REDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR 99
             D++  + A G  +P   Q R+ +    GR V+    + +GK+  + + +L +L    R
Sbjct: 22  HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPR 81

Query: 100 ETQVLCLSPTRELAVQIQKVVLALG 124
            T  L L+PT+ LA    + V  L 
Sbjct: 82  AT-ALYLAPTKALAADQLRAVRELT 105

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. Length = 742

>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 6/73 (8%)

Query: 52  FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSL----DTQLRETQVLCL- 106
           F   +  Q+ +I  I +G++V+  + +G+GKT    ++I+  L         E +V CL 
Sbjct: 30  FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLY 89

Query: 107 -SPTRELAVQIQK 118
            SP R L   I +
Sbjct: 90  VSPLRALNNDIHR 102

Length = 876

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	178
KOG0330|consensus	476		100.0
KOG0331|consensus	519		100.0
KOG0338|consensus	691		100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PTZ00110	545	helicase; Provisional	99.98
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.98
KOG0348|consensus	708		99.97
KOG0340|consensus	442		99.97
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.97
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.97
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.97
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.97
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.97
KOG0345|consensus	567		99.97
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.96
KOG0328|consensus	400		99.96
KOG0342|consensus	543		99.96
KOG0346|consensus	569		99.96
PTZ00424	401	helicase 45; Provisional	99.96
KOG0334|consensus	997		99.96
KOG0335|consensus	482		99.96
KOG0339|consensus	731		99.96
KOG0343|consensus	758		99.95
KOG0333|consensus	673		99.95
KOG0347|consensus	731		99.95
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.95
KOG0326|consensus	459		99.95
KOG0341|consensus	610		99.94
KOG0336|consensus	629		99.93
KOG0329|consensus	387		99.93
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.93
KOG0327|consensus	397		99.93
KOG0350|consensus	620		99.93
KOG0337|consensus	529		99.93
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.92
PRK02362	737	ski2-like helicase; Provisional	99.92
PRK00254	720	ski2-like helicase; Provisional	99.91
PRK13767	876	ATP-dependent helicase; Provisional	99.9
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.89
KOG4284|consensus	980		99.89
KOG0332|consensus	477		99.88
PRK01172	674	ski2-like helicase; Provisional	99.87
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.87
COG1205	851	Distinct helicase family with a unique C-terminal	99.87
KOG0344|consensus	593		99.86
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.82
PRK14701	1638	reverse gyrase; Provisional	99.82
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.82
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.81
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.81
PRK09401	1176	reverse gyrase; Reviewed	99.81
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.81
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.79
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.79
COG1204	766	Superfamily II helicase [General function predicti	99.78
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.77
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.77
PRK10689	1147	transcription-repair coupling factor; Provisional	99.76
KOG0952|consensus	1230		99.75
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.73
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.7
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.69
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.69
COG1202	830	Superfamily II helicase, archaea-specific [General	99.67
KOG0349|consensus	725		99.64
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.63
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.61
PHA02558	501	uvsW UvsW helicase; Provisional	99.61
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.61
PRK05580	679	primosome assembly protein PriA; Validated	99.6
KOG0951|consensus	1674		99.59
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.59
PRK13766	773	Hef nuclease; Provisional	99.57
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.56
KOG0354|consensus	746		99.5
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.48
PHA02653	675	RNA helicase NPH-II; Provisional	99.43
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.41
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.4
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.4
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.39
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.38
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.37
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.36
KOG0353|consensus	695		99.34
KOG0352|consensus	641		99.29
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.29
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.29
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.29
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.19
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.18
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.18
KOG0351|consensus	941		99.16
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.12
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.05
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.05
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.02
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.01
PRK09694	878	helicase Cas3; Provisional	99.0
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.99
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.99
KOG0951|consensus	1674		98.99
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.96
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.91
KOG0947|consensus	1248		98.88
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.85
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.79
KOG0949|consensus	1330		98.79
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.76
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.76
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.72
KOG0948|consensus	1041		98.6
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.59
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	98.56
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.53
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.51
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.44
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.38
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.34
PF13245	76	AAA_19: Part of AAA domain	98.32
KOG0952|consensus	1230		98.23
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.22
COG4096	875	HsdR Type I site-specific restriction-modification	98.2
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.18
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.17
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.16
KOG0950|consensus	1008		98.15
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.1
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	98.09
PRK15483	986	type III restriction-modification system StyLTI en	98.04
PRK14873	665	primosome assembly protein PriA; Provisional	97.99
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.86
KOG1802|consensus	935		97.84
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.78
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.74
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.73
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.7
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.61
KOG1123|consensus	776		97.55
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.53
COG4889	1518	Predicted helicase [General function prediction on	97.52
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.4
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.33
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.33
KOG1803|consensus	649		97.32
PRK04914	956	ATP-dependent helicase HepA; Validated	97.24
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.23
PRK10536	262	hypothetical protein; Provisional	97.22
PRK05298	652	excinuclease ABC subunit B; Provisional	97.22
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	97.2
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	97.18
PRK11054	684	helD DNA helicase IV; Provisional	97.08
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.07
KOG0920|consensus	924		97.04
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	97.04
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.04
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.04
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.95
KOG4150|consensus	1034		96.86
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	96.83
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.83
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	96.82
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.81
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.81
COG3587	985	Restriction endonuclease [Defense mechanisms]	96.8
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.73
COG0610	962	Type I site-specific restriction-modification syst	96.68
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.64
PRK10875	615	recD exonuclease V subunit alpha; Provisional	96.62
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.54
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.47
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.45
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.39
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	96.37
PRK05973	237	replicative DNA helicase; Provisional	96.35
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.31
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.31
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.28
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.26
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.17
KOG1132|consensus	945		96.17
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.14
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.1
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.02
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	96.0
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.99
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.98
COG1484	254	DnaC DNA replication protein [DNA replication, rec	95.93
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.87
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	95.84
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.8
PRK13851	344	type IV secretion system protein VirB11; Provision	95.74
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.74
KOG1133|consensus	821		95.68
PRK08181	269	transposase; Validated	95.64
PRK06835	329	DNA replication protein DnaC; Validated	95.64
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.63
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	95.61
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	95.57
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.55
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.54
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.53
KOG0390|consensus	776		95.48
KOG4439|consensus	901		95.46
TIGR00959	428	ffh signal recognition particle protein. This mode	95.41
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.4
PRK13764	602	ATPase; Provisional	95.39
PRK06921	266	hypothetical protein; Provisional	95.36
KOG0953|consensus	700		95.27
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.27
PRK08769	319	DNA polymerase III subunit delta'; Validated	95.19
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.17
PRK13826	1102	Dtr system oriT relaxase; Provisional	95.15
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.14
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.1
PRK06526	254	transposase; Provisional	95.04
KOG0387|consensus	923		95.02
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.0
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.98
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.95
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	94.88
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	94.87
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	94.84
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	94.83
PRK04328	249	hypothetical protein; Provisional	94.82
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.8
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	94.8
KOG1131|consensus	755		94.79
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	94.74
TIGR02533	486	type_II_gspE general secretory pathway protein E.	94.73
PRK10436	462	hypothetical protein; Provisional	94.73
KOG1805|consensus	1100		94.7
PRK11823	446	DNA repair protein RadA; Provisional	94.67
PRK13897	606	type IV secretion system component VirD4; Provisio	94.65
KOG1002|consensus	791		94.64
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	94.63
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	94.62
PRK12377	248	putative replication protein; Provisional	94.61
PRK06871	325	DNA polymerase III subunit delta'; Validated	94.57
PF12846	304	AAA_10: AAA-like domain	94.55
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.53
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	94.53
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	94.53
PRK08533	230	flagellar accessory protein FlaH; Reviewed	94.48
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	94.47
PHA02244	383	ATPase-like protein	94.47
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.44
PRK10416	318	signal recognition particle-docking protein FtsY;	94.4
smart00382	148	AAA ATPases associated with a variety of cellular	94.38
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	94.38
PHA02533	534	17 large terminase protein; Provisional	94.37
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	94.35
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	94.34
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.33
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	94.31
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.28
KOG0385|consensus	971		94.28
KOG0389|consensus	941		94.21
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	94.2
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.16
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	94.14
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	94.09
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	94.04
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	93.99
PRK07952	244	DNA replication protein DnaC; Validated	93.94
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	93.94
PRK08116	268	hypothetical protein; Validated	93.94
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.93
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	93.91
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	93.84
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	93.84
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	93.82
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.72
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	93.7
KOG0744|consensus	423		93.69
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	93.65
PRK14974	336	cell division protein FtsY; Provisional	93.61
PRK09183	259	transposase/IS protein; Provisional	93.59
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	93.56
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	93.52
KOG0331|consensus	519		93.49
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.49
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	93.4
PRK10867	433	signal recognition particle protein; Provisional	93.37
KOG0729|consensus	435		93.36
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	93.35
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	93.26
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	93.25
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	93.24
KOG0922|consensus	674		93.23
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	93.21
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	93.13
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	93.06
PF13555	62	AAA_29: P-loop containing region of AAA domain	92.99
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.98
TIGR02237	209	recomb_radB DNA repair and recombination protein R	92.96
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.95
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	92.9
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	92.9
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	92.89
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	92.84
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	92.83
KOG0333|consensus	673		92.82
PF09439	181	SRPRB: Signal recognition particle receptor beta s	92.77
PRK06964	342	DNA polymerase III subunit delta'; Validated	92.72
PRK06090	319	DNA polymerase III subunit delta'; Validated	92.68
PRK05642	234	DNA replication initiation factor; Validated	92.63
COG0606	490	Predicted ATPase with chaperone activity [Posttran	92.61
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	92.57
PRK13822	641	conjugal transfer coupling protein TraG; Provision	92.55
PRK13531	498	regulatory ATPase RavA; Provisional	92.51
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	92.51
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	92.46
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	92.46
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	92.43
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	92.35
KOG0925|consensus	699		92.34
PRK03992	389	proteasome-activating nucleotidase; Provisional	92.33
PTZ00110	545	helicase; Provisional	92.3
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	92.29
cd03115	173	SRP The signal recognition particle (SRP) mediates	92.25
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	92.24
PRK04296	190	thymidine kinase; Provisional	92.18
PRK14087	450	dnaA chromosomal replication initiation protein; P	92.18
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	92.17
PF00004	132	AAA: ATPase family associated with various cellula	92.17
PRK06067	234	flagellar accessory protein FlaH; Validated	92.13
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	92.07
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	92.05
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	92.03
KOG0926|consensus	1172		92.01
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	92.0
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	91.99
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	91.99
PRK08727	233	hypothetical protein; Validated	91.97
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	91.96
PRK07993	334	DNA polymerase III subunit delta'; Validated	91.96
KOG1806|consensus	1320		91.88
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.86
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	91.85
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	91.78
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	91.76
PTZ00424	401	helicase 45; Provisional	91.76
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	91.74
PRK08939	306	primosomal protein DnaI; Reviewed	91.7
PRK00149	450	dnaA chromosomal replication initiation protein; R	91.66
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	91.63
cd01394	218	radB RadB. The archaeal protein radB shares simila	91.61
PRK13876	663	conjugal transfer coupling protein TraG; Provision	91.58
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	91.5
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	91.49
KOG0733|consensus	802		91.49
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	91.45
PHA02535	581	P terminase ATPase subunit; Provisional	91.44
COG0593	408	DnaA ATPase involved in DNA replication initiation	91.42
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	91.41
PRK13700	732	conjugal transfer protein TraD; Provisional	91.32
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	91.23
cd00983	325	recA RecA is a bacterial enzyme which has roles in	91.2
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	90.98
PRK13880	636	conjugal transfer coupling protein TraG; Provision	90.96
CHL00181	287	cbbX CbbX; Provisional	90.89
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	90.89
PRK08084	235	DNA replication initiation factor; Provisional	90.83
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	90.83
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	90.81
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	90.8
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	90.79
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	90.69
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	90.67
PRK09354	349	recA recombinase A; Provisional	90.63
PRK14088	440	dnaA chromosomal replication initiation protein; P	90.61
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	90.41
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	90.35
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	90.23
KOG0738|consensus	491		90.18
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	90.1
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	90.09
) 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	90.05
PRK09302	509	circadian clock protein KaiC; Reviewed	90.0
KOG0745|consensus	564		89.86
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	89.85
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	89.81
KOG0652|consensus	424		89.8
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	89.78
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	89.76
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	89.75
COG3451	796	VirB4 Type IV secretory pathway, VirB4 components	89.74
PRK06893	229	DNA replication initiation factor; Validated	89.7
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	89.7
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	89.69
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	89.69
KOG2340|consensus	698		89.64
PRK08903	227	DnaA regulatory inactivator Hda; Validated	89.58
PRK08118	167	topology modulation protein; Reviewed	89.53
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	89.5
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	89.43
PRK00131	175	aroK shikimate kinase; Reviewed	89.4
PF05729	166	NACHT: NACHT domain	89.4
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	89.33
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	89.32
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	89.32
KOG0924|consensus	1042		89.27
PLN02165	334	adenylate isopentenyltransferase	89.26
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	89.24
PRK12402	337	replication factor C small subunit 2; Reviewed	89.22
KOG0060|consensus	659		89.2
PRK10689	1147	transcription-repair coupling factor; Provisional	89.18
PRK12678	672	transcription termination factor Rho; Provisional	89.18
KOG0332|consensus	477		89.18
PRK09302	509	circadian clock protein KaiC; Reviewed	89.14
PTZ00035	337	Rad51 protein; Provisional	89.06
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	89.02
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	89.0
KOG0989|consensus	346		88.95
KOG1807|consensus	1025		88.89
PRK00411	394	cdc6 cell division control protein 6; Reviewed	88.84
PTZ00301	210	uridine kinase; Provisional	88.73
PRK07261	171	topology modulation protein; Provisional	88.71
PRK14530	215	adenylate kinase; Provisional	88.68
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	88.66
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	88.65
KOG0391|consensus	1958		88.59
COG0714	329	MoxR-like ATPases [General function prediction onl	88.59
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	88.58
COG2256	436	MGS1 ATPase related to the helicase subunit of the	88.43
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	88.38
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	88.37
TIGR00767	415	rho transcription termination factor Rho. Members	88.31
PRK07399	314	DNA polymerase III subunit delta'; Validated	88.23
PRK00300	205	gmk guanylate kinase; Provisional	88.19
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	88.18
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	88.14
KOG2373|consensus	514		88.12
KOG0392|consensus	1549		88.08
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	88.08
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	87.97
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	87.95
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	87.92
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	87.88
KOG1533|consensus	290		87.84
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	87.82
PRK04220	301	2-phosphoglycerate kinase; Provisional	87.72
PF00005	137	ABC_tran: ABC transporter This structure is on hol	87.69
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	87.68
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	87.67
PHA03333	752	putative ATPase subunit of terminase; Provisional	87.64
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	87.6
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	87.56
PRK14737	186	gmk guanylate kinase; Provisional	87.45
KOG1205|consensus	282		87.36
TIGR00665	434	DnaB replicative DNA helicase. This model describe	87.32
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	87.28
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	87.19
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	87.16
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	87.16
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	87.05
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	86.91
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	86.75
COG1855	604	ATPase (PilT family) [General function prediction	86.72
cd01918	149	HprK_C HprK/P, the bifunctional histidine-containi	86.69
PRK04914	956	ATP-dependent helicase HepA; Validated	86.68
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	86.65
PRK11608	326	pspF phage shock protein operon transcriptional ac	86.63
PRK09694	878	helicase Cas3; Provisional	86.55
KOG4150|consensus	1034		86.54
PRK13767	876	ATP-dependent helicase; Provisional	86.52
COG4525	259	TauB ABC-type taurine transport system, ATPase com	86.47
KOG0340|consensus	442		86.39
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	86.39
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	86.33
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	86.3
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	86.28
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	86.2
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	86.18
PRK13342	413	recombination factor protein RarA; Reviewed	86.11
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	86.1
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	86.0
KOG0731|consensus	774		85.99
PHA00729	226	NTP-binding motif containing protein	85.92
KOG0733|consensus	802		85.92
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	85.82
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	85.82
PRK13891	852	conjugal transfer protein TrbE; Provisional	85.8
PHA02544	316	44 clamp loader, small subunit; Provisional	85.79
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	85.77
KOG0330|consensus	476		85.74
COG1702	348	PhoH Phosphate starvation-inducible protein PhoH,	85.74
TIGR02236	310	recomb_radA DNA repair and recombination protein R	85.72
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	85.68
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	85.68
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	85.66
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	85.59
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	85.56
PLN02796	347	D-glycerate 3-kinase	85.51
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	85.41
TIGR02773	1158	addB_Gpos ATP-dependent nuclease subunit B. DNA re	85.38
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	85.38
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	85.34

>KOG0330|consensus

Probab=100.00  E-value=3.2e-34  Score=226.41  Aligned_cols=147  Identities=33%  Similarity=0.560  Sum_probs=140.2

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      ..+..++|.++++++++++++++.|++.||++|+++||.++.|+|++..|.||||||.+|++|+++++..+...++++|+
T Consensus        56 ~~e~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVL  135 (476)
T KOG0330|consen   56 TDESFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVL  135 (476)
T ss_pred             hhhhhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEe
Confidence            35678899999999999999999999999999999999999999999999999999999999999999988888999999


Q ss_pred             cCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         107 SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       107 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      +||||||.|+...+..++...|+++.++.||.+...+...+.+.|||+|+|||+|.+++.++.++..
T Consensus       136 tPtRELA~QI~e~fe~Lg~~iglr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~l  202 (476)
T KOG0330|consen  136 TPTRELAQQIAEQFEALGSGIGLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSL  202 (476)
T ss_pred             cCcHHHHHHHHHHHHHhccccCeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccH
Confidence            9999999999999999999999999999999999999999999999999999999999998776643

>KOG0331|consensus

Probab=100.00  E-value=9.5e-33  Score=228.02  Aligned_cols=142  Identities=33%  Similarity=0.588  Sum_probs=135.5

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh------cCCCceEEE
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT------QLRETQVLC  105 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~------~~~~~~~li  105 (178)
                      ..|.+++|+++...+++..||..|||+|.+.||.++.|+|++..|.||||||++|++|++.++..      ..+++++|+
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            37999999999999999999999999999999999999999999999999999999999999875      345789999


Q ss_pred             EcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         106 LSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       106 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      |+||||||.|+...+.+++..+.+++++++||.+...|...+.++.+|+|+|||||.|++..+.+++.
T Consensus       171 L~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~  238 (519)
T KOG0331|consen  171 LAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLS  238 (519)
T ss_pred             EcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999988764

>KOG0338|consensus

Probab=100.00  E-value=6.3e-33  Score=225.31  Aligned_cols=145  Identities=34%  Similarity=0.567  Sum_probs=136.6

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCC---ceEEEEc
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE---TQVLCLS  107 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~---~~~lil~  107 (178)
                      ..+|.+++|+-.+++++..+||..|||+|..+||..+-|+|++.||-||||||.+|++|+|.++.....+   .++|||+
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            5589999999999999999999999999999999999999999999999999999999999999765443   4899999


Q ss_pred             CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCccc
Q psy9277         108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN  175 (178)
Q Consensus       108 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~~~  175 (178)
                      |||+|+.|++.+.+++++...+.+++++||.+.+.+...++.+|||+|+|||||.|+|+|...+..++
T Consensus       260 PTRELaiQv~sV~~qlaqFt~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~lds  327 (691)
T KOG0338|consen  260 PTRELAIQVHSVTKQLAQFTDITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDS  327 (691)
T ss_pred             ccHHHHHHHHHHHHHHHhhccceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999998876654

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

Probab=100.00  E-value=6.4e-32  Score=227.83  Aligned_cols=141  Identities=38%  Similarity=0.640  Sum_probs=130.7

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh--cCCCceEEEEcCc
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT--QLRETQVLCLSPT  109 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~--~~~~~~~lil~Pt  109 (178)
                      ..|++++|++++++++.+.||..||++|..+||.++.|+|+++.|+||||||++|++|+++.+..  ......+||++||
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            78999999999999999999999999999999999999999999999999999999999999874  2222229999999


Q ss_pred             HHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         110 RELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      |+||.|+++.+..+.... +++++.++||.+...+...+..++||||+|||||+|++.++.+++
T Consensus       109 RELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l  172 (513)
T COG0513         109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDL  172 (513)
T ss_pred             HHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcch
Confidence            999999999999999998 799999999999999999999899999999999999999986554

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.4e-31  Score=221.63  Aligned_cols=143  Identities=29%  Similarity=0.468  Sum_probs=131.6

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-------CCCce
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-------LRETQ  102 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-------~~~~~  102 (178)
                      ...+|++++|+++++++|.++||.+||++|.++||.+++|+|++++||||||||++|++|+++.+...       ..+++
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            45789999999999999999999999999999999999999999999999999999999999988642       23478


Q ss_pred             EEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         103 VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       103 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      +|||+||++||.|+++.+..+....++++..++|+...+.+...+.+++||+|+||++|.+++.++.+++
T Consensus        86 ~lil~PtreLa~Qi~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l  155 (423)
T PRK04837         86 ALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINL  155 (423)
T ss_pred             EEEECCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccc
Confidence            9999999999999999999999999999999999999988888888889999999999999998776544

>PTZ00110 helicase; Provisional

Probab=99.98  E-value=2.6e-31  Score=225.76  Aligned_cols=148  Identities=27%  Similarity=0.448  Sum_probs=135.5

Q ss_pred             cccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-----C
Q psy9277          24 TSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-----L   98 (178)
Q Consensus        24 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-----~   98 (178)
                      ..+.+.++.+|++++|+++++++|.++||.+||++|.++||.+++|+|++++||||||||++|++|++..+...     .
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            34567788999999999999999999999999999999999999999999999999999999999999887543     2


Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      .++++|||+||++||.|+++.+..+....++++.+++|+.+...+...+..+++|+|+||++|.+++.++...
T Consensus       202 ~gp~~LIL~PTreLa~Qi~~~~~~~~~~~~i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~  274 (545)
T PTZ00110        202 DGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTN  274 (545)
T ss_pred             CCcEEEEECChHHHHHHHHHHHHHHhcccCccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCC
Confidence            3678999999999999999999999998899999999999998888888889999999999999999876544

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

Probab=99.98  E-value=4.1e-31  Score=223.61  Aligned_cols=152  Identities=28%  Similarity=0.529  Sum_probs=137.4

Q ss_pred             cccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh---
Q psy9277          20 VEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT---   96 (178)
Q Consensus        20 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~---   96 (178)
                      +.+.....++++.+|++++|++.++++|.+.||..||++|.++||.+++|+|++++||||||||++|++|++.++..   
T Consensus       109 i~~~g~~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~  188 (518)
T PLN00206        109 IHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRS  188 (518)
T ss_pred             CEecCCCCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcc
Confidence            34445567789999999999999999999999999999999999999999999999999999999999999988743   


Q ss_pred             ----cCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277          97 ----QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus        97 ----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                          ...++++|||+||++||.|+++.++.+.+..++++..++||.....+...+..+++|+|+||++|.+++..+.+.
T Consensus       189 ~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~~~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~  267 (518)
T PLN00206        189 GHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIE  267 (518)
T ss_pred             ccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCcc
Confidence                224679999999999999999999999998899999999999988888888889999999999999999877544

>KOG0348|consensus

Probab=99.97  E-value=2.7e-31  Score=216.76  Aligned_cols=150  Identities=29%  Similarity=0.489  Sum_probs=133.2

Q ss_pred             ccccccccccccCCCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh------c
Q psy9277          25 SEDVEVVSTFDNMGLREDLLRGI-YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT------Q   97 (178)
Q Consensus        25 ~~~~~~~~~f~~~~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~------~   97 (178)
                      ++.+..-..|..+|||+.+...| ..+++..||.+|.++||.+++|+|++|.++||||||++|++|+++.+..      .
T Consensus       129 ~e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~R  208 (708)
T KOG0348|consen  129 SEAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQR  208 (708)
T ss_pred             cccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCccccc
Confidence            44455567799999999999999 5889999999999999999999999999999999999999999999854      3


Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHhccCCCc-eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCcc
Q psy9277          98 LRETQVLCLSPTRELAVQIQKVVLALGDFMNV-QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTT  174 (178)
Q Consensus        98 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~-~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~~  174 (178)
                      ..|+.+|+|+||||||.|+|+.+.++.+.+-. .-+.+.||...+.+...+++|++|+|+|||||+|+|.++......
T Consensus       209 s~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s  286 (708)
T KOG0348|consen  209 SDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFS  286 (708)
T ss_pred             cCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheee
Confidence            46789999999999999999999999887653 346678999999998999999999999999999999998765543

>KOG0340|consensus

Probab=99.97  E-value=4e-31  Score=206.86  Aligned_cols=140  Identities=39%  Similarity=0.608  Sum_probs=135.0

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      ...+.|+++||++|+.+.|+.+|+++|||+|..|||.|++|+|++-+|.||||||.+|.+|+++++.....+.++++++|
T Consensus         4 ~t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP   83 (442)
T KOG0340|consen    4 KTAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP   83 (442)
T ss_pred             cccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCCcceEEEecc
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         109 TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       109 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      ||+||.|+.+.|..+++..++++.+++||++.-.+...+...+||+|+||||+.+++.++
T Consensus        84 TrELA~QiaEQF~alGk~l~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn  143 (442)
T KOG0340|consen   84 TRELALQIAEQFIALGKLLNLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSN  143 (442)
T ss_pred             hHHHHHHHHHHHHHhcccccceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccC
Confidence            999999999999999999999999999999999998999999999999999999998877

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.97  E-value=6.3e-30  Score=213.54  Aligned_cols=141  Identities=38%  Similarity=0.671  Sum_probs=129.1

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC------CCceEEE
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL------RETQVLC  105 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~------~~~~~li  105 (178)
                      ++|++++|+++++++|.++||..||++|.++||.+++|+|+++++|||||||++|++|+++.+....      ...++||
T Consensus         1 ~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLi   80 (456)
T PRK10590          1 MSFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALI   80 (456)
T ss_pred             CCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEE
Confidence            3799999999999999999999999999999999999999999999999999999999999886432      2358999


Q ss_pred             EcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         106 LSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       106 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      |+||++||.|+++.++.+.+..++++..++|+.+.+.+...+..+++|+|+||++|++++....+.+
T Consensus        81 l~PtreLa~Qi~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l  147 (456)
T PRK10590         81 LTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKL  147 (456)
T ss_pred             EeCcHHHHHHHHHHHHHHhccCCCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCccc
Confidence            9999999999999999999999999999999999998888888889999999999999988766543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.97  E-value=9.8e-30  Score=217.04  Aligned_cols=138  Identities=33%  Similarity=0.555  Sum_probs=127.9

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC-------CCceEE
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL-------RETQVL  104 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~-------~~~~~l  104 (178)
                      .+|++++|++.++++|.++||..||++|.++||.+++|+|+++++|||||||++|++|+++.+....       ..+++|
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            5799999999999999999999999999999999999999999999999999999999999885421       247999


Q ss_pred             EEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         105 CLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       105 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      ||+||++|+.|+++.+..++...++++..++|+.+.+.+...+.++++|+|+||++|++++.+..
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~  153 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHK  153 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhcc
Confidence            99999999999999999999999999999999999998888888889999999999999997653

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.97  E-value=8.6e-30  Score=212.98  Aligned_cols=141  Identities=37%  Similarity=0.648  Sum_probs=130.5

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ..+|++++|++.++++|.++||..||++|.++||.+++|+|++++||||||||++|++|+++.+.......+++|++||+
T Consensus         3 ~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~Ptr   82 (460)
T PRK11776          3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTR   82 (460)
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCH
Confidence            35799999999999999999999999999999999999999999999999999999999999987665567999999999


Q ss_pred             HHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         111 ELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +||.|+++.++.+.... ++++..++|+.+...+...+..+++|+|+||++|.+++.++.+.
T Consensus        83 eLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~  144 (460)
T PRK11776         83 ELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLD  144 (460)
T ss_pred             HHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCcc
Confidence            99999999999988754 78999999999999888888889999999999999999876654

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.97  E-value=1.1e-29  Score=218.30  Aligned_cols=143  Identities=40%  Similarity=0.697  Sum_probs=132.1

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      ...+|++++|++.++++|.++||.+|+++|.++||.+++|+|++++||||||||++|++|+++.+......+++|||+||
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            45679999999999999999999999999999999999999999999999999999999999998776667899999999


Q ss_pred             HHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         110 RELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      ++||.|+++.+..+.... ++.++.++|+.+.+.+...+..+++|+|+||++|.+++.++.+++
T Consensus        84 reLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l  147 (629)
T PRK11634         84 RELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDL  147 (629)
T ss_pred             HHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcch
Confidence            999999999999987765 799999999999998888888899999999999999998876553

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.97  E-value=2.4e-29  Score=208.83  Aligned_cols=141  Identities=33%  Similarity=0.539  Sum_probs=129.7

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----CCCceEEEEc
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----LRETQVLCLS  107 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----~~~~~~lil~  107 (178)
                      ++|++++|++.++++|.++||.+|+++|.++|+.+++|+|+++++|||+|||++|++|+++.+...    ....++||++
T Consensus         1 ~~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~   80 (434)
T PRK11192          1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILT   80 (434)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEEC
Confidence            379999999999999999999999999999999999999999999999999999999999988542    2346899999


Q ss_pred             CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       108 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      ||++||.|+++.+..+....++.+..++|+.....+...+.++++|+|+||++|++++.++.++.
T Consensus        81 Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~  145 (434)
T PRK11192         81 PTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDC  145 (434)
T ss_pred             CcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCc
Confidence            99999999999999999999999999999999988888888889999999999999998876543

>KOG0345|consensus

Probab=99.97  E-value=1.3e-29  Score=204.20  Aligned_cols=143  Identities=31%  Similarity=0.572  Sum_probs=125.3

Q ss_pred             ccccccCC--CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC---C--ceE
Q psy9277          31 VSTFDNMG--LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR---E--TQV  103 (178)
Q Consensus        31 ~~~f~~~~--l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~---~--~~~  103 (178)
                      ...|++++  |++++++++.+.||+.+||+|..+||.+++++||++.++||||||++|++|++..+.....   +  .-+
T Consensus         3 ~~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vga   82 (567)
T KOG0345|consen    3 PKSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGA   82 (567)
T ss_pred             CcchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeE
Confidence            45788776  5599999999999999999999999999999999999999999999999999998854321   1  368


Q ss_pred             EEEcCcHHHHHHHHHHHHHhccC-CCceEEEEEcCccHHHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         104 LCLSPTRELAVQIQKVVLALGDF-MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       104 lil~Pt~~L~~q~~~~~~~~~~~-~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      +||+|||+|+.|+.++...|... .++.+.+++||.+.++....+. ++++|+|||||||.+++++..-.++
T Consensus        83 lIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~  154 (567)
T KOG0345|consen   83 LIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLS  154 (567)
T ss_pred             EEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhcc
Confidence            99999999999999999988877 6889999999999888877776 5789999999999999998554444

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=1.7e-28  Score=205.96  Aligned_cols=145  Identities=32%  Similarity=0.509  Sum_probs=129.7

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC-------C
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR-------E  100 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~-------~  100 (178)
                      .+....|.+++|++.++++|.+.||.+|+++|.++|+.+++|+|+++++|||||||++|++|+++.+.....       .
T Consensus        83 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~  162 (475)
T PRK01297         83 QEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGE  162 (475)
T ss_pred             ccCCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCC
Confidence            455678999999999999999999999999999999999999999999999999999999999998865421       4


Q ss_pred             ceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         101 TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      +++|||+||++||.|+++.++.+.+..++++..++||.+.+.+...+. ..++|+|+||++|++++.+....+
T Consensus       163 ~~aLil~PtreLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l  235 (475)
T PRK01297        163 PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHL  235 (475)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHhhccCCCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCccc
Confidence            699999999999999999999999989999999999988877766664 468999999999999988765443

>KOG0328|consensus

Probab=99.96  E-value=2.6e-30  Score=197.43  Aligned_cols=158  Identities=80%  Similarity=1.197  Sum_probs=148.8

Q ss_pred             CCCCCcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          15 EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      +..+...++.+++..+..+|+++||++++++++...||++|+.+|+.|++.|++|+|++.++.+|+|||..|.+.+++.+
T Consensus        10 ~~~~~~~feTs~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~   89 (400)
T KOG0328|consen   10 EDMDTVEFETSEKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSL   89 (400)
T ss_pred             ccccceeEeeccCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeec
Confidence            34556677778999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277          95 DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus        95 ~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      .-+.+..+++|++|||+||.|+.+.+..++..+++++..+.||.+..+.+..+..|+|++.||||+++++++.+.+..
T Consensus        90 d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~~mnvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~t  167 (400)
T KOG0328|consen   90 DISVRETQALILSPTRELAVQIQKVILALGDYMNVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRT  167 (400)
T ss_pred             ccccceeeEEEecChHHHHHHHHHHHHHhcccccceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccc
Confidence            877778899999999999999999999999999999999999999999999999999999999999999999887654

>KOG0342|consensus

Probab=99.96  E-value=1.4e-29  Score=204.91  Aligned_cols=149  Identities=34%  Similarity=0.524  Sum_probs=137.4

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----CCCceE
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----LRETQV  103 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----~~~~~~  103 (178)
                      ......|+++.|++..+++++++||.++|++|..+++.++.|+|+++.|.||+|||++|++|+++.+.+.    +++..+
T Consensus        78 ~~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~v  157 (543)
T KOG0342|consen   78 ITTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGV  157 (543)
T ss_pred             hhhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeE
Confidence            3345678999999999999999999999999999999999999999999999999999999999988653    345679


Q ss_pred             EEEcCcHHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCcccc
Q psy9277         104 LCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQ  176 (178)
Q Consensus       104 lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~~~~  176 (178)
                      +|++|||+||.|++.+++.+.++. ++.+..+.||.........+.++|+|+|+|||||+|++++...+...|+
T Consensus       158 lIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~  231 (543)
T KOG0342|consen  158 LIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNL  231 (543)
T ss_pred             EEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhcc
Confidence            999999999999999999999988 8999999999999888888888999999999999999999999887765

>KOG0346|consensus

Probab=99.96  E-value=1.8e-29  Score=202.22  Aligned_cols=139  Identities=31%  Similarity=0.471  Sum_probs=125.0

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc------CCCceEEE
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ------LRETQVLC  105 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~------~~~~~~li  105 (178)
                      ++|++|+|++++++++.++||++||.+|..+||.+++|+|++..|.||||||.+|++|+++.+...      ..++.++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            899999999999999999999999999999999999999999999999999999999999998543      34679999


Q ss_pred             EcCcHHHHHHHHHHHHHhccCCC--ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         106 LSPTRELAVQIQKVVLALGDFMN--VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       106 l~Pt~~L~~q~~~~~~~~~~~~~--~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      ++||++||+|+|..+.++...+.  ++++-+.++++.+.....+.+.+||+|+||+++++++..+.+
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~  165 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVL  165 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccc
Confidence            99999999999999988877653  666666767777766677888899999999999999988774

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=4.5e-28  Score=199.12  Aligned_cols=143  Identities=64%  Similarity=1.011  Sum_probs=131.3

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      .+...+|+++++++.++++|.+.||..|+++|.++|+.+++|+|+++++|||||||++|++|+++.+.....+.++||++
T Consensus        24 ~~~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~  103 (401)
T PTZ00424         24 DEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILA  103 (401)
T ss_pred             ccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEEC
Confidence            44578999999999999999999999999999999999999999999999999999999999999886555667999999


Q ss_pred             CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       108 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      |+++|+.|+++.+..++...++.+..+.|+....++...+..+++|+|+||++|.+++.++..
T Consensus       104 Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~  166 (401)
T PTZ00424        104 PTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHL  166 (401)
T ss_pred             CCHHHHHHHHHHHHHHhhhcCceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCc
Confidence            999999999999999988888999999999988888888888899999999999999886654

>KOG0334|consensus

Probab=99.96  E-value=6.5e-29  Score=215.26  Aligned_cols=160  Identities=31%  Similarity=0.566  Sum_probs=147.0

Q ss_pred             cCCCCCCcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          13 IPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      .+..++.+.+...+-+.++++|.+.|++..++..++++||.+|+++|.+|||+|+.|+||+.+|-||||||++|++|++.
T Consensus       346 yr~~l~~i~v~g~~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmir  425 (997)
T KOG0334|consen  346 YRCELDGIKVKGKECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIR  425 (997)
T ss_pred             hhcCccceeeccCCCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhh
Confidence            45566667888888899999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             Hhhh-----cCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277          93 SLDT-----QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus        93 ~l~~-----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      ++..     ...+|.++|++||++|+.|+++.++.|++.+++++++++|+....+++..+++++.|+|+|||+..|++--
T Consensus       426 hi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~  505 (997)
T KOG0334|consen  426 HIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLLGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCA  505 (997)
T ss_pred             hhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhcCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhh
Confidence            7643     24589999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             CCCCC
Q psy9277         168 SQGRR  172 (178)
Q Consensus       168 ~~~~~  172 (178)
                      +.+.+
T Consensus       506 n~grv  510 (997)
T KOG0334|consen  506 NSGRV  510 (997)
T ss_pred             cCCcc
Confidence            55443

>KOG0335|consensus

Probab=99.96  E-value=4.4e-29  Score=203.66  Aligned_cols=149  Identities=34%  Similarity=0.464  Sum_probs=137.6

Q ss_pred             ccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC-----
Q psy9277          25 SEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR-----   99 (178)
Q Consensus        25 ~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~-----   99 (178)
                      ..-+.++.+|.+..+.+.+..+++..||..|||+|+.+||.+..|+++++||+||||||.+|++|++..+.....     
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            344566779999999999999999999999999999999999999999999999999999999999999866432     


Q ss_pred             -----CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         100 -----ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       100 -----~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                           .++++|++|||+||.|+|+.++++.-..+++++.++|+.+...+.+.+..+|||+|+|||+|.+++..+.+.+.
T Consensus       147 ~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~  225 (482)
T KOG0335|consen  147 SGGGVYPRALILAPTRELVDQIYNEARKFSYLSGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLD  225 (482)
T ss_pred             cCCCCCCceEEEeCcHHHhhHHHHHHHhhcccccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceeehh
Confidence                 48999999999999999999999998899999999999999999999999999999999999999999887664

>KOG0339|consensus

Probab=99.96  E-value=1.4e-28  Score=200.04  Aligned_cols=153  Identities=31%  Similarity=0.476  Sum_probs=142.0

Q ss_pred             ccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc---
Q psy9277          21 EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ---   97 (178)
Q Consensus        21 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~---   97 (178)
                      .+.....++++++|+.+++++.++.++.+.-|++||++|.+++|..+.|++++-+|-||||||.+|+.|++.++..+   
T Consensus       212 rv~g~s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL  291 (731)
T KOG0339|consen  212 RVSGSSPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPEL  291 (731)
T ss_pred             eeccCCCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhh
Confidence            34456678899999999999999999999999999999999999999999999999999999999999999888542   


Q ss_pred             --CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277          98 --LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus        98 --~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                        ..+|..||++||++||.|++..+++|++..++++++++||.+..++...+..+|.|||+|||||+++++-+..++.
T Consensus       292 ~~g~gPi~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~  369 (731)
T KOG0339|consen  292 KPGEGPIGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKMKATNLS  369 (731)
T ss_pred             cCCCCCeEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHhhcccce
Confidence              4678999999999999999999999999999999999999999999999999999999999999999987776654

>KOG0343|consensus

Probab=99.95  E-value=2.5e-28  Score=200.19  Aligned_cols=148  Identities=28%  Similarity=0.477  Sum_probs=135.7

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----CCCceE
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----LRETQV  103 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----~~~~~~  103 (178)
                      ....+.|.+|+|+..++++|++.+|..+|.+|+.+||..+.|+||+..|.||||||++|++|+++++.+.    ..|.-|
T Consensus        65 ~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGa  144 (758)
T KOG0343|consen   65 STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGA  144 (758)
T ss_pred             hhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCCCCCcee
Confidence            3456789999999999999999999999999999999999999999999999999999999999999763    345679


Q ss_pred             EEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCcccc
Q psy9277         104 LCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTNQ  176 (178)
Q Consensus       104 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~~~~  176 (178)
                      |||+|||+||.|+++.+.+.++..++..+++.||...+.+...+. +++|+|||||||+.+|..+......++
T Consensus       145 lIISPTRELA~QtFevL~kvgk~h~fSaGLiiGG~~~k~E~eRi~-~mNILVCTPGRLLQHmde~~~f~t~~l  216 (758)
T KOG0343|consen  145 LIISPTRELALQTFEVLNKVGKHHDFSAGLIIGGKDVKFELERIS-QMNILVCTPGRLLQHMDENPNFSTSNL  216 (758)
T ss_pred             EEecchHHHHHHHHHHHHHHhhccccccceeecCchhHHHHHhhh-cCCeEEechHHHHHHhhhcCCCCCCcc
Confidence            999999999999999999999999999999999999888766665 689999999999999999888877765

>KOG0333|consensus

Probab=99.95  E-value=4.7e-28  Score=197.50  Aligned_cols=148  Identities=29%  Similarity=0.474  Sum_probs=136.7

Q ss_pred             cccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----
Q psy9277          22 FETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----   97 (178)
Q Consensus        22 ~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----   97 (178)
                      .+...-+.|+..|++.+|+.++++.+.+.||..|+|+|..++|..++.+|++..+.||||||++|++|++..+...    
T Consensus       235 ~kg~~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~  314 (673)
T KOG0333|consen  235 IKGGRLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMA  314 (673)
T ss_pred             ecCCCCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcc
Confidence            3444567899999999999999999999999999999999999999999999999999999999999999877442    


Q ss_pred             -----CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277          98 -----LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus        98 -----~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                           ..++.++|++|||+|++|+.+.-.+|++.++++++.++||.+.+++-..+..||+|+|+||++|.+.|.+.-
T Consensus       315 ~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~lg~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Lenr~  391 (673)
T KOG0333|consen  315 RLENNIEGPYAIILAPTRELAQQIEEETNKFGKPLGIRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLENRY  391 (673)
T ss_pred             hhhhcccCceeeeechHHHHHHHHHHHHHHhcccccceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHHHH
Confidence                 347899999999999999999999999999999999999999999988999999999999999999987653

>KOG0347|consensus

Probab=99.95  E-value=3e-28  Score=199.66  Aligned_cols=144  Identities=28%  Similarity=0.528  Sum_probs=131.3

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC-CcEEEEcCCCChHHHHHHHHHHHHhhhc--------
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQ--------   97 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g-~~v~v~aptGsGKTl~~ll~il~~l~~~--------   97 (178)
                      ....+..|.+|+|+.+++++|..+||.+||++|+.++|.+..| .|++..|.||||||++|-+|+++++...        
T Consensus       176 ~~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~  255 (731)
T KOG0347|consen  176 SKVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELS  255 (731)
T ss_pred             cccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhh
Confidence            3455778999999999999999999999999999999999998 7999999999999999999999966332        


Q ss_pred             ---CCCce--EEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277          98 ---LRETQ--VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus        98 ---~~~~~--~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                         ...++  +||++|||+||.|+...+..+....++++..++||.....+.+.+...+||+|+|||||+.++.....
T Consensus       256 ~~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~  333 (731)
T KOG0347|consen  256 NTSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNT  333 (731)
T ss_pred             hHHhccCcceeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhh
Confidence               12344  99999999999999999999999999999999999999999899999999999999999999987765

>cd00268 DEADc DEAD-box helicases

Probab=99.95  E-value=1.7e-26  Score=173.38  Aligned_cols=137  Identities=50%  Similarity=0.841  Sum_probs=126.6

Q ss_pred             cccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc--CCCceEEEEcCcHH
Q psy9277          34 FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQVLCLSPTRE  111 (178)
Q Consensus        34 f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~--~~~~~~lil~Pt~~  111 (178)
                      |+++++++.+.+.+.+.|+..|+++|.++++.+.+|+|+++++|||+|||++|++|+++.+...  ..+++++|++|+++
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            7899999999999999999999999999999999999999999999999999999999998876  46789999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      |+.|+...++.+....++.+..+.|+.+.......+.++++|+|+||++|.+++.+...
T Consensus        81 L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~  139 (203)
T cd00268          81 LALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKL  139 (203)
T ss_pred             HHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCC
Confidence            99999999999988888999999999988777777777899999999999999987753

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=99.95  E-value=1.2e-28  Score=191.06  Aligned_cols=142  Identities=39%  Similarity=0.695  Sum_probs=135.9

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      ..|+++.|..+++..+.+.||++|+|+|.++||.++.|+|++..|..|+|||.+|.+|+++++....+..+++|++|||+
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~IQ~~ilVPtre  164 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVIQAIILVPTRE  164 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCccccceeEEEEeecch
Confidence            45999999999999999999999999999999999999999999999999999999999999998888889999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      ||.|....|+++++.+++++...+||++..+.+..+.+..|++|+||||++|++..+..++.
T Consensus       165 lALQtSqvc~~lskh~~i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls  226 (459)
T KOG0326|consen  165 LALQTSQVCKELSKHLGIKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLS  226 (459)
T ss_pred             hhHHHHHHHHHHhcccCeEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccch
Confidence            99999999999999999999999999999999889999999999999999999998877654

>KOG0341|consensus

Probab=99.94  E-value=7e-28  Score=191.04  Aligned_cols=154  Identities=28%  Similarity=0.467  Sum_probs=138.1

Q ss_pred             CcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh--
Q psy9277          19 NVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT--   96 (178)
Q Consensus        19 ~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~--   96 (178)
                      .+.++....++|+++|.++.++..+++.|++.|+..|||+|.+-+|.+++|+|.+-.|.||||||++|++|++.....  
T Consensus       157 ~I~veGd~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE  236 (610)
T KOG0341|consen  157 HILVEGDDIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQE  236 (610)
T ss_pred             eEEeeCCCCCCchhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHH
Confidence            355666778899999999999999999999999999999999999999999999999999999999999998765422  


Q ss_pred             ------cCCCceEEEEcCcHHHHHHHHHHHHHhccCC------CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHH
Q psy9277          97 ------QLRETQVLCLSPTRELAVQIQKVVLALGDFM------NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDM  164 (178)
Q Consensus        97 ------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~------~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~  164 (178)
                            ...++..+|+||+|+||.|.++.+..|...+      .++..++.||.+..++...++.|.||+|+|||||.|+
T Consensus       237 ~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~Dm  316 (610)
T KOG0341|consen  237 MMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDM  316 (610)
T ss_pred             hcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHH
Confidence                  3467899999999999999999988776543      4799999999999999999999999999999999999


Q ss_pred             HHcCCCCC
Q psy9277         165 IRSSQGRR  172 (178)
Q Consensus       165 l~~~~~~~  172 (178)
                      |..+.+++
T Consensus       317 L~KK~~sL  324 (610)
T KOG0341|consen  317 LAKKIMSL  324 (610)
T ss_pred             HHHhhccH
Confidence            98877654

>KOG0336|consensus

Probab=99.93  E-value=1.5e-26  Score=184.49  Aligned_cols=147  Identities=32%  Similarity=0.483  Sum_probs=133.2

Q ss_pred             ccccccccccc-CCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh------cC
Q psy9277          26 EDVEVVSTFDN-MGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT------QL   98 (178)
Q Consensus        26 ~~~~~~~~f~~-~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~------~~   98 (178)
                      .-+.|.-+|++ |...+++++.+++.||.+|||+|+++||.+++|.|++..|.||+|||++|++|-+.++..      +.
T Consensus       213 pIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr  292 (629)
T KOG0336|consen  213 PIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQR  292 (629)
T ss_pred             cCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhcc
Confidence            35677888988 678899999999999999999999999999999999999999999999999998876632      45


Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      .++.+|+++||++|+.|+.-.+.++ .+.+.+.++++|+-+..++.+.++.+.+|+|+||++|.++.-.+.+++.
T Consensus       293 ~~p~~lvl~ptreLalqie~e~~ky-syng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~  366 (629)
T KOG0336|consen  293 NGPGVLVLTPTRELALQIEGEVKKY-SYNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLA  366 (629)
T ss_pred             CCCceEEEeccHHHHHHHHhHHhHh-hhcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeee
Confidence            6789999999999999999999877 4558999999999999999999999999999999999999988887765

>KOG0329|consensus

Probab=99.93  E-value=8.3e-26  Score=170.89  Aligned_cols=143  Identities=36%  Similarity=0.569  Sum_probs=134.0

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      .+.|.++-|.|++++++-..||+.|+.+|.+|||...-|.|++++|.+|.|||.+|+++.++.+........++++|.||
T Consensus        41 ssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv~g~vsvlvmchtr  120 (387)
T KOG0329|consen   41 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVSVLVMCHTR  120 (387)
T ss_pred             ccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCCCCeEEEEEEeccH
Confidence            56699999999999999999999999999999999999999999999999999999999999998776667899999999


Q ss_pred             HHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         111 ELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      +||-|+.+...+|++++ ++++.+++||...+...+.+++.|||+||||||++.+.+++.+++.
T Consensus       121 elafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk  184 (387)
T KOG0329|consen  121 ELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLK  184 (387)
T ss_pred             HHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchh
Confidence            99999999999999886 6999999999999988889999899999999999999999988764

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

Probab=99.93  E-value=8.2e-25  Score=191.40  Aligned_cols=124  Identities=23%  Similarity=0.305  Sum_probs=110.6

Q ss_pred             CCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          38 GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        38 ~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      .|++++.++|++.||++|+++|.++|+.+++|+|+++++|||||||++|++|+++.+..+ .+.++|||+||++|+.|++
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            489999999999999999999999999999999999999999999999999999998764 4579999999999999999


Q ss_pred             HHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHH
Q psy9277         118 KVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDM  164 (178)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~  164 (178)
                      +.++.+. ..++++..+.|+.+.+++ ..+.++++|+|+||++|...
T Consensus        99 ~~l~~l~-~~~i~v~~~~Gdt~~~~r-~~i~~~~~IivtTPd~L~~~  143 (742)
T TIGR03817        99 RAVRELT-LRGVRPATYDGDTPTEER-RWAREHARYVLTNPDMLHRG  143 (742)
T ss_pred             HHHHHhc-cCCeEEEEEeCCCCHHHH-HHHhcCCCEEEEChHHHHHh
Confidence            9999987 457888888888876554 55666799999999998743

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

>KOG0327|consensus

Probab=99.93  E-value=3.1e-26  Score=180.87  Aligned_cols=154  Identities=62%  Similarity=0.895  Sum_probs=138.8

Q ss_pred             cccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC
Q psy9277          20 VEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR   99 (178)
Q Consensus        20 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~   99 (178)
                      ..+-.+++.+...+|++++|++++++.+...||++|+.+|+.||..+..|.|+.+.+++|+|||.+|.+++++.+.....
T Consensus        14 ~~~iesn~~evvdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~k   93 (397)
T KOG0327|consen   14 EGVIESNWNEVVDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVK   93 (397)
T ss_pred             cccccccHHHHhhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchH
Confidence            44556788899999999999999999999999999999999999999999999999999999999999999999987777


Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL-DYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      ..++++++|+++||.|+..+...++...++++..+.|+.....+...+ ..+++|+|+|||++.+++..+.+...
T Consensus        94 e~qalilaPtreLa~qi~~v~~~lg~~~~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~  168 (397)
T KOG0327|consen   94 ETQALILAPTRELAQQIQKVVRALGDHMDVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTD  168 (397)
T ss_pred             HHHHHHhcchHHHHHHHHHHHHhhhcccceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhcccccccc
Confidence            789999999999999999999999999999999999998877444444 45799999999999999987755543

>KOG0350|consensus

Probab=99.93  E-value=1.8e-25  Score=181.62  Aligned_cols=145  Identities=22%  Similarity=0.385  Sum_probs=123.5

Q ss_pred             ccccccccCCCCHHHH----------HHHHhCCCCCCcHHHHHHHHHHHc---------CCcEEEEcCCCChHHHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLL----------RGIYAYGFEKPSAIQQRSIKPIVK---------GRDVIAQAQSGTGKTATFSIS   89 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~----------~~l~~~g~~~~~~~Q~~~i~~i~~---------g~~v~v~aptGsGKTl~~ll~   89 (178)
                      .....|+.+++++.+.          +++.++++.+..|+|..++|.++.         ++|+.|.||||||||++|.+|
T Consensus       124 nslq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iP  203 (620)
T KOG0350|consen  124 NSLQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIP  203 (620)
T ss_pred             CceeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhH
Confidence            3355577777766444          458999999999999999998864         579999999999999999999


Q ss_pred             HHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCC-C----cEEEeChHHHHH
Q psy9277          90 ILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYG-Q----HVVSGTPGRVFD  163 (178)
Q Consensus        90 il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-~----~IlV~TP~~l~~  163 (178)
                      |++.+... -+..+|+||+||++|+.|+++.+..+....|+.|+.+.|..+...+...+.+. +    ||+|+|||||.|
T Consensus       204 IVQ~L~~R~v~~LRavVivPtr~L~~QV~~~f~~~~~~tgL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVD  283 (620)
T KOG0350|consen  204 IVQLLSSRPVKRLRAVVIVPTRELALQVYDTFKRLNSGTGLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVD  283 (620)
T ss_pred             HHHHHccCCccceEEEEEeeHHHHHHHHHHHHHHhccCCceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHH
Confidence            99998754 34469999999999999999999999999999999999999998888877642 3    999999999999


Q ss_pred             HHHcCCCCCc
Q psy9277         164 MIRSSQGRRT  173 (178)
Q Consensus       164 ~l~~~~~~~~  173 (178)
                      ++++...+..
T Consensus       284 Hl~~~k~f~L  293 (620)
T KOG0350|consen  284 HLNNTKSFDL  293 (620)
T ss_pred             hccCCCCcch
Confidence            9997665443

>KOG0337|consensus

Probab=99.93  E-value=7.2e-26  Score=180.75  Aligned_cols=139  Identities=36%  Similarity=0.588  Sum_probs=129.8

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC-CCceEEEEcCc
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL-RETQVLCLSPT  109 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~-~~~~~lil~Pt  109 (178)
                      ...|..+||+..+++++.+.||..|||+|+..+|.++.+++++-.+.||||||.||++|+++++.... .+.++++++||
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~Ralilspt   99 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPT   99 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhccccccceeeccCc
Confidence            67899999999999999999999999999999999999999999999999999999999999986533 45699999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      ++|+.|..+.++++++..++++++++|+.+.+++...+..++|||++||++++.+.....
T Consensus       100 reLa~qtlkvvkdlgrgt~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~  159 (529)
T KOG0337|consen  100 RELALQTLKVVKDLGRGTKLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMT  159 (529)
T ss_pred             HHHHHHHHHHHHHhccccchhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehhee
Confidence            999999999999999999999999999999999999999999999999999977655444

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

Probab=99.92  E-value=1.4e-24  Score=188.14  Aligned_cols=129  Identities=21%  Similarity=0.250  Sum_probs=120.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-----CCCceEEEEcCcHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-----LRETQVLCLSPTRELA  113 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-----~~~~~~lil~Pt~~L~  113 (178)
                      |++.+.+.+++. |..||+.|.+|||.+.+|+|++++||||||||+++++|++..+...     ..+..+|||+|.++|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            789999999886 9999999999999999999999999999999999999999999876     2346899999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         114 VQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       114 ~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .++.+.+...+..+|+.+.+.+|+++..++.+..++.|||+|||||.|.-++.+.
T Consensus        87 ~Di~~rL~~~~~~~G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~  141 (814)
T COG1201          87 NDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSP  141 (814)
T ss_pred             HHHHHHHHHHHHHcCCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCH
Confidence            9999999999999999999999999999998999999999999999998888764

>PRK02362 ski2-like helicase; Provisional

Probab=99.92  E-value=4.6e-24  Score=187.28  Aligned_cols=130  Identities=18%  Similarity=0.312  Sum_probs=114.7

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ..|++++|++++++++++.||.+|+|+|.+|++. +..|+|+++++|||||||++|.+|+++.+.   .+.++||++|++
T Consensus         1 ~~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~---~~~kal~i~P~r   77 (737)
T PRK02362          1 MKIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIA---RGGKALYIVPLR   77 (737)
T ss_pred             CChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHh---cCCcEEEEeChH
Confidence            3689999999999999999999999999999998 778999999999999999999999999885   456899999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      +||.|+++.++.+.. .++++..++|+...+..   ....++|+|+||+++..+++++
T Consensus        78 aLa~q~~~~~~~~~~-~g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~  131 (737)
T PRK02362         78 ALASEKFEEFERFEE-LGVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNG  131 (737)
T ss_pred             HHHHHHHHHHHHhhc-CCCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcC
Confidence            999999999998753 58999999998765432   2245899999999999988864

>PRK00254 ski2-like helicase; Provisional

Probab=99.91  E-value=1.8e-23  Score=183.19  Aligned_cols=131  Identities=15%  Similarity=0.258  Sum_probs=115.1

Q ss_pred             ccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        33 ~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      +|+++++++.+.+.+++.||.+|+++|.++++. +.+|+|+++++|||||||++|.+|+++.+..  .+.++||++|+++
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            688999999999999999999999999999986 7889999999999999999999999998765  3569999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      |+.|+++.+..+. ..++++..++|+.+.+...   ...++|+|+||+++..+++++.
T Consensus        80 La~q~~~~~~~~~-~~g~~v~~~~Gd~~~~~~~---~~~~~IiV~Tpe~~~~ll~~~~  133 (720)
T PRK00254         80 LAEEKYREFKDWE-KLGLRVAMTTGDYDSTDEW---LGKYDIIIATAEKFDSLLRHGS  133 (720)
T ss_pred             HHHHHHHHHHHHh-hcCCEEEEEeCCCCCchhh---hccCCEEEEcHHHHHHHHhCCc
Confidence            9999999998864 4689999999988754332   2468999999999998887643

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.90  E-value=7.7e-23  Score=181.94  Aligned_cols=129  Identities=22%  Similarity=0.291  Sum_probs=109.8

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc------CCCceEEEEcCcHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ------LRETQVLCLSPTREL  112 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~------~~~~~~lil~Pt~~L  112 (178)
                      |++.+.+.+++ +|..|+++|.++|+.+++|+|++++||||||||++|++|+++.+...      .++.++||++|+++|
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            67777777766 79999999999999999999999999999999999999999988642      235689999999999


Q ss_pred             HHHHHHHHHH-------hc----cCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         113 AVQIQKVVLA-------LG----DFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       113 ~~q~~~~~~~-------~~----~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      +.|+++.+..       +.    ... ++++...+|+.+..++...+.+.++|+||||++|..++.+.
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~  164 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSP  164 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcCh
Confidence            9999986642       22    233 67889999999998887788888999999999998887654

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

Probab=99.89  E-value=3.5e-22  Score=145.42  Aligned_cols=114  Identities=27%  Similarity=0.452  Sum_probs=101.1

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEE
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI  135 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  135 (178)
                      |++|.++|+.+.+|+++++.+|||+|||++|++++++.+... +..+++|++|+++|+.|+++.+..+....++++..++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-~~~~~lii~P~~~l~~q~~~~~~~~~~~~~~~~~~~~   79 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-KDARVLIIVPTRALAEQQFERLRKFFSNTNVRVVLLH   79 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-SSSEEEEEESSHHHHHHHHHHHHHHTTTTTSSEEEES
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-CCceEEEEeeccccccccccccccccccccccccccc
Confidence            789999999999999999999999999999999999988876 5569999999999999999999999988889999999


Q ss_pred             cCccHH-HHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         136 GGTNLS-EDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       136 g~~~~~-~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      ++...+ +....+.++++|+|+||++|.+++.+...
T Consensus        80 ~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~  115 (169)
T PF00270_consen   80 GGQSISEDQREVLSNQADILVTTPEQLLDLISNGKI  115 (169)
T ss_dssp             TTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSS
T ss_pred             ccccccccccccccccccccccCcchhhcccccccc
Confidence            998866 44455556799999999999999987443

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>KOG4284|consensus

Probab=99.89  E-value=8.6e-24  Score=176.36  Aligned_cols=144  Identities=34%  Similarity=0.545  Sum_probs=131.9

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      .....|+++.|..+++..|+..+|..||++|..|||.++.+.|++|++.+|+|||++|...+++.+..+...++++||+|
T Consensus        22 ~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~P  101 (980)
T KOG4284|consen   22 NCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTP  101 (980)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEec
Confidence            34678999999999999999999999999999999999999999999999999999999999999988778889999999


Q ss_pred             cHHHHHHHHHHHHHhccC-CCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         109 TRELAVQIQKVVLALGDF-MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       109 t~~L~~q~~~~~~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      ||++|.|+.+.+..++.. .|.++.++.||+........++ .|+|+|||||||..++..+..+..
T Consensus       102 TREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk-~~rIvIGtPGRi~qL~el~~~n~s  166 (980)
T KOG4284|consen  102 TREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLK-QTRIVIGTPGRIAQLVELGAMNMS  166 (980)
T ss_pred             chhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhh-hceEEecCchHHHHHHHhcCCCcc
Confidence            999999999999999875 4899999999999887766655 689999999999999998877654

>KOG0332|consensus

Probab=99.88  E-value=9.5e-23  Score=160.96  Aligned_cols=141  Identities=36%  Similarity=0.657  Sum_probs=122.9

Q ss_pred             cccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCc
Q psy9277          24 TSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLDTQLRET  101 (178)
Q Consensus        24 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~  101 (178)
                      .+.+.-..++|++++|.|++++++..++|.+|+.+|..++|.++.  .+|.+.++.+|+|||.||++.+|.++......|
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~~~~P  161 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPDVVVP  161 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCccccCC
Confidence            344455689999999999999999999999999999999999998  589999999999999999999999998888889


Q ss_pred             eEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         102 QVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       102 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      +++.|+||++||.|..+++.++++..+++..+..-+.....- ..  -..+|+|+|||.+.|++..
T Consensus       162 Q~iCLaPtrELA~Q~~eVv~eMGKf~~ita~yair~sk~~rG-~~--i~eqIviGTPGtv~Dlm~k  224 (477)
T KOG0332|consen  162 QCICLAPTRELAPQTGEVVEEMGKFTELTASYAIRGSKAKRG-NK--LTEQIVIGTPGTVLDLMLK  224 (477)
T ss_pred             CceeeCchHHHHHHHHHHHHHhcCceeeeEEEEecCcccccC-Cc--chhheeeCCCccHHHHHHH
Confidence            999999999999999999999999988888888766622211 01  1248999999999999876

>PRK01172 ski2-like helicase; Provisional

Probab=99.87  E-value=1.7e-21  Score=169.76  Aligned_cols=130  Identities=20%  Similarity=0.266  Sum_probs=112.2

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      +.|++++|++.+++.+.+.+|+ ++++|.++++.+.+|+|+++++|||||||+++.++++..+..   +.++||++|+++
T Consensus         1 ~~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~---~~k~v~i~P~ra   76 (674)
T PRK01172          1 MKISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA---GLKSIYIVPLRS   76 (674)
T ss_pred             CcHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh---CCcEEEEechHH
Confidence            3688999999999999999996 999999999999999999999999999999999999987763   468999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      ||.|+++.+.++. ..|+++...+|+.......   ...++|+|+||+++..++++..
T Consensus        77 La~q~~~~~~~l~-~~g~~v~~~~G~~~~~~~~---~~~~dIiv~Tpek~~~l~~~~~  130 (674)
T PRK01172         77 LAMEKYEELSRLR-SLGMRVKISIGDYDDPPDF---IKRYDVVILTSEKADSLIHHDP  130 (674)
T ss_pred             HHHHHHHHHHHHh-hcCCeEEEEeCCCCCChhh---hccCCEEEECHHHHHHHHhCCh
Confidence            9999999998764 4688888888887654321   2368999999999988887643

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.87  E-value=2e-21  Score=169.53  Aligned_cols=134  Identities=19%  Similarity=0.249  Sum_probs=119.5

Q ss_pred             ccCCCCHHHHHHHH-----hCCCCCC---cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          35 DNMGLREDLLRGIY-----AYGFEKP---SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        35 ~~~~l~~~i~~~l~-----~~g~~~~---~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      +.|++..++.+.+.     .+||..|   +|+|.++++.+..++++++.++||+|||++|++|++..+...   ..++||
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g---~~v~IV  141 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG---KPVHLV  141 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc---CCeEEE
Confidence            55778888888876     6799988   999999999999999999999999999999999999877642   248999


Q ss_pred             cCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCCCCCc
Q psy9277         107 SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQGRRT  173 (178)
Q Consensus       107 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~~~~~  173 (178)
                      +||++||.|.++.+..+.+.+++++.+++||.+..++...+  +|||+||||++| .|+++.+.+.+.
T Consensus       142 TpTrELA~Qdae~m~~L~k~lGLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~  207 (970)
T PRK12899        142 TVNDYLAQRDCEWVGSVLRWLGLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATR  207 (970)
T ss_pred             eCCHHHHHHHHHHHHHHHhhcCCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcC
Confidence            99999999999999999999999999999999998886554  599999999999 999998865544

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

Probab=99.87  E-value=2.2e-21  Score=171.17  Aligned_cols=125  Identities=23%  Similarity=0.303  Sum_probs=113.5

Q ss_pred             CHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          40 REDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        40 ~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      ...+..++.+.|+..++++|.+|+..+.+|+|++|++|||||||.+|++||++.+..... .++|+|+||++||++|.+.
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~-a~AL~lYPtnALa~DQ~~r  134 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPS-ARALLLYPTNALANDQAER  134 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcC-ccEEEEechhhhHhhHHHH
Confidence            445678888889999999999999999999999999999999999999999999987654 4999999999999999999


Q ss_pred             HHHhccCCC--ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHH
Q psy9277         120 VLALGDFMN--VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI  165 (178)
Q Consensus       120 ~~~~~~~~~--~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l  165 (178)
                      ++++...++  +++..+.|++...+....+.+.++||+|||..|..++
T Consensus       135 l~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~l  182 (851)
T COG1205         135 LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLL  182 (851)
T ss_pred             HHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHh
Confidence            999998887  8889999999998887788889999999999997744

>KOG0344|consensus

Probab=99.86  E-value=9.7e-22  Score=162.45  Aligned_cols=151  Identities=26%  Similarity=0.377  Sum_probs=123.9

Q ss_pred             Cccccccccccccccccc----CCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          19 NVEFETSEDVEVVSTFDN----MGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        19 ~~~~~~~~~~~~~~~f~~----~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .+.+...+-+.++.+|.+    +.+++.+++.+...||..|+++|.+|+|.++.+++++.|+|||||||++|.+|+++++
T Consensus       119 k~~v~G~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L  198 (593)
T KOG0344|consen  119 KINVDGFHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHL  198 (593)
T ss_pred             eeeccCCCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHH
Confidence            355566666888999987    6789999999999999999999999999999999999999999999999999999998


Q ss_pred             hhc-----CCCceEEEEcCcHHHHHHHHHHHHHhc--cCCCceEEEEEcCccHHHHH-HHhcCCCcEEEeChHHHHHHHH
Q psy9277          95 DTQ-----LRETQVLCLSPTRELAVQIQKVVLALG--DFMNVQCHACIGGTNLSEDL-RKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus        95 ~~~-----~~~~~~lil~Pt~~L~~q~~~~~~~~~--~~~~~~~~~~~g~~~~~~~~-~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      ...     ..+.+++|+.||++|+.|+++.++++.  ...+.++..........+.. ......++|+|+||-+|..++.
T Consensus       199 ~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~  278 (593)
T KOG0344|consen  199 KDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLG  278 (593)
T ss_pred             HHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhc
Confidence            543     345799999999999999999999998  66666665554333222221 1222357999999999999998


Q ss_pred             cCC
Q psy9277         167 SSQ  169 (178)
Q Consensus       167 ~~~  169 (178)
                      .+.
T Consensus       279 ~~~  281 (593)
T KOG0344|consen  279 LGK  281 (593)
T ss_pred             CCC
Confidence            765

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

Probab=99.82  E-value=5.1e-19  Score=157.34  Aligned_cols=122  Identities=20%  Similarity=0.245  Sum_probs=100.4

Q ss_pred             cccccc--CCCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          31 VSTFDN--MGLREDLLRGI-YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        31 ~~~f~~--~~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      .+.|..  ++....+...+ .-+||..++++|.++|+.++.|+|+++++|||+|||+||++|++.      ....+|||+
T Consensus       434 ~~~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~------~~GiTLVIS  507 (1195)
T PLN03137        434 DKKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALI------CPGITLVIS  507 (1195)
T ss_pred             CccccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHH------cCCcEEEEe
Confidence            344554  45556666666 457999999999999999999999999999999999999999986      246899999


Q ss_pred             CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc------CCCcEEEeChHHHH
Q psy9277         108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD------YGQHVVSGTPGRVF  162 (178)
Q Consensus       108 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~------~~~~IlV~TP~~l~  162 (178)
                      |+++|++++...+...    ++....+.++....++...+.      ..++||++||++|.
T Consensus       508 PLiSLmqDQV~~L~~~----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~  564 (1195)
T PLN03137        508 PLVSLIQDQIMNLLQA----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVA  564 (1195)
T ss_pred             CHHHHHHHHHHHHHhC----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhh
Confidence            9999999877776543    788999999988776655443      35799999999985

>PRK14701 reverse gyrase; Provisional

Probab=99.82  E-value=3.2e-19  Score=165.23  Aligned_cols=122  Identities=16%  Similarity=0.146  Sum_probs=100.2

Q ss_pred             HHHHHHHh-CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          42 DLLRGIYA-YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        42 ~i~~~l~~-~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      ++.+.+++ .|| .||++|..+++.+++|+|++++||||+|||++++++.+...   .++.+++||+||++|+.|+++.+
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            45555655 899 69999999999999999999999999999997776665432   24579999999999999999999


Q ss_pred             HHhccCC--CceEEEEEcCccHHHHHH---HhcC-CCcEEEeChHHHHHHHHc
Q psy9277         121 LALGDFM--NVQCHACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       121 ~~~~~~~--~~~~~~~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~~~l~~  167 (178)
                      +.++...  ++++..++|+.+.+++..   .+.. .++|+|+||++|.+.+..
T Consensus       143 ~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~  195 (1638)
T PRK14701        143 ESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPE  195 (1638)
T ss_pred             HHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHH
Confidence            9998765  567788899988776643   3444 489999999999887653

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.82  E-value=2.6e-19  Score=155.94  Aligned_cols=120  Identities=21%  Similarity=0.272  Sum_probs=101.7

Q ss_pred             HHHHHHH-HhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHH
Q psy9277          41 EDLLRGI-YAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELA  113 (178)
Q Consensus        41 ~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~  113 (178)
                      ..+.+.+ ..++| +||++|.++++.+.++      ++++++||||||||++|++|++..+.   .+.+++|++||++||
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            4455554 67788 5999999999999986      48999999999999999999998775   467999999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEEcCccHHHHHH---HhcC-CCcEEEeChHHHHHH
Q psy9277         114 VQIQKVVLALGDFMNVQCHACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFDM  164 (178)
Q Consensus       114 ~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~~~  164 (178)
                      .|+++.+++++...++++..++|+.+..++..   .+.+ .++|+||||+.+.+.
T Consensus       324 ~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~  378 (681)
T PRK10917        324 EQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDD  378 (681)
T ss_pred             HHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhccc
Confidence            99999999999999999999999998654433   3344 489999999988653

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.81  E-value=3.9e-19  Score=153.77  Aligned_cols=117  Identities=22%  Similarity=0.284  Sum_probs=100.0

Q ss_pred             HHHHHHhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          43 LLRGIYAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        43 i~~~l~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +.+.+.+++| +||+.|.++++.++++      .+.+++||||||||++|++|++..+.   .+.+++|++||++||.|+
T Consensus       225 ~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~---~g~qvlilaPT~~LA~Q~  300 (630)
T TIGR00643       225 LTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIE---AGYQVALMAPTEILAEQH  300 (630)
T ss_pred             HHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHH---cCCcEEEECCHHHHHHHH
Confidence            3445588899 6999999999999985      36899999999999999999998765   467999999999999999


Q ss_pred             HHHHHHhccCCCceEEEEEcCccHHHHHH---HhcC-CCcEEEeChHHHHH
Q psy9277         117 QKVVLALGDFMNVQCHACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFD  163 (178)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~~  163 (178)
                      ++.+++++...++++..++|+.+..++..   .+.. .++|+||||+.+.+
T Consensus       301 ~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~  351 (630)
T TIGR00643       301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE  351 (630)
T ss_pred             HHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc
Confidence            99999999988999999999988765433   3333 47999999998864

>TIGR01054 rgy reverse gyrase

Probab=99.81  E-value=4.6e-19  Score=160.88  Aligned_cols=123  Identities=17%  Similarity=0.183  Sum_probs=97.6

Q ss_pred             HHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          42 DLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        42 ~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      ++.+.+.+.....||++|..+++.++.|+|++++||||+|||+ |.+|++..+..  .+++++||+||++||.|+++.++
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            4444554433347999999999999999999999999999997 65666665543  46799999999999999999999


Q ss_pred             HhccCCCceEE---EEEcCccHHHHHH---HhcC-CCcEEEeChHHHHHHHHc
Q psy9277         122 ALGDFMNVQCH---ACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       122 ~~~~~~~~~~~---~~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~~~l~~  167 (178)
                      .++...++.+.   .++|+.+..++..   .+.+ +++|+|+||++|.+.+..
T Consensus       143 ~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~  195 (1171)
T TIGR01054       143 SLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE  195 (1171)
T ss_pred             HHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH
Confidence            99887776543   4678887765433   3333 589999999999988765

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.81  E-value=7.1e-19  Score=159.61  Aligned_cols=114  Identities=20%  Similarity=0.232  Sum_probs=92.9

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      ..|+ +||++|..++|.++.|+|++++||||+|||. |.++++..+..  ++.+++||+||++||.|+++.++.++...+
T Consensus        76 ~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--~g~~alIL~PTreLa~Qi~~~l~~l~~~~~  151 (1176)
T PRK09401         76 KTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--KGKKSYIIFPTRLLVEQVVEKLEKFGEKVG  151 (1176)
T ss_pred             hcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--cCCeEEEEeccHHHHHHHHHHHHHHhhhcC
Confidence            3477 7999999999999999999999999999996 44455444433  467999999999999999999999999888


Q ss_pred             ceEEEEEcCcc-----HHHHHHHhc-CCCcEEEeChHHHHHHHH
Q psy9277         129 VQCHACIGGTN-----LSEDLRKLD-YGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       129 ~~~~~~~g~~~-----~~~~~~~~~-~~~~IlV~TP~~l~~~l~  166 (178)
                      +.+..++|+..     ..+....+. .+++|+|+||++|.+++.
T Consensus       152 ~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~  195 (1176)
T PRK09401        152 CGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD  195 (1176)
T ss_pred             ceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH
Confidence            88887776653     222333444 358999999999999876

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.81  E-value=5e-19  Score=148.57  Aligned_cols=105  Identities=18%  Similarity=0.237  Sum_probs=88.3

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +.+||..|+|+|.++|+.+++|+|+++++|||+|||++|++|++.      .+..+|||+|+++|+.|+++.+..+    
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~------~~~~~lVi~P~~~L~~dq~~~l~~~----   74 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC------SDGITLVISPLISLMEDQVLQLKAS----   74 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHH------cCCcEEEEecHHHHHHHHHHHHHHc----
Confidence            357999999999999999999999999999999999999999986      3458999999999999999988754    


Q ss_pred             CceEEEEEcCccHHHHHHH---h-cCCCcEEEeChHHHH
Q psy9277         128 NVQCHACIGGTNLSEDLRK---L-DYGQHVVSGTPGRVF  162 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~---~-~~~~~IlV~TP~~l~  162 (178)
                      ++.+..+.++....+....   + ...++|+++||+++.
T Consensus        75 gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~  113 (470)
T TIGR00614        75 GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCS  113 (470)
T ss_pred             CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHc
Confidence            7777778877766543322   2 234799999999974

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

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.79  E-value=2e-18  Score=153.52  Aligned_cols=119  Identities=19%  Similarity=0.103  Sum_probs=98.9

Q ss_pred             CCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          38 GLREDLLRGI-YAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        38 ~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ..+....+.+ ..++|+ ||+.|..||+.+.++      +|++++||||+|||.+|++|++..+.   .+.+++|++||+
T Consensus       435 ~~~~~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~---~g~qvlvLvPT~  510 (926)
T TIGR00580       435 PPDLEWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVL---DGKQVAVLVPTT  510 (926)
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHH---hCCeEEEEeCcH
Confidence            3455666666 556884 999999999999985      79999999999999999999998775   357999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH---hcC-CCcEEEeChHH
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK---LDY-GQHVVSGTPGR  160 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~-~~~IlV~TP~~  160 (178)
                      +||.|+++.++++....++++..+.|+.+..++...   +.. .++|+||||..
T Consensus       511 ~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l  564 (926)
T TIGR00580       511 LLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL  564 (926)
T ss_pred             HHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH
Confidence            999999999999888889999999888776544333   333 48999999953

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.

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

Probab=99.79  E-value=1.6e-18  Score=151.45  Aligned_cols=116  Identities=19%  Similarity=0.212  Sum_probs=95.4

Q ss_pred             CCCCCCcHHHHHHHHHHHcCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEE-EcCcHHHHHHHHHHHHHhccCC
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLC-LSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~li-l~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      .||+ |+++|.++++.++.|+ ++++++|||||||.++.++.+. +......++.++ ++|||+||.|+++.++++++.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~-~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k~l   89 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLA-VEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGERL   89 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhcc-ccccccccceEEEeCchHHHHHHHHHHHHHHHHHh
Confidence            5887 9999999999999998 6788899999999976554443 222233455555 7799999999999998888754


Q ss_pred             -----------------------CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         128 -----------------------NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       128 -----------------------~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                                             ++++..++||.+.+.++..+..+++|||||+    |++.++.++
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~----D~i~sr~L~  152 (844)
T TIGR02621        90 PDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTV----DMIGSRLLF  152 (844)
T ss_pred             cccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECH----HHHcCCccc
Confidence                                   4889999999999999999999999999994    788777763

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.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.78  E-value=1.9e-18  Score=150.99  Aligned_cols=127  Identities=20%  Similarity=0.292  Sum_probs=107.1

Q ss_pred             CCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          38 GLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        38 ~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      .+++.+.+.++..|+.++.+.|+.++..... ++|+++|+|||||||+++++.+++.+...  +.+++|+||+++||.+.
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--~~k~vYivPlkALa~Ek   92 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALAEEK   92 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--CCcEEEEeChHHHHHHH
Confidence            4777888888888888888888888876554 69999999999999999999999998863  56999999999999999


Q ss_pred             HHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         117 QKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       117 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      ++.+.++ ..+|+++...+|+.+.....  + .+++|+|+|||++-.++++...
T Consensus        93 ~~~~~~~-~~~GirV~~~TgD~~~~~~~--l-~~~~ViVtT~EK~Dsl~R~~~~  142 (766)
T COG1204          93 YEEFSRL-EELGIRVGISTGDYDLDDER--L-ARYDVIVTTPEKLDSLTRKRPS  142 (766)
T ss_pred             HHHhhhH-HhcCCEEEEecCCcccchhh--h-ccCCEEEEchHHhhHhhhcCcc
Confidence            9999843 56799999999999866532  2 3689999999999777776654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.77  E-value=6.3e-18  Score=145.50  Aligned_cols=107  Identities=18%  Similarity=0.224  Sum_probs=90.7

Q ss_pred             HHH-hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          46 GIY-AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        46 ~l~-~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|+ -+||..++++|.++|+.+++|+|+++++|||+|||++|++|++.      .+..++|++|+++|+.|+++.++.+ 
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~------~~g~~lVisPl~sL~~dq~~~l~~~-   76 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALL------LKGLTVVISPLISLMKDQVDQLRAA-   76 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHH------cCCcEEEEcCCHHHHHHHHHHHHHc-
Confidence            443 47999999999999999999999999999999999999999985      2457899999999999999998875 


Q ss_pred             cCCCceEEEEEcCccHHHHHHHh----cCCCcEEEeChHHHH
Q psy9277         125 DFMNVQCHACIGGTNLSEDLRKL----DYGQHVVSGTPGRVF  162 (178)
Q Consensus       125 ~~~~~~~~~~~g~~~~~~~~~~~----~~~~~IlV~TP~~l~  162 (178)
                         ++.+..+.++.+.++....+    ....+|+++||++|.
T Consensus        77 ---gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~  115 (591)
T TIGR01389        77 ---GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLE  115 (591)
T ss_pred             ---CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhc
Confidence               67888888888776554332    245799999999985

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.77  E-value=1.2e-17  Score=143.95  Aligned_cols=114  Identities=20%  Similarity=0.258  Sum_probs=92.8

Q ss_pred             CCHHHHHHHH-hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          39 LREDLLRGIY-AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        39 l~~~i~~~l~-~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      ..+...+.|+ .+||..|+++|.++++.+++|+|+++++|||+|||++|++|++..      ...+||++|+++|+.|+.
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            4444455553 479999999999999999999999999999999999999999862      357999999999999999


Q ss_pred             HHHHHhccCCCceEEEEEcCccHHHHHHH---hc-CCCcEEEeChHHHH
Q psy9277         118 KVVLALGDFMNVQCHACIGGTNLSEDLRK---LD-YGQHVVSGTPGRVF  162 (178)
Q Consensus       118 ~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~-~~~~IlV~TP~~l~  162 (178)
                      +.++.+    ++....+.++...++....   +. ...+|+++||+++.
T Consensus        83 ~~l~~~----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~  127 (607)
T PRK11057         83 DQLLAN----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLM  127 (607)
T ss_pred             HHHHHc----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhc
Confidence            998765    6777777777766654332   22 34689999999986

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.76  E-value=1.8e-17  Score=150.22  Aligned_cols=116  Identities=18%  Similarity=0.113  Sum_probs=97.4

Q ss_pred             HHHHHHHhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHH
Q psy9277          42 DLLRGIYAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ  115 (178)
Q Consensus        42 ~i~~~l~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q  115 (178)
                      +..+...+++| .||+.|.+||+.++++      +|++++++||+|||.+|+.++...+.   ++.+++|++||++||.|
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            34444578888 6999999999999997      89999999999999999988776554   46799999999999999


Q ss_pred             HHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeChHHH
Q psy9277         116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTPGRV  161 (178)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP~~l  161 (178)
                      +++.+++.....++++..+.|+.+..++...+.    ..++|+||||+.+
T Consensus       665 ~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL  714 (1147)
T PRK10689        665 HYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL  714 (1147)
T ss_pred             HHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH
Confidence            999999877777889888888888777655443    3589999999744

>KOG0952|consensus

Probab=99.75  E-value=7.6e-18  Score=146.85  Aligned_cols=116  Identities=18%  Similarity=0.326  Sum_probs=100.0

Q ss_pred             CCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhh-------cCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          50 YGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDT-------QLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~-------~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      ++|.+++.+|+.++|.+++ +.|.+||||||||||-.|+|.|++.+..       .++..++|||+|+++||.++++.+.
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            4788999999999999887 7899999999999999999999998874       2356799999999999999999998


Q ss_pred             HhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         122 ALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       122 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +-+...|+.|.-++|++...... .  ..++|||+|||+. |.+.++.
T Consensus       186 kkl~~~gi~v~ELTGD~ql~~te-i--~~tqiiVTTPEKw-DvvTRk~  229 (1230)
T KOG0952|consen  186 KKLAPLGISVRELTGDTQLTKTE-I--ADTQIIVTTPEKW-DVVTRKS  229 (1230)
T ss_pred             hhcccccceEEEecCcchhhHHH-H--HhcCEEEecccce-eeeeeee
Confidence            77788899999999999877653 2  2589999999997 5554443

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.73  E-value=6.9e-17  Score=138.37  Aligned_cols=113  Identities=20%  Similarity=0.272  Sum_probs=99.0

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+|. +|+++|..+++.++.|+  +..+.||+|||++|++|++....   .+..++||+||++||.|.+..+..+++.+|
T Consensus        99 ~lg~-~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al---~G~~v~VvTptreLA~qdae~~~~l~~~lG  172 (656)
T PRK12898         99 VLGQ-RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAAL---AGLPVHVITVNDYLAERDAELMRPLYEALG  172 (656)
T ss_pred             HhCC-CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhh---cCCeEEEEcCcHHHHHHHHHHHHHHHhhcC
Confidence            4466 69999999999999999  99999999999999999998755   467999999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQ  169 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~  169 (178)
                      +++++++|+.+...  +....+|||++||...| .|+|+.+-
T Consensus       173 lsv~~i~gg~~~~~--r~~~y~~dIvygT~~e~~FDyLrd~~  212 (656)
T PRK12898        173 LTVGCVVEDQSPDE--RRAAYGADITYCTNKELVFDYLRDRL  212 (656)
T ss_pred             CEEEEEeCCCCHHH--HHHHcCCCEEEECCCchhhhhccccc
Confidence            99999999987543  34446899999999999 67776653

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.70  E-value=9.5e-17  Score=147.24  Aligned_cols=95  Identities=21%  Similarity=0.271  Sum_probs=81.3

Q ss_pred             EEcCCCChHHHHHHHHHHHHhhhcC----------CCceEEEEcCcHHHHHHHHHHHHHhc------------cCCCceE
Q psy9277          74 AQAQSGTGKTATFSISILQSLDTQL----------RETQVLCLSPTRELAVQIQKVVLALG------------DFMNVQC  131 (178)
Q Consensus        74 v~aptGsGKTl~~ll~il~~l~~~~----------~~~~~lil~Pt~~L~~q~~~~~~~~~------------~~~~~~~  131 (178)
                      |++|||||||++|++|++.++..+.          ++.++|||+|+++|+.|+++.++...            ...++++
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            5799999999999999999986531          35799999999999999999886421            1347899


Q ss_pred             EEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       132 ~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      ...+|+.+.+++...+++.+||||+||++|..++.++
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk  117 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSR  117 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhh
Confidence            9999999999988788888999999999999988764

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.69  E-value=4.8e-16  Score=134.22  Aligned_cols=113  Identities=21%  Similarity=0.280  Sum_probs=96.9

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +.+|. +|+++|..+...+..|+  +..++||+|||++|++|++-....   +..+.|++||+.||.|.++.+..+.+.+
T Consensus        51 R~lg~-~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~---G~~V~VvTpt~~LA~qdae~~~~l~~~L  124 (745)
T TIGR00963        51 RVLGM-RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT---GKGVHVVTVNDYLAQRDAEWMGQVYRFL  124 (745)
T ss_pred             HHhCC-CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh---CCCEEEEcCCHHHHHHHHHHHHHHhccC
Confidence            34576 69999999998888776  999999999999999999533332   4479999999999999999999999999


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      |+++.+++|+.+..++....  .+||++|||++| .|+++.+
T Consensus       125 GLsv~~i~g~~~~~~r~~~y--~~dIvyGT~~rlgfDyLrd~  164 (745)
T TIGR00963       125 GLSVGLILSGMSPEERREAY--ACDITYGTNNELGFDYLRDN  164 (745)
T ss_pred             CCeEEEEeCCCCHHHHHHhc--CCCEEEECCCchhhHHHhcc
Confidence            99999999999877654443  589999999999 9999876

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.69  E-value=4.7e-16  Score=135.78  Aligned_cols=113  Identities=20%  Similarity=0.293  Sum_probs=96.9

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +.+|. +|+++|..+++.+..|+  +..+.||+|||++|++|++....   .+..+.|++||++||.|.+..+..+.+.+
T Consensus        73 R~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al---~G~~v~VvTpt~~LA~qd~e~~~~l~~~l  146 (790)
T PRK09200         73 RVLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNAL---EGKGVHLITVNDYLAKRDAEEMGQVYEFL  146 (790)
T ss_pred             HHhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHH---cCCCeEEEeCCHHHHHHHHHHHHHHHhhc
Confidence            34476 79999999999888887  99999999999999999986544   46789999999999999999999999999


Q ss_pred             CceEEEEEcCcc-HHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         128 NVQCHACIGGTN-LSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       128 ~~~~~~~~g~~~-~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      |+++.++.|+.+ .++. +. ..++||++|||++| .|+|+..
T Consensus       147 Gl~v~~i~g~~~~~~~r-~~-~y~~dIvygT~~~l~fDyLrd~  187 (790)
T PRK09200        147 GLTVGLNFSDIDDASEK-KA-IYEADIIYTTNSELGFDYLRDN  187 (790)
T ss_pred             CCeEEEEeCCCCcHHHH-HH-hcCCCEEEECCccccchhHHhc
Confidence            999999999998 4444 33 34699999999999 6776654

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

Probab=99.67  E-value=4.9e-16  Score=129.13  Aligned_cols=136  Identities=15%  Similarity=0.215  Sum_probs=117.4

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      -...+++.+++...+.|+..|++.+.|+|.-++.. +++|.|.+|.++|+||||++.-++-+.++..  .+.+.++++|.
T Consensus       193 r~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~--~g~KmlfLvPL  270 (830)
T COG1202         193 RVPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS--GGKKMLFLVPL  270 (830)
T ss_pred             cccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh--CCCeEEEEehh
Confidence            36788999999999999999999999999999986 8889999999999999999999988888775  46689999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh----cCCCcEEEeChHHHHHHHHcC
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL----DYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .+||+|-|+.|++-...+++++..-+|-..........    ....||||||.+-+-.+|+.+
T Consensus       271 VALANQKy~dF~~rYs~LglkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg  333 (830)
T COG1202         271 VALANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG  333 (830)
T ss_pred             HHhhcchHHHHHHHhhcccceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC
Confidence            99999999999877788999998888776655442211    124699999999998888875

>KOG0349|consensus

Probab=99.64  E-value=1.8e-16  Score=128.01  Aligned_cols=63  Identities=30%  Similarity=0.554  Sum_probs=60.1

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      ..|+++|.-+++-.+..++.+.-||.+|.++||.|+.|-|++..|.||||||-+|.+|+++-.
T Consensus         2 ~af~e~gv~pel~~a~~e~dw~lptdvqaeaiplilgggdvlmaaetgsgktgaf~lpilqiv   64 (725)
T KOG0349|consen    2 TAFEEFGVLPELGMATDELDWTLPTDVQAEAIPLILGGGDVLMAAETGSGKTGAFCLPILQIV   64 (725)
T ss_pred             cchHhhCcchHhhhhhhhhccccccccccccccEEecCCcEEEEeccCCCCccceehhhHHHH
Confidence            469999999999999999999999999999999999999999999999999999999999865

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.63  E-value=2.7e-15  Score=130.23  Aligned_cols=112  Identities=15%  Similarity=0.210  Sum_probs=85.1

Q ss_pred             CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      +|. +|+++|......+  +++.++.++||+|||++|++|++....   .+..++|++|+++||.|.++.+..+.+.+|+
T Consensus        67 lgl-rpydVQlig~l~l--~~G~Iaem~TGeGKTLta~Lpa~l~aL---~g~~V~VVTpn~yLA~Rdae~m~~l~~~LGL  140 (762)
T TIGR03714        67 LGM-FPYDVQVLGAIVL--HQGNIAEMKTGEGKTLTATMPLYLNAL---TGKGAMLVTTNDYLAKRDAEEMGPVYEWLGL  140 (762)
T ss_pred             cCC-CccHHHHHHHHHh--cCCceeEecCCcchHHHHHHHHHHHhh---cCCceEEeCCCHHHHHHHHHHHHHHHhhcCC
Confidence            354 4555555555444  444799999999999999999876554   3457999999999999999999999999999


Q ss_pred             eEEEEEcCcc---HHHHHHHhcCCCcEEEeChHHH-HHHHHc
Q psy9277         130 QCHACIGGTN---LSEDLRKLDYGQHVVSGTPGRV-FDMIRS  167 (178)
Q Consensus       130 ~~~~~~g~~~---~~~~~~~~~~~~~IlV~TP~~l-~~~l~~  167 (178)
                      .+.+++++..   ..........+|||++|||++| .++|+.
T Consensus       141 sv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD  182 (762)
T TIGR03714       141 TVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLID  182 (762)
T ss_pred             cEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHH
Confidence            9988876521   2222233346899999999999 666654

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.61  E-value=1.1e-14  Score=118.36  Aligned_cols=104  Identities=17%  Similarity=0.174  Sum_probs=80.0

Q ss_pred             HHHHHHHHHHcCCc--EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC----CCceE
Q psy9277          58 IQQRSIKPIVKGRD--VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF----MNVQC  131 (178)
Q Consensus        58 ~Q~~~i~~i~~g~~--v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~----~~~~~  131 (178)
                      +|.++++.+.++.+  +++++|||||||++|++|++.      ...+++|++|+++|+.|+++.++.+...    .++.+
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~------~~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v   74 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLH------GENDTIALYPTNALIEDQTEAIKEFVDVFKPERDVNL   74 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHH------cCCCEEEEeChHHHHHHHHHHHHHHHHhcCCCCCceE
Confidence            59999999999874  889999999999999999985      2357899999999999999999888643    25666


Q ss_pred             EEEEcCccHH--HH------------------HHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         132 HACIGGTNLS--ED------------------LRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       132 ~~~~g~~~~~--~~------------------~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      ..+.|....+  ..                  .......++|++|||+.|..++++
T Consensus        75 ~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~  130 (357)
T TIGR03158        75 LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRF  130 (357)
T ss_pred             EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhh
Confidence            6666653222  00                  011123689999999999877664

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.

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.61  E-value=1e-14  Score=123.38  Aligned_cols=104  Identities=17%  Similarity=0.111  Sum_probs=81.1

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEE
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCH  132 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  132 (178)
                      ..|+++|.++++.++.+.+.++++|||+|||+++...+ ..+.. ....++|||+||++|+.|..+.+.++.......+.
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~-~~~~~-~~~~~vLilvpt~eL~~Q~~~~l~~~~~~~~~~~~  190 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLS-RYYLE-NYEGKVLIIVPTTSLVTQMIDDFVDYRLFPREAMH  190 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHH-HHHHh-cCCCeEEEEECcHHHHHHHHHHHHHhcccccccee
Confidence            47999999999999999999999999999999765432 22222 23459999999999999999999998765445555


Q ss_pred             EEEcCccHHHHHHHhcCCCcEEEeChHHHHHHH
Q psy9277         133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI  165 (178)
Q Consensus       133 ~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l  165 (178)
                      .+.+|....       .+++|+|+||+++.+..
T Consensus       191 ~i~~g~~~~-------~~~~I~VaT~qsl~~~~  216 (501)
T PHA02558        191 KIYSGTAKD-------TDAPIVVSTWQSAVKQP  216 (501)
T ss_pred             EEecCcccC-------CCCCEEEeeHHHHhhch
Confidence            666665432       35789999999997653

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.61  E-value=5.3e-14  Score=103.49  Aligned_cols=120  Identities=35%  Similarity=0.581  Sum_probs=97.3

Q ss_pred             hCCCCCCcHHHHHHHHHHHcC-CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g-~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      ..++..++++|.+++..+..+ +++++.+++|+|||.++..+++..+.... ..++++++|+++++.|....+..+....
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-~~~~l~~~p~~~~~~~~~~~~~~~~~~~   81 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-GKRVLVLVPTRELAEQWAEELKKLGPSL   81 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-CCcEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            346778999999999999998 99999999999999999999988776532 3589999999999999999998887665


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCC-cEEEeChHHHHHHHHcCC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~-~IlV~TP~~l~~~l~~~~  169 (178)
                      ........++.........+..+. +|+++|++.+.+.+....
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~  124 (201)
T smart00487       82 GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDL  124 (201)
T ss_pred             CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCC
Confidence            534455555655444555555565 999999999999887754

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.60  E-value=3.7e-14  Score=123.67  Aligned_cols=103  Identities=21%  Similarity=0.235  Sum_probs=85.7

Q ss_pred             CCcHHHHHHHHHHHcC---CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce
Q psy9277          54 KPSAIQQRSIKPIVKG---RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ  130 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g---~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (178)
                      .+++.|.+++..+.++   +++++.++||||||.+|+.++...+.   .+.++||++|+++|+.|+++.+++..   +.+
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~---~g~~vLvLvPt~~L~~Q~~~~l~~~f---g~~  217 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLA---QGKQALVLVPEIALTPQMLARFRARF---GAP  217 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHHHHHHHHHHh---CCC
Confidence            5899999999999884   78999999999999999988777665   35689999999999999999997653   678


Q ss_pred             EEEEEcCccHHHHHHHh----cCCCcEEEeChHHHH
Q psy9277         131 CHACIGGTNLSEDLRKL----DYGQHVVSGTPGRVF  162 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~----~~~~~IlV~TP~~l~  162 (178)
                      +..++|+.+..++...+    ...++|+||||+.+.
T Consensus       218 v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~  253 (679)
T PRK05580        218 VAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF  253 (679)
T ss_pred             EEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc
Confidence            88999998776554332    245799999998874

>KOG0951|consensus

Probab=99.59  E-value=1.1e-14  Score=129.08  Aligned_cols=168  Identities=19%  Similarity=0.211  Sum_probs=125.5

Q ss_pred             CCCCccceeccCCCCCCcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCCh
Q psy9277           3 AGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTG   81 (178)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsG   81 (178)
                      |.|+-+.+++-.+++..............+-+.-..++.|-..++.  |...++.+|.......+. ..|+++|||||+|
T Consensus       260 P~GS~rl~kk~yeevhVPa~~~~pf~~~Ekl~~iselP~Wnq~aF~--g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaG  337 (1674)
T KOG0951|consen  260 PQGSFRLKKKGYEEVHVPAPSYFPFHKEEKLVKISELPKWNQPAFF--GKQSLNRIQSKVYDAALRGDENMLLCAPTGAG  337 (1674)
T ss_pred             CCccEEEecCCceEEeCCCCCCCCCCccceeEeecCCcchhhhhcc--cchhhhHHHHHHHHHHhcCcCcEEEeccCCCC
Confidence            3444444444444443333322222233333444567888888875  566799999999999888 4799999999999


Q ss_pred             HHHHHHHHHHHHhhhcCC--------CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcE
Q psy9277          82 KTATFSISILQSLDTQLR--------ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHV  153 (178)
Q Consensus        82 KTl~~ll~il~~l~~~~~--------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I  153 (178)
                      ||-.+++.+++.+....+        ..+.+|++|+++|++.+...+.+....+|++|.-.+|+.....+.-   .+.+|
T Consensus       338 KTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLvqE~VgsfSkRla~~GI~V~ElTgD~~l~~~qi---eeTqV  414 (1674)
T KOG0951|consen  338 KTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALVQEMVGSFSKRLAPLGITVLELTGDSQLGKEQI---EETQV  414 (1674)
T ss_pred             chHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHHHHHHHHHHhhccccCcEEEEecccccchhhhh---hccee
Confidence            999999999999865332        3589999999999999999998888999999999999987654321   35789


Q ss_pred             EEeChHHHHHHHHcCCCCCcccc
Q psy9277         154 VSGTPGRVFDMIRSSQGRRTTNQ  176 (178)
Q Consensus       154 lV~TP~~l~~~l~~~~~~~~~~~  176 (178)
                      +||||++- |.+.++..+..+++
T Consensus       415 IV~TPEK~-DiITRk~gdraY~q  436 (1674)
T KOG0951|consen  415 IVTTPEKW-DIITRKSGDRAYEQ  436 (1674)
T ss_pred             EEeccchh-hhhhcccCchhHHH
Confidence            99999997 78888877776653

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.59  E-value=1.5e-14  Score=126.88  Aligned_cols=111  Identities=17%  Similarity=0.204  Sum_probs=92.3

Q ss_pred             CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      +|. +++++|...--.+  ...-+..++||+|||++|.+|++..+..   +..++||+||++||.|.++.+..+.+.+|+
T Consensus        79 lg~-~~ydvQliGg~~L--h~G~Iaem~TGeGKTL~a~Lpa~~~al~---G~~V~VvTpn~yLA~qd~e~m~~l~~~lGL  152 (896)
T PRK13104         79 LGL-RHFDVQLIGGMVL--HEGNIAEMRTGEGKTLVATLPAYLNAIS---GRGVHIVTVNDYLAKRDSQWMKPIYEFLGL  152 (896)
T ss_pred             cCC-CcchHHHhhhhhh--ccCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEcCCHHHHHHHHHHHHHHhcccCc
Confidence            354 4667766544333  4455899999999999999999977653   456999999999999999999999999999


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      ++.+++|+.+..++....  .+||++|||++| .|+|+.+
T Consensus       153 tv~~i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~  190 (896)
T PRK13104        153 TVGVIYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDN  190 (896)
T ss_pred             eEEEEeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcC
Confidence            999999999887765543  689999999999 9999887

>PRK13766 Hef nuclease; Provisional

Probab=99.57  E-value=8.8e-14  Score=123.26  Aligned_cols=116  Identities=19%  Similarity=0.167  Sum_probs=95.0

Q ss_pred             CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce
Q psy9277          51 GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ  130 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (178)
                      +..+++++|.+++..++.+ |+++++|||+|||+++++++...+.  ..+.++|||+||++|+.|+.+.++.+....+..
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~--~~~~~vLvl~Pt~~L~~Q~~~~~~~~~~~~~~~   88 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLH--KKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEK   88 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHH--hCCCeEEEEeCcHHHHHHHHHHHHHHhCCCCce
Confidence            4457899999999888887 9999999999999999999888773  245699999999999999999998886554567


Q ss_pred             EEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         131 CHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      +..+.|+.+..++.. +..+++|+|+||+.+...+..+.+
T Consensus        89 v~~~~g~~~~~~r~~-~~~~~~iiv~T~~~l~~~l~~~~~  127 (773)
T PRK13766         89 IVVFTGEVSPEKRAE-LWEKAKVIVATPQVIENDLIAGRI  127 (773)
T ss_pred             EEEEeCCCCHHHHHH-HHhCCCEEEECHHHHHHHHHcCCC
Confidence            888888887765543 344679999999999877765544

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

Probab=99.56  E-value=5.7e-14  Score=115.37  Aligned_cols=119  Identities=18%  Similarity=0.146  Sum_probs=101.8

Q ss_pred             CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceE
Q psy9277          52 FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC  131 (178)
Q Consensus        52 ~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  131 (178)
                      ..+++.+|.......+.+ |++++.|||-|||+++++-+..++....  .++|+++||+.|+.|+++.|+++..-..-.+
T Consensus        13 ~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~--~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i   89 (542)
T COG1111          13 TIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFG--GKVLFLAPTKPLVLQHAEFCRKVTGIPEDEI   89 (542)
T ss_pred             cccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcC--CeEEEecCCchHHHHHHHHHHHHhCCChhhe
Confidence            346888998887776666 9999999999999999999988877643  2899999999999999999999987777788


Q ss_pred             EEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCcc
Q psy9277         132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTT  174 (178)
Q Consensus       132 ~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~~  174 (178)
                      +.++|..+.+++...+. ..+|+|+||+.+..-|..+.+++..
T Consensus        90 ~~ltGev~p~~R~~~w~-~~kVfvaTPQvveNDl~~Grid~~d  131 (542)
T COG1111          90 AALTGEVRPEEREELWA-KKKVFVATPQVVENDLKAGRIDLDD  131 (542)
T ss_pred             eeecCCCChHHHHHHHh-hCCEEEeccHHHHhHHhcCccChHH
Confidence            99999999888766655 5689999999999999999887643

>KOG0354|consensus

Probab=99.50  E-value=9.5e-14  Score=119.29  Aligned_cols=130  Identities=18%  Similarity=0.167  Sum_probs=99.7

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      +++...+.+.--..-.++.+|.+.....+ |+|++|++|||+|||+++...+.+++..... .++|+++|++.|+.|+..
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            44444444432234478999999999999 9999999999999999999999888766544 799999999999999997


Q ss_pred             HHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         119 VVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       119 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      .+..++..  ..+....||.........+-..++|+|.||+-|.+.|.++..+-
T Consensus       125 ~~~~~~~~--~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~  176 (746)
T KOG0354|consen  125 CFSIYLIP--YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDE  176 (746)
T ss_pred             HHhhccCc--ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccc
Confidence            77777665  45555556643333333555678999999999999998776554

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.48  E-value=3.6e-13  Score=117.92  Aligned_cols=113  Identities=19%  Similarity=0.278  Sum_probs=95.3

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHH-HHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL-QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il-~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      -+|. +|+++|....-.+..|+  +..+.||+|||+++.+|++ +.+.    +..+-|++||..||.|.++.+..+.+.+
T Consensus        77 ~lg~-~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~----G~~V~IvTpn~yLA~rd~e~~~~l~~~L  149 (830)
T PRK12904         77 VLGM-RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT----GKGVHVVTVNDYLAKRDAEWMGPLYEFL  149 (830)
T ss_pred             HhCC-CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc----CCCEEEEecCHHHHHHHHHHHHHHHhhc
Confidence            3465 68889888776665554  9999999999999999996 5442    3357799999999999999999999999


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCCC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQG  170 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~~  170 (178)
                      |+++.++.|+.+..++....  .+||++|||++| .|+|+.+..
T Consensus       150 Glsv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~  191 (830)
T PRK12904        150 GLSVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMV  191 (830)
T ss_pred             CCeEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccc
Confidence            99999999999988776664  499999999999 999987653

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.43  E-value=1.1e-12  Score=113.70  Aligned_cols=104  Identities=15%  Similarity=0.133  Sum_probs=79.4

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHH---------HHHHHHHHhh---hcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTAT---------FSISILQSLD---TQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~---------~ll~il~~l~---~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      -.+|.++++.+.+|++++++|+||||||.+         |++|.+..+.   ....+.++++++|+++||.|+...+.+.
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            358999999999999999999999999997         5555555443   2334568999999999999999998765


Q ss_pred             ccC---CCceEEEEEcCccHHHHHHHhcCCCcEEEeChHH
Q psy9277         124 GDF---MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGR  160 (178)
Q Consensus       124 ~~~---~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~  160 (178)
                      ...   .+..+...+|+.+.. .......+.+|+|+|++.
T Consensus       246 vg~~~~~g~~v~v~~Gg~~~~-~~~t~~k~~~Ilv~T~~L  284 (675)
T PHA02653        246 LGFDEIDGSPISLKYGSIPDE-LINTNPKPYGLVFSTHKL  284 (675)
T ss_pred             hCccccCCceEEEEECCcchH-HhhcccCCCCEEEEeCcc
Confidence            443   367788889998732 222222367999999864

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

Probab=99.41  E-value=3.4e-12  Score=108.57  Aligned_cols=123  Identities=24%  Similarity=0.282  Sum_probs=103.2

Q ss_pred             CCCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          37 MGLREDLLRGI-YAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        37 ~~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      +..+..+++.+ .++.| ++|..|..++..|..+      .+-+++|.-|||||++++++++..+.   .+.++..++||
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            34455666665 78888 5999999999999874      58899999999999999999998776   57899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---cCC-CcEEEeChHHHHH
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---DYG-QHVVSGTPGRVFD  163 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~~-~~IlV~TP~~l~~  163 (178)
                      .-||.|.++.+.++...+|+++..++|....+.+...+   .+| .||+|||-.-+.|
T Consensus       321 EILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd  378 (677)
T COG1200         321 EILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQD  378 (677)
T ss_pred             HHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhc
Confidence            99999999999999999999999999998776554443   345 7999999755543

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.40  E-value=2.6e-12  Score=113.77  Aligned_cols=101  Identities=17%  Similarity=0.217  Sum_probs=80.5

Q ss_pred             HHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH-HHhccCCCceEEEEEcC
Q psy9277          59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV-LALGDFMNVQCHACIGG  137 (178)
Q Consensus        59 Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~-~~~~~~~~~~~~~~~g~  137 (178)
                      -.+.+..+.++++++++|+||||||.+|.+++++...   ...+++++.|+|++|.|+++.+ ..+....|..+...+++
T Consensus        10 ~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~---~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~   86 (812)
T PRK11664         10 LPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG---INGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRA   86 (812)
T ss_pred             HHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC---cCCeEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecC
Confidence            3455566777899999999999999999999997543   2358999999999999999998 45566677788877766


Q ss_pred             ccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         138 TNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       138 ~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .+..      ....+|+|+|||+|++++.+.
T Consensus        87 ~~~~------~~~t~I~v~T~G~Llr~l~~d  111 (812)
T PRK11664         87 ESKV------GPNTRLEVVTEGILTRMIQRD  111 (812)
T ss_pred             cccc------CCCCcEEEEChhHHHHHHhhC
Confidence            5432      234689999999999998764

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

Probab=99.40  E-value=2.3e-12  Score=109.16  Aligned_cols=107  Identities=20%  Similarity=0.264  Sum_probs=92.2

Q ss_pred             HHH-HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          45 RGI-YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        45 ~~l-~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..| +-+||..+.+-|.++|..+++|+|+++..|||.||++||.+|.+-.      .+.+|+|+|..+|++++.+.++..
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~------~G~TLVVSPLiSLM~DQV~~l~~~   80 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL------EGLTLVVSPLISLMKDQVDQLEAA   80 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc------CCCEEEECchHHHHHHHHHHHHHc
Confidence            344 3469999999999999999999999999999999999999999863      448999999999999999999876


Q ss_pred             ccCCCceEEEEEcCccHHHHHHHhc---C-CCcEEEeChHHH
Q psy9277         124 GDFMNVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTPGRV  161 (178)
Q Consensus       124 ~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~IlV~TP~~l  161 (178)
                          |+....+.+..+.+++...+.   . ..+++.-+|++|
T Consensus        81 ----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl  118 (590)
T COG0514          81 ----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERL  118 (590)
T ss_pred             ----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhh
Confidence                788888888888777655443   2 369999999998

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.39  E-value=3.4e-12  Score=103.63  Aligned_cols=93  Identities=15%  Similarity=0.148  Sum_probs=67.1

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHH---------
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS---------  141 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~---------  141 (178)
                      ++++.+|||||||++|+++++..+.. ....+++|++|+++|+.|+++.+..+...   .+..++++....         
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~-~~~~~ii~v~P~~~L~~q~~~~l~~~f~~---~~~~~~~~~~~~~~~~~~~~~   76 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS-QKADRVIIALPTRATINAMYRRAKELFGS---NLGLLHSSSSFKRIKEMGDSE   76 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh-CCCCeEEEEeehHHHHHHHHHHHHHHhCc---ccEEeeccHHHHHHhccCCch
Confidence            58999999999999999999987654 34569999999999999999999887432   233334332211         


Q ss_pred             ---HHHHHh-c-----CCCcEEEeChHHHHHHHHc
Q psy9277         142 ---EDLRKL-D-----YGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       142 ---~~~~~~-~-----~~~~IlV~TP~~l~~~l~~  167 (178)
                         ...... .     ...+|+|+||+++...+.+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~  111 (358)
T TIGR01587        77 EFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFG  111 (358)
T ss_pred             hHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhc
Confidence               100010 0     1357999999999887765

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.

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

Probab=99.38  E-value=1.5e-11  Score=108.21  Aligned_cols=114  Identities=18%  Similarity=0.218  Sum_probs=88.7

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      ..|+ +||..|+.+...+..|+++-+.||||.|||..-++..+....   ++.+++||+||..|+.|.++.+.++....+
T Consensus        78 ~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~---kgkr~yii~PT~~Lv~Q~~~kl~~~~e~~~  153 (1187)
T COG1110          78 ATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAK---KGKRVYIIVPTTTLVRQVYERLKKFAEDAG  153 (1187)
T ss_pred             hhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHHHHh---cCCeEEEEecCHHHHHHHHHHHHHHHhhcC
Confidence            3466 799999999999999999999999999999877666655333   457999999999999999999999987655


Q ss_pred             -ceEEE-EEcCccHHHHHH---HhcC-CCcEEEeChHHHHHHHH
Q psy9277         129 -VQCHA-CIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       129 -~~~~~-~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~~~l~  166 (178)
                       ..+.. +++..+.++...   .+.+ +.||+|+|.+.|...+.
T Consensus       154 ~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e  197 (1187)
T COG1110         154 SLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFE  197 (1187)
T ss_pred             CcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHH
Confidence             33333 566655554333   3333 58999999999966654

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.37  E-value=2.5e-11  Score=84.26  Aligned_cols=97  Identities=37%  Similarity=0.534  Sum_probs=79.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcC
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY  149 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  149 (178)
                      +++++.+|||+|||..++..+....... ...+++|++|++.++.|..+.+...... +..+..+.+.............
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~-~~~~~lv~~p~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   78 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE-GIKVGYLIGGTSIKQQEKLLSG   78 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhcc-cCCCEEEEcCcHHHHHHHHHHHHHHhhC-CcEEEEEecCcchhHHHHHhcC
Confidence            4789999999999999988888766542 3469999999999999999998877665 6777778877776666555556


Q ss_pred             CCcEEEeChHHHHHHHHcC
Q psy9277         150 GQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       150 ~~~IlV~TP~~l~~~l~~~  168 (178)
                      +.+|+++|++.+...+...
T Consensus        79 ~~~i~i~t~~~~~~~~~~~   97 (144)
T cd00046          79 KTDIVVGTPGRLLDELERL   97 (144)
T ss_pred             CCCEEEECcHHHHHHHHcC
Confidence            7899999999998877654

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

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.36  E-value=1.2e-11  Score=109.55  Aligned_cols=101  Identities=19%  Similarity=0.274  Sum_probs=80.2

Q ss_pred             HHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH-HhccCCCceEEEEEcC
Q psy9277          59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL-ALGDFMNVQCHACIGG  137 (178)
Q Consensus        59 Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~-~~~~~~~~~~~~~~g~  137 (178)
                      -.+.+..+.++.+++++|+||||||.+|.+++++...   .+.+++++.|+|++|.|+++.+. .+....|..+...+.+
T Consensus         7 ~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~   83 (819)
T TIGR01970         7 LPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRG   83 (819)
T ss_pred             HHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEcc
Confidence            3455666777899999999999999999999998753   34699999999999999999884 5555667777666655


Q ss_pred             ccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         138 TNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       138 ~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .+      ......+|+|+|||+|++++.+.
T Consensus        84 ~~------~~s~~t~I~v~T~G~Llr~l~~d  108 (819)
T TIGR01970        84 EN------KVSRRTRLEVVTEGILTRMIQDD  108 (819)
T ss_pred             cc------ccCCCCcEEEECCcHHHHHHhhC
Confidence            43      22345789999999999999764

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.

>KOG0353|consensus

Probab=99.34  E-value=8.4e-12  Score=100.01  Aligned_cols=118  Identities=16%  Similarity=0.236  Sum_probs=94.4

Q ss_pred             ccCCCCHHHHHHHH-hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHH
Q psy9277          35 DNMGLREDLLRGIY-AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELA  113 (178)
Q Consensus        35 ~~~~l~~~i~~~l~-~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~  113 (178)
                      ++|+.+.+..+.|+ .+..++++|.|..+|...+.|+++++..|||.||++||.+|.+-      ....+++++|..+|+
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~------adg~alvi~plislm  147 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALC------ADGFALVICPLISLM  147 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHh------cCCceEeechhHHHH
Confidence            56778888888774 55678899999999999999999999999999999999999986      456999999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEEcCccHHHHHHH---h-c--CCCcEEEeChHHHH
Q psy9277         114 VQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK---L-D--YGQHVVSGTPGRVF  162 (178)
Q Consensus       114 ~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~-~--~~~~IlV~TP~~l~  162 (178)
                      .++.-.++.+    |+....+....+.++....   + .  ....++..||+++.
T Consensus       148 edqil~lkql----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekia  198 (695)
T KOG0353|consen  148 EDQILQLKQL----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIA  198 (695)
T ss_pred             HHHHHHHHHh----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHH
Confidence            9999999877    6665566656555443221   1 1  13578899999984

>KOG0352|consensus

Probab=99.29  E-value=1.7e-11  Score=99.45  Aligned_cols=110  Identities=22%  Similarity=0.283  Sum_probs=87.2

Q ss_pred             HHHHHHH-hCCCCCC-cHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          42 DLLRGIY-AYGFEKP-SAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        42 ~i~~~l~-~~g~~~~-~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+.++|+ -+|+.++ ++.|.+++..+.. .+||.|++|||+||++||.+|.|-      .+...|+++|..+|++++.+
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~------~~gITIV~SPLiALIkDQiD   79 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALV------HGGITIVISPLIALIKDQID   79 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHH------hCCeEEEehHHHHHHHHHHH
Confidence            4556664 4466544 8999999999877 579999999999999999999986      34589999999999999999


Q ss_pred             HHHHhccCCCceEEEEEcCccHHHHHHHhc------CCCcEEEeChHHH
Q psy9277         119 VVLALGDFMNVQCHACIGGTNLSEDLRKLD------YGQHVVSGTPGRV  161 (178)
Q Consensus       119 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~------~~~~IlV~TP~~l  161 (178)
                      .+..+    .+.+..+.+..+..++.+.+.      ....++.-||+.-
T Consensus        80 HL~~L----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~A  124 (641)
T KOG0352|consen   80 HLKRL----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGA  124 (641)
T ss_pred             HHHhc----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhh
Confidence            99877    677777777777766655442      2457999999863

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

Probab=99.29  E-value=3.2e-11  Score=107.99  Aligned_cols=98  Identities=21%  Similarity=0.278  Sum_probs=77.9

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHH----HHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIK----PIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAV  114 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~----~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~  114 (178)
                      +++...+.+...||+ +++.|.+++.    .+.+++++++.||||+|||++|++|++....   .+.+++|.+||++|..
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~---~~~~vvi~t~t~~Lq~  306 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI---TEKPVVISTNTKVLQS  306 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc---CCCeEEEEeCcHHHHH
Confidence            345677778788986 8999998776    4445899999999999999999999988655   3458999999999999


Q ss_pred             HHHH-HHHHhccCCC--ceEEEEEcCccH
Q psy9277         115 QIQK-VVLALGDFMN--VQCHACIGGTNL  140 (178)
Q Consensus       115 q~~~-~~~~~~~~~~--~~~~~~~g~~~~  140 (178)
                      |+.. .+..+.+.++  ++++.+.|....
T Consensus       307 Ql~~~~~~~l~~~~~~~~~~~~~kG~~~y  335 (850)
T TIGR01407       307 QLLEKDIPLLNEILNFKINAALIKGKSNY  335 (850)
T ss_pred             HHHHHHHHHHHHHcCCCceEEEEEcchhh
Confidence            9876 4655555444  888888877644

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

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

Probab=99.29  E-value=2.1e-11  Score=108.56  Aligned_cols=113  Identities=20%  Similarity=0.218  Sum_probs=90.2

Q ss_pred             HHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          46 GIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        46 ~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .....+| .+.++|++++-.+.+|.+|+|+||||+|||++...++...+.   ++.+++|.+|.++|.+|.++.+.....
T Consensus       112 ~~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~---~~qrviYTsPIKALsNQKyrdl~~~fg  187 (1041)
T COG4581         112 PAREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALR---DGQRVIYTSPIKALSNQKYRDLLAKFG  187 (1041)
T ss_pred             HHHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHH---cCCceEeccchhhhhhhHHHHHHHHhh
Confidence            3466788 599999999999999999999999999999999888877665   455799999999999999998854433


Q ss_pred             CCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         126 FMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       126 ~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      ...-.+.+.+|+.+..       .+..++|.|-+-|-.|+..+.
T Consensus       188 dv~~~vGL~TGDv~IN-------~~A~clvMTTEILRnMlyrg~  224 (1041)
T COG4581         188 DVADMVGLMTGDVSIN-------PDAPCLVMTTEILRNMLYRGS  224 (1041)
T ss_pred             hhhhhccceecceeeC-------CCCceEEeeHHHHHHHhccCc
Confidence            2222356667776654       346788888899999988773

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.29  E-value=1.1e-11  Score=108.85  Aligned_cols=110  Identities=21%  Similarity=0.256  Sum_probs=89.4

Q ss_pred             CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce
Q psy9277          51 GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ  130 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (178)
                      |. .|+++|...-  +.-...-+..++||.|||++|.+|++.....   +..+.||+|+..||.+..+.+..+.+.+|++
T Consensus        80 gm-~~ydVQliGg--l~L~~G~IaEm~TGEGKTL~a~lp~~l~al~---g~~VhIvT~ndyLA~RD~e~m~~l~~~lGls  153 (908)
T PRK13107         80 EM-RHFDVQLLGG--MVLDSNRIAEMRTGEGKTLTATLPAYLNALT---GKGVHVITVNDYLARRDAENNRPLFEFLGLT  153 (908)
T ss_pred             CC-CcCchHHhcc--hHhcCCccccccCCCCchHHHHHHHHHHHhc---CCCEEEEeCCHHHHHHHHHHHHHHHHhcCCe
Confidence            44 4666766433  3334566999999999999999999876653   4459999999999999999999999999999


Q ss_pred             EEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         131 CHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      +.++.++.+..+...  ..+|||++|||++| .|+|+.+
T Consensus       154 v~~i~~~~~~~~r~~--~Y~~dI~YgT~~e~gfDyLrdn  190 (908)
T PRK13107        154 VGINVAGLGQQEKKA--AYNADITYGTNNEFGFDYLRDN  190 (908)
T ss_pred             EEEecCCCCHHHHHh--cCCCCeEEeCCCcccchhhhcc
Confidence            999999888754322  23799999999999 9999877

>TIGR00595 priA primosomal protein N'

Probab=99.19  E-value=1.4e-10  Score=98.25  Aligned_cols=84  Identities=26%  Similarity=0.236  Sum_probs=64.9

Q ss_pred             EEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---c-
Q psy9277          73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---D-  148 (178)
Q Consensus        73 ~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~-  148 (178)
                      ++.||||||||.+|+..+...+.   .+.+++|++|+++|+.|+++.+++..   +..+..++++.+..++...+   . 
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~---~g~~vLvlvP~i~L~~Q~~~~l~~~f---~~~v~vlhs~~~~~er~~~~~~~~~   74 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLA---LGKSVLVLVPEIALTPQMIQRFKYRF---GSQVAVLHSGLSDSEKLQAWRKVKN   74 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCcHHHHHHHHHHHHHHh---CCcEEEEECCCCHHHHHHHHHHHHc
Confidence            46899999999999776655443   35689999999999999999997653   56778888888766543332   2 


Q ss_pred             CCCcEEEeChHHHH
Q psy9277         149 YGQHVVSGTPGRVF  162 (178)
Q Consensus       149 ~~~~IlV~TP~~l~  162 (178)
                      ...+|+|||+..+.
T Consensus        75 g~~~IVVGTrsalf   88 (505)
T TIGR00595        75 GEILVVIGTRSALF   88 (505)
T ss_pred             CCCCEEECChHHHc
Confidence            34799999998774

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).

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

Probab=99.18  E-value=1.4e-10  Score=103.16  Aligned_cols=88  Identities=26%  Similarity=0.406  Sum_probs=71.8

Q ss_pred             HhCCCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH-HHHHH
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ-KVVLA  122 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~-~~~~~  122 (178)
                      .-.|| ++++-|.++...+..    +..+++.|+||+|||++|++|++...    .+.++||++||++|++|+. +.+..
T Consensus       240 ~~~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----~~~~vvI~t~T~~Lq~Ql~~~~i~~  314 (820)
T PRK07246        240 ALLGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQIMAEEVKA  314 (820)
T ss_pred             ccCCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----CCCcEEEEeCcHHHHHHHHHHHHHH
Confidence            33466 589999997765544    78999999999999999999988753    3468999999999999994 66777


Q ss_pred             hccCCCceEEEEEcCccH
Q psy9277         123 LGDFMNVQCHACIGGTNL  140 (178)
Q Consensus       123 ~~~~~~~~~~~~~g~~~~  140 (178)
                      +.+.+++.+..+.|+.+.
T Consensus       315 l~~~~~~~~~~~kg~~~y  332 (820)
T PRK07246        315 IQEVFHIDCHSLKGPQNY  332 (820)
T ss_pred             HHHhcCCcEEEEECCccc
Confidence            777788888888877653

>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=99.18  E-value=3.6e-10  Score=82.68  Aligned_cols=108  Identities=21%  Similarity=0.189  Sum_probs=74.5

Q ss_pred             CCcHHHHHHHHHHHc-------CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          54 KPSAIQQRSIKPIVK-------GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~-------g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      +++++|.+++..+..       .+++++.+|||||||.+++..+.....      ++++++|+..|+.|..+.+..+...
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            589999999999884       589999999999999998854544322      8999999999999999999766543


Q ss_pred             CCceEEE-----------EEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         127 MNVQCHA-----------CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       127 ~~~~~~~-----------~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      .......           ..................+++++|.+.+......
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~  128 (184)
T PF04851_consen   77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKE  128 (184)
T ss_dssp             SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH
T ss_pred             hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhccc
Confidence            2111100           0111111122223345678999999999888654

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 ....

>KOG0351|consensus

Probab=99.16  E-value=8.4e-11  Score=104.78  Aligned_cols=110  Identities=18%  Similarity=0.195  Sum_probs=90.6

Q ss_pred             HHHHH-HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          43 LLRGI-YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        43 i~~~l-~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      ....+ ..+|.+.+.+-|.++|..++.|+|++|.+|||.||++||.+|++-      .++-.|+|.|..+|++++...+.
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l------~~gitvVISPL~SLm~DQv~~L~  325 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALL------LGGVTVVISPLISLMQDQVTHLS  325 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeeccccc------cCCceEEeccHHHHHHHHHHhhh
Confidence            44444 677999999999999999999999999999999999999999875      34589999999999999988884


Q ss_pred             HhccCCCceEEEEEcCccHHHHHH---HhcC---CCcEEEeChHHHH
Q psy9277         122 ALGDFMNVQCHACIGGTNLSEDLR---KLDY---GQHVVSGTPGRVF  162 (178)
Q Consensus       122 ~~~~~~~~~~~~~~g~~~~~~~~~---~~~~---~~~IlV~TP~~l~  162 (178)
                      .    .++....+.++....++..   .+.+   .++|+.-||+++.
T Consensus       326 ~----~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~  368 (941)
T KOG0351|consen  326 K----KGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVV  368 (941)
T ss_pred             h----cCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhh
Confidence            3    3788888888887764433   3333   4699999999984

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

Probab=99.12  E-value=5e-10  Score=96.55  Aligned_cols=75  Identities=21%  Similarity=0.225  Sum_probs=61.3

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc-cC--CCceEEEEEcCccH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG-DF--MNVQCHACIGGTNL  140 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~--~~~~~~~~~g~~~~  140 (178)
                      .+.+++.+++.|+||+|||++|++|++..+... .+.++||++||++|+.|+++.+..+. +.  .+++++.+.|..++
T Consensus        12 al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-~~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i~~~~lkGr~nY   89 (636)
T TIGR03117        12 SLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-PDQKIAIAVPTLALMGQLWSELERLTAEGLAGPVQAGFFPGSQEF   89 (636)
T ss_pred             HHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-cCceEEEECCcHHHHHHHHHHHHHHHHhhcCCCeeEEEEECCccc
Confidence            344588999999999999999999999876532 34699999999999999999988887 43  36777777777654

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.05  E-value=1.6e-09  Score=94.50  Aligned_cols=98  Identities=16%  Similarity=0.116  Sum_probs=74.4

Q ss_pred             CCcHHHHHHHHHHHc-C--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce
Q psy9277          54 KPSAIQQRSIKPIVK-G--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ  130 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~-g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (178)
                      .++++|.+++..+.. |  ++.++++|||+|||+..+..+.. +     +.++|||||+..|+.|..+.+.++.......
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~-l-----~k~tLILvps~~Lv~QW~~ef~~~~~l~~~~  328 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACT-V-----KKSCLVLCTSAVSVEQWKQQFKMWSTIDDSQ  328 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHH-h-----CCCEEEEeCcHHHHHHHHHHHHHhcCCCCce
Confidence            589999999998874 4  47899999999999998765543 2     2479999999999999999999886544456


Q ss_pred             EEEEEcCccHHHHHHHhcCCCcEEEeChHHHH
Q psy9277         131 CHACIGGTNLSEDLRKLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~  162 (178)
                      +..+.|+....     ......|+|+|.+.+.
T Consensus       329 I~~~tg~~k~~-----~~~~~~VvVtTYq~l~  355 (732)
T TIGR00603       329 ICRFTSDAKER-----FHGEAGVVVSTYSMVA  355 (732)
T ss_pred             EEEEecCcccc-----cccCCcEEEEEHHHhh
Confidence            66666653221     1123679999998764

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).

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

Probab=99.05  E-value=5.1e-09  Score=94.00  Aligned_cols=119  Identities=18%  Similarity=0.121  Sum_probs=95.2

Q ss_pred             CCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          38 GLREDLLRGI-YAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        38 ~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      .-+.+..+.+ ..++|. -|+-|..||..+.++      +|-++||.-|-|||-+++=++.....   ++.++.++|||.
T Consensus       578 ~~d~~~q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~---~GKQVAvLVPTT  653 (1139)
T COG1197         578 PPDTEWQEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVM---DGKQVAVLVPTT  653 (1139)
T ss_pred             CCChHHHHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhc---CCCeEEEEcccH
Confidence            3455556666 456775 699999999999873      59999999999999998776665554   568999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---cC-CCcEEEeChHH
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---DY-GQHVVSGTPGR  160 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~-~~~IlV~TP~~  160 (178)
                      -||+|.++.+++-...+++++..+.-=.+.+++...+   .+ ..||||||-.-
T Consensus       654 lLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrL  707 (1139)
T COG1197         654 LLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRL  707 (1139)
T ss_pred             HhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHh
Confidence            9999999999999999999998887666666655444   34 47999999643

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

Probab=99.02  E-value=3.2e-09  Score=97.01  Aligned_cols=109  Identities=18%  Similarity=0.135  Sum_probs=75.2

Q ss_pred             CCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .++++|.+|+..+..     .++.+++++||||||.+.+ .++.++.......++|+|+|+++|+.|..+.+..+.....
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai-~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~~~~  491 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI-ALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKIEGD  491 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH-HHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhcccccc
Confidence            589999999987763     4689999999999998854 3445555544556999999999999999999987743222


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHH
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI  165 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l  165 (178)
                      ..+..+++.....+.  .......|+|+|.+++...+
T Consensus       492 ~~~~~i~~i~~L~~~--~~~~~~~I~iaTiQtl~~~~  526 (1123)
T PRK11448        492 QTFASIYDIKGLEDK--FPEDETKVHVATVQGMVKRI  526 (1123)
T ss_pred             cchhhhhchhhhhhh--cccCCCCEEEEEHHHHHHhh
Confidence            111111211111111  11235689999999987664

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.01  E-value=3.1e-09  Score=93.25  Aligned_cols=113  Identities=17%  Similarity=0.221  Sum_probs=93.8

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +.+|. +|+++|...--.+..|+  +..+.||+|||+++.+|++....   .+..+-+++|+.-||.|-++.+..+.+.+
T Consensus        75 R~~g~-~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al---~G~~v~vvT~neyLA~Rd~e~~~~~~~~L  148 (796)
T PRK12906         75 RVLGL-RPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNAL---TGKGVHVVTVNEYLSSRDATEMGELYRWL  148 (796)
T ss_pred             HHhCC-CCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHH---cCCCeEEEeccHHHHHhhHHHHHHHHHhc
Confidence            34465 68999988776666666  99999999999999998887655   46789999999999999999999999999


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      |+++.++.++.+..++....  .|||+.+|...| .|+|+.+
T Consensus       149 Gl~vg~i~~~~~~~~r~~~y--~~dI~Y~t~~e~gfDyLRD~  188 (796)
T PRK12906        149 GLTVGLNLNSMSPDEKRAAY--NCDITYSTNSELGFDYLRDN  188 (796)
T ss_pred             CCeEEEeCCCCCHHHHHHHh--cCCCeecCCccccccchhhc
Confidence            99999999988877665443  589999999888 4566654

>PRK09694 helicase Cas3; Provisional

Probab=99.00  E-value=6e-09  Score=93.00  Aligned_cols=86  Identities=19%  Similarity=0.134  Sum_probs=64.0

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC--Cce
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM--NVQ  130 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~--~~~  130 (178)
                      ..|+|+|..+......+..+++.+|||+|||.+++..+.. +.......+++|..||++.++++++++.++.+..  ...
T Consensus       285 ~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~-l~~~~~~~gi~~aLPT~Atan~m~~Rl~~~~~~~f~~~~  363 (878)
T PRK09694        285 YQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWR-LIDQGLADSIIFALPTQATANAMLSRLEALASKLFPSPN  363 (878)
T ss_pred             CCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHH-HHHhCCCCeEEEECcHHHHHHHHHHHHHHHHHHhcCCCc
Confidence            4799999988655445678999999999999998776654 3333334689999999999999999987654321  345


Q ss_pred             EEEEEcCcc
Q psy9277         131 CHACIGGTN  139 (178)
Q Consensus       131 ~~~~~g~~~  139 (178)
                      +.+.+|...
T Consensus       364 v~L~Hg~a~  372 (878)
T PRK09694        364 LILAHGNSR  372 (878)
T ss_pred             eEeecCcch
Confidence            666666543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.99  E-value=4.3e-09  Score=83.42  Aligned_cols=73  Identities=23%  Similarity=0.244  Sum_probs=58.8

Q ss_pred             CCCCCcHHHHHHHHH----HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC---CceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          51 GFEKPSAIQQRSIKP----IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR---ETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~----i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .|+ |++.|.+.+..    +.+|.++++.||||+|||++|++|++..+.....   +.+++|.++|.++..|....+++.
T Consensus         6 Py~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        6 PYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            454 69999996554    4458999999999999999999999987654332   238999999999999988888766


Q ss_pred             c
Q psy9277         124 G  124 (178)
Q Consensus       124 ~  124 (178)
                      .
T Consensus        85 ~   85 (289)
T smart00488       85 M   85 (289)
T ss_pred             c
Confidence            4

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.99  E-value=4.3e-09  Score=83.42  Aligned_cols=73  Identities=23%  Similarity=0.244  Sum_probs=58.8

Q ss_pred             CCCCCcHHHHHHHHH----HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC---CceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          51 GFEKPSAIQQRSIKP----IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR---ETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~----i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~---~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .|+ |++.|.+.+..    +.+|.++++.||||+|||++|++|++..+.....   +.+++|.++|.++..|....+++.
T Consensus         6 Py~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        6 PYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccHHHHHHHHHHHHhc
Confidence            454 69999996554    4458999999999999999999999987654332   238999999999999988888766


Q ss_pred             c
Q psy9277         124 G  124 (178)
Q Consensus       124 ~  124 (178)
                      .
T Consensus        85 ~   85 (289)
T smart00489       85 M   85 (289)
T ss_pred             c
Confidence            4

>KOG0951|consensus

Probab=98.99  E-value=5.6e-10  Score=100.02  Aligned_cols=106  Identities=20%  Similarity=0.308  Sum_probs=88.0

Q ss_pred             CCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH-HHhccCCCce
Q psy9277          53 EKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV-LALGDFMNVQ  130 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~-~~~~~~~~~~  130 (178)
                      ...+++|.++++.+.+ +.++++++|+|||||.|+-++++.    .....++++++|..+.+..+++.+ +++.+..|.+
T Consensus      1142 ~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~G~~ 1217 (1674)
T KOG0951|consen 1142 QDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLLGLR 1217 (1674)
T ss_pred             cccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----CccceEEEEecchHHHHHHHHHHHHHhhccccCce
Confidence            3458999999999887 689999999999999999998876    334569999999999999999887 6777778999


Q ss_pred             EEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         131 CHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      ++.+.|..+.+-.   +....+|+|+||++. ++++
T Consensus      1218 ~~~l~ge~s~~lk---l~~~~~vii~tpe~~-d~lq 1249 (1674)
T KOG0951|consen 1218 IVKLTGETSLDLK---LLQKGQVIISTPEQW-DLLQ 1249 (1674)
T ss_pred             EEecCCccccchH---HhhhcceEEechhHH-HHHh
Confidence            9999998887744   233568999999998 4444

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.96  E-value=9.3e-09  Score=89.10  Aligned_cols=112  Identities=16%  Similarity=0.191  Sum_probs=93.6

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      -+|. +|+++|....-.++.|.  +..+.||+|||++..+|+.....   .+..+.+++|+.-||.|-++.+..+...+|
T Consensus        74 ~lg~-r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL---~G~~VhvvT~NdyLA~RDae~m~~ly~~LG  147 (764)
T PRK12326         74 TLGL-RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYAL---QGRRVHVITVNDYLARRDAEWMGPLYEALG  147 (764)
T ss_pred             HcCC-CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHH---cCCCeEEEcCCHHHHHHHHHHHHHHHHhcC
Confidence            3465 68999999988888774  77999999999999998887654   466899999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      +++.++.++.+.+++....  .|||+.+|...| .|+|+.+
T Consensus       148 Lsvg~i~~~~~~~err~aY--~~DItYgTn~e~gFDyLRDn  186 (764)
T PRK12326        148 LTVGWITEESTPEERRAAY--ACDVTYASVNEIGFDVLRDQ  186 (764)
T ss_pred             CEEEEECCCCCHHHHHHHH--cCCCEEcCCcccccccchhh
Confidence            9999999988877665444  589999999877 4455544

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

Probab=98.91  E-value=9.1e-09  Score=86.07  Aligned_cols=96  Identities=21%  Similarity=0.215  Sum_probs=69.7

Q ss_pred             CCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      .++++|.+++..+.+    ++..++++|||+|||.+++..+...      +..++||+|+++|+.|..+.+....... .
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~------~~~~Lvlv~~~~L~~Qw~~~~~~~~~~~-~  108 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAEL------KRSTLVLVPTKELLDQWAEALKKFLLLN-D  108 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHh------cCCEEEEECcHHHHHHHHHHHHHhcCCc-c
Confidence            599999999999998    8999999999999999987666542      2249999999999999987776554322 1


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~  163 (178)
                      .+.. +|+......     . ..|.|+|-+.+..
T Consensus       109 ~~g~-~~~~~~~~~-----~-~~i~vat~qtl~~  135 (442)
T COG1061         109 EIGI-YGGGEKELE-----P-AKVTVATVQTLAR  135 (442)
T ss_pred             ccce-ecCceeccC-----C-CcEEEEEhHHHhh
Confidence            1222 233222211     0 3699999888765

>KOG0947|consensus

Probab=98.88  E-value=1.8e-08  Score=88.67  Aligned_cols=107  Identities=19%  Similarity=0.198  Sum_probs=87.7

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      ...+| ++...|++||-++.+|.+|+|.|+|.+|||+++-.++.-   ...+..+++|-+|-++|.+|-++.|+.-....
T Consensus       292 ~~~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAial---aq~h~TR~iYTSPIKALSNQKfRDFk~tF~Dv  367 (1248)
T KOG0947|consen  292 LIYPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIAL---AQKHMTRTIYTSPIKALSNQKFRDFKETFGDV  367 (1248)
T ss_pred             hhCCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHH---HHhhccceEecchhhhhccchHHHHHHhcccc
Confidence            45567 599999999999999999999999999999998766643   23367799999999999999999998776654


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      |    +++|+.+..       ....++|.|-+-|-.||.++.
T Consensus       368 g----LlTGDvqin-------PeAsCLIMTTEILRsMLYrga  398 (1248)
T KOG0947|consen  368 G----LLTGDVQIN-------PEASCLIMTTEILRSMLYRGA  398 (1248)
T ss_pred             c----eeecceeeC-------CCcceEeehHHHHHHHHhccc
Confidence            4    667777654       246789999999988887664

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.85  E-value=1.7e-08  Score=89.21  Aligned_cols=113  Identities=17%  Similarity=0.175  Sum_probs=90.0

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      -+|. .|+++|...-  +.-...-+..+.||+|||+++.+|++-...   .+..+.+++|+.-||.+-+..+..+.+.+|
T Consensus        78 ~lGm-~~ydVQliGg--~~Lh~G~iaEM~TGEGKTLvA~l~a~l~al---~G~~VhvvT~ndyLA~RD~e~m~~l~~~lG  151 (913)
T PRK13103         78 VMGM-RHFDVQLIGG--MTLHEGKIAEMRTGEGKTLVGTLAVYLNAL---SGKGVHVVTVNDYLARRDANWMRPLYEFLG  151 (913)
T ss_pred             HhCC-CcchhHHHhh--hHhccCccccccCCCCChHHHHHHHHHHHH---cCCCEEEEeCCHHHHHHHHHHHHHHhcccC
Confidence            3354 5777776543  333556689999999999999998876554   467899999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQ  169 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~  169 (178)
                      +++.++.++.+.+++.....  +||++||..-| .|+|+.+.
T Consensus       152 l~v~~i~~~~~~~err~~Y~--~dI~YGT~~e~gFDYLrD~~  191 (913)
T PRK13103        152 LSVGIVTPFQPPEEKRAAYA--ADITYGTNNEFGFDYLRDNM  191 (913)
T ss_pred             CEEEEECCCCCHHHHHHHhc--CCEEEEcccccccchhhccc
Confidence            99999998888777655543  99999999887 55555543

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

Probab=98.79  E-value=5.4e-08  Score=85.06  Aligned_cols=102  Identities=24%  Similarity=0.253  Sum_probs=80.6

Q ss_pred             CCcHHHHHHHHHHHcC----CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPIVKG----RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g----~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      .+++-|..+...+.+.    ...++.+.||||||.+|+-.+-..+.   .+.++|+|+|-.+|..|+...++...   |.
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~---~GkqvLvLVPEI~Ltpq~~~rf~~rF---g~  271 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLA---QGKQVLVLVPEIALTPQLLARFKARF---GA  271 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHH---cCCEEEEEeccccchHHHHHHHHHHh---CC
Confidence            5788999999998775    68999999999999999988777666   46799999999999999999997664   46


Q ss_pred             eEEEEEcCccHHHHHHHh----cCCCcEEEeChHHH
Q psy9277         130 QCHACIGGTNLSEDLRKL----DYGQHVVSGTPGRV  161 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~----~~~~~IlV~TP~~l  161 (178)
                      ++..++++.+..++...+    .....|+|||=-.|
T Consensus       272 ~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl  307 (730)
T COG1198         272 KVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL  307 (730)
T ss_pred             ChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh
Confidence            677777776554433333    34579999995443

>KOG0949|consensus

Probab=98.79  E-value=1.5e-08  Score=89.27  Aligned_cols=112  Identities=17%  Similarity=0.207  Sum_probs=84.4

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc-CCCceEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD-FMNVQCH  132 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~-~~~~~~~  132 (178)
                      .|..||.+.+..+-.++++++.|||.+|||++-...+ ....+.....-+|+++|+++|+.|+...+..... ..-.+..
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~i-EKVLResD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~  589 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAI-EKVLRESDSDVVIYVAPTKALVNQVSANVYARFDTKTFLRGV  589 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceeccHHHH-HHHHhhcCCCEEEEecchHHHhhhhhHHHHHhhccCccccch
Confidence            5899999999999999999999999999998754444 4444445666899999999999999888755442 2223444


Q ss_pred             EEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       133 ~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .+.|....+-+..  .-.|+|+|+.|+.+..+|-+.
T Consensus       590 sl~g~ltqEYsin--p~nCQVLITvPecleslLlsp  623 (1330)
T KOG0949|consen  590 SLLGDLTQEYSIN--PWNCQVLITVPECLESLLLSP  623 (1330)
T ss_pred             hhHhhhhHHhcCC--chhceEEEEchHHHHHHhcCc
Confidence            4455555544433  236999999999998888663

>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=98.76  E-value=4.5e-07  Score=70.80  Aligned_cols=113  Identities=19%  Similarity=0.292  Sum_probs=87.3

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +..|+ +|+++|..++-.+..|+  ++...||-|||++..+|+.-...   .+..+-|++.+..||..=++.+..+.+.+
T Consensus        72 r~~g~-~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL---~G~~V~vvT~NdyLA~RD~~~~~~~y~~L  145 (266)
T PF07517_consen   72 RTLGL-RPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNAL---QGKGVHVVTSNDYLAKRDAEEMRPFYEFL  145 (266)
T ss_dssp             HHTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHT---TSS-EEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             HHcCC-cccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHH---hcCCcEEEeccHHHhhccHHHHHHHHHHh
Confidence            35566 69999999997776666  99999999999998887765444   45689999999999999999999999999


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      |+.+....++.+.+++....  .++|+.+|...+ .|+|+..
T Consensus       146 Glsv~~~~~~~~~~~r~~~Y--~~dI~Y~t~~~~~fD~Lrd~  185 (266)
T PF07517_consen  146 GLSVGIITSDMSSEERREAY--AADIVYGTNSEFGFDYLRDN  185 (266)
T ss_dssp             T--EEEEETTTEHHHHHHHH--HSSEEEEEHHHHHHHHHHHT
T ss_pred             hhccccCccccCHHHHHHHH--hCcccccccchhhHHHHHHH
Confidence            99999999998876654443  478999999998 4566653

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 ....

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

Probab=98.76  E-value=7.5e-08  Score=87.16  Aligned_cols=85  Identities=18%  Similarity=0.217  Sum_probs=65.8

Q ss_pred             CCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH----HHH
Q psy9277          51 GFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV----VLA  122 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~----~~~  122 (178)
                      || ++++-|.+++..+..    +..+++.||||+|||++|++|++.....  .+.++||-++|+.|-+|+...    +++
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            56 589999998776654    7899999999999999999999875543  456899999999999998774    333


Q ss_pred             hccCCCceEEEEEcCcc
Q psy9277         123 LGDFMNVQCHACIGGTN  139 (178)
Q Consensus       123 ~~~~~~~~~~~~~g~~~  139 (178)
                      .. ..+++++++-|..+
T Consensus       332 ~~-~~~~~~~~lKGr~n  347 (928)
T PRK08074        332 IF-PFPVEAALLKGRSH  347 (928)
T ss_pred             Hc-CCCceEEEEEcccc
Confidence            32 23567777666544

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

Probab=98.72  E-value=1e-07  Score=83.55  Aligned_cols=105  Identities=22%  Similarity=0.201  Sum_probs=74.0

Q ss_pred             CCcHHHHHHHHHHHc----------CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          54 KPSAIQQRSIKPIVK----------GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----------g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .+..+|..++..+..          .+..++..+||||||++.+..+.. +......+++|+|+|+.+|..|..+.+..+
T Consensus       238 ~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~-l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~  316 (667)
T TIGR00348       238 YQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARK-ALELLKNPKVFFVVDRRELDYQLMKEFQSL  316 (667)
T ss_pred             ehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHH-HHhhcCCCeEEEEECcHHHHHHHHHHHHhh
Confidence            378899999987643          257899999999999887655543 334445679999999999999999999888


Q ss_pred             ccCCCceEEEEEcCccHHHHHHHhcC-CCcEEEeChHHHHHHH
Q psy9277         124 GDFMNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMI  165 (178)
Q Consensus       124 ~~~~~~~~~~~~g~~~~~~~~~~~~~-~~~IlV~TP~~l~~~l  165 (178)
                      .... +     .+..+.......+.. ...|+|+|.++|...+
T Consensus       317 ~~~~-~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~  353 (667)
T TIGR00348       317 QKDC-A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKL  353 (667)
T ss_pred             CCCC-C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhH
Confidence            5321 1     111223333233332 4689999999997644

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

>KOG0948|consensus

Probab=98.60  E-value=2.3e-07  Score=80.19  Aligned_cols=101  Identities=22%  Similarity=0.232  Sum_probs=82.7

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA  133 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  133 (178)
                      .+.|.|..+|..+-++.+|+|.|.|.+|||.++-.+|.+.+..   +-|+||-+|-++|.+|-|+.+..=.+.    +++
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~---kQRVIYTSPIKALSNQKYREl~~EF~D----VGL  201 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE---KQRVIYTSPIKALSNQKYRELLEEFKD----VGL  201 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh---cCeEEeeChhhhhcchhHHHHHHHhcc----cce
Confidence            5889999999999999999999999999999999999887764   458999999999999999998544444    344


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .+|+....       .....+|.|-+-|-.||.++
T Consensus       202 MTGDVTIn-------P~ASCLVMTTEILRsMLYRG  229 (1041)
T KOG0948|consen  202 MTGDVTIN-------PDASCLVMTTEILRSMLYRG  229 (1041)
T ss_pred             eecceeeC-------CCCceeeeHHHHHHHHHhcc
Confidence            55665543       23457888999998887655

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.59  E-value=3.4e-07  Score=80.81  Aligned_cols=75  Identities=23%  Similarity=0.273  Sum_probs=64.1

Q ss_pred             CCCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          50 YGFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      +-|..++|.|.+.+..+..    +.+.++.+|||+|||++.+.|++..........+++|.+.|.+-..|..+.++++.
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRThsQl~q~i~Elk~~~   84 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTHSQLEQATEELRKLM   84 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccchHHHHHHHHHHhhh
Confidence            3466679999998876654    89999999999999999999999977655445799999999999999999998854

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).

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=98.56  E-value=4.3e-07  Score=83.56  Aligned_cols=100  Identities=21%  Similarity=0.254  Sum_probs=62.1

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE--cC----cHHHHHHHHHHHHH-hccCCC
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL--SP----TRELAVQIQKVVLA-LGDFMN  128 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil--~P----t~~L~~q~~~~~~~-~~~~~~  128 (178)
                      +....+.+..+..+..++++|+||||||.  .+|.+-...  ..+....|+  -|    ++++|.++.+.+.. ++...|
T Consensus        76 ~~~r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~--g~g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~VG  151 (1294)
T PRK11131         76 SQKKQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLEL--GRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCVG  151 (1294)
T ss_pred             HHHHHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHc--CCCCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcceec
Confidence            33444556666677888999999999998  467332211  122222232  35    57888888888754 444444


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +.+       ..++   ....+++|+|+|||+|++.+.+..
T Consensus       152 Y~v-------rf~~---~~s~~t~I~v~TpG~LL~~l~~d~  182 (1294)
T PRK11131        152 YKV-------RFND---QVSDNTMVKLMTDGILLAEIQQDR  182 (1294)
T ss_pred             eee-------cCcc---ccCCCCCEEEEChHHHHHHHhcCC
Confidence            432       1111   113468999999999999987654

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.53  E-value=6.2e-07  Score=79.03  Aligned_cols=66  Identities=26%  Similarity=0.398  Sum_probs=54.7

Q ss_pred             CCCCCcHHHHHHHHHHHc---C------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          51 GFEKPSAIQQRSIKPIVK---G------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~---g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      || +.++-|.+++..+.+   +      +.+++.||||+|||++|++|++.....  .+.++||-+.|++|=+|+...
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~--~~k~vVIST~T~~LQeQL~~k   97 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARA--EKKKLVISTATVALQEQLVSK   97 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHH--cCCeEEEEcCCHHHHHHHHhh
Confidence            66 589999998877663   3      678999999999999999999875554  345899999999999998753

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

Probab=98.51  E-value=5.5e-07  Score=78.88  Aligned_cols=74  Identities=22%  Similarity=0.333  Sum_probs=60.9

Q ss_pred             HhCCCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..+...++++.|.+++..+..    ++.+++.||||+|||++|++|++......  +..++|.++|+.|-.|+.+....+
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~--~~~viist~t~~lq~q~~~~~~~~   86 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREE--GKKVIISTRTKALQEQLLEEDLPI   86 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHc--CCcEEEECCCHHHHHHHHHhhcch
Confidence            344455799999999976553    66799999999999999999999876553  368999999999999999887544

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.44  E-value=6.5e-07  Score=79.16  Aligned_cols=112  Identities=19%  Similarity=0.215  Sum_probs=88.4

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+|. +|+++|....  +.-..+-+..+.||.|||+++.+|+.-...   .+..+.|++++..||.+-++.+..+.+.+|
T Consensus        72 ~lG~-r~ydvQlig~--l~L~~G~IaEm~TGEGKTL~a~l~ayl~aL---~G~~VhVvT~NdyLA~RD~e~m~pvy~~LG  145 (870)
T CHL00122         72 TLGL-RHFDVQLIGG--LVLNDGKIAEMKTGEGKTLVATLPAYLNAL---TGKGVHIVTVNDYLAKRDQEWMGQIYRFLG  145 (870)
T ss_pred             HhCC-CCCchHhhhh--HhhcCCccccccCCCCchHHHHHHHHHHHh---cCCceEEEeCCHHHHHHHHHHHHHHHHHcC
Confidence            4465 4788887654  334567899999999999999998854333   356799999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      +.+.+..++.+..++...  ..|||+.+|...| .|+|+.+
T Consensus       146 Lsvg~i~~~~~~~err~a--Y~~DItYgTn~e~gFDyLRDn  184 (870)
T CHL00122        146 LTVGLIQEGMSSEERKKN--YLKDITYVTNSELGFDYLRDN  184 (870)
T ss_pred             CceeeeCCCCChHHHHHh--cCCCCEecCCccccccchhhc
Confidence            999999888888766444  3589999999766 3555544

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.38  E-value=1.7e-06  Score=76.66  Aligned_cols=110  Identities=16%  Similarity=0.185  Sum_probs=86.7

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+|. +|+++|...--.+  ...-+..+.||-|||+++.+|+.-...   .+..+-||+++.-||..=++.+..+.+.+|
T Consensus        81 ~lG~-r~ydVQliGgl~L--h~G~IAEM~TGEGKTL~atlpaylnAL---~GkgVhVVTvNdYLA~RDae~m~~vy~~LG  154 (939)
T PRK12902         81 VLGM-RHFDVQLIGGMVL--HEGQIAEMKTGEGKTLVATLPSYLNAL---TGKGVHVVTVNDYLARRDAEWMGQVHRFLG  154 (939)
T ss_pred             HhCC-CcchhHHHhhhhh--cCCceeeecCCCChhHHHHHHHHHHhh---cCCCeEEEeCCHHHHHhHHHHHHHHHHHhC
Confidence            3455 5777776644333  566689999999999999998876444   456799999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHH
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIR  166 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~  166 (178)
                      +.+.+..++.+..++...  ..|||+.||+..| .|+|+
T Consensus       155 Ltvg~i~~~~~~~err~a--Y~~DItYgTn~e~gFDYLR  191 (939)
T PRK12902        155 LSVGLIQQDMSPEERKKN--YACDITYATNSELGFDYLR  191 (939)
T ss_pred             CeEEEECCCCChHHHHHh--cCCCeEEecCCcccccchh
Confidence            999999888777665433  4799999999988 34443

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

Probab=98.34  E-value=3.5e-06  Score=63.73  Aligned_cols=68  Identities=25%  Similarity=0.374  Sum_probs=51.4

Q ss_pred             CCcHHHHHHHHHHHcCCc-EEEEcCCCChHHHHHHHHHHHHh------hhcCCCceEEEEcCcHHHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKGRD-VIAQAQSGTGKTATFSISILQSL------DTQLRETQVLCLSPTRELAVQIQKVVLA  122 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~-v~v~aptGsGKTl~~ll~il~~l------~~~~~~~~~lil~Pt~~L~~q~~~~~~~  122 (178)
                      ++++.|.+|+..++.... .+|.||+|+|||....- ++..+      .....+.++++++|+.+-+..+.+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~~-~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTTLAS-IIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHHH-HHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHHH-HHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            368899999999999998 99999999999965443 33333      1244667999999999999999999877

>PF13245 AAA_19: Part of AAA domain

Probab=98.32  E-value=4.2e-06  Score=53.12  Aligned_cols=59  Identities=29%  Similarity=0.456  Sum_probs=41.5

Q ss_pred             HHHHHHcCCc-EEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          62 SIKPIVKGRD-VIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        62 ~i~~i~~g~~-v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      ++...+.+.+ ++|.+|+|||||...+-.+...+.. ...+.++++++|++..+.++.+.+
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            3443333444 5559999999997766555554431 222668999999999999998888

>KOG0952|consensus

Probab=98.23  E-value=3.2e-07  Score=81.57  Aligned_cols=113  Identities=17%  Similarity=0.220  Sum_probs=89.7

Q ss_pred             CCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceE
Q psy9277          53 EKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC  131 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  131 (178)
                      ..+.+.|.+.+-.+.. ..++++.+|||+|||++|.+++...+... .+.+++|++|.++|+..-.+.+.......|+++
T Consensus       926 ~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~-p~~kvvyIap~kalvker~~Dw~~r~~~~g~k~ 1004 (1230)
T KOG0952|consen  926 KYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYY-PGSKVVYIAPDKALVKERSDDWSKRDELPGIKV 1004 (1230)
T ss_pred             cccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccC-CCccEEEEcCCchhhcccccchhhhcccCCcee
Confidence            3567788888877666 78999999999999999999988876654 347999999999999999988866655559999


Q ss_pred             EEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       132 ~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +-+.|+...+-.  .+ ...+|+|+||++.-...++-+
T Consensus      1005 ie~tgd~~pd~~--~v-~~~~~~ittpek~dgi~Rsw~ 1039 (1230)
T KOG0952|consen 1005 IELTGDVTPDVK--AV-READIVITTPEKWDGISRSWQ 1039 (1230)
T ss_pred             EeccCccCCChh--he-ecCceEEcccccccCcccccc
Confidence            999888876622  22 257899999999866665433

>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=98.22  E-value=1.1e-05  Score=63.47  Aligned_cols=92  Identities=18%  Similarity=0.090  Sum_probs=58.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCC---ceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRE---TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR  145 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~---~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  145 (178)
                      .+..+++-..|.|||+..+..+. .+......   ..+|||+|. .+..+-...+.++......++..+.|.........
T Consensus        25 ~~g~lL~de~GlGKT~~~i~~~~-~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~~~~~~~~v~~~~~~~~~~~~~~  102 (299)
T PF00176_consen   25 PRGGLLADEMGLGKTITAIALIS-YLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKWFDPDSLRVIIYDGDSERRRLSK  102 (299)
T ss_dssp             T-EEEE---TTSSHHHHHHHHHH-HHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHHSGT-TS-EEEESSSCHHHHTTS
T ss_pred             CCCEEEEECCCCCchhhhhhhhh-hhhhccccccccceeEeecc-chhhhhhhhhccccccccccccccccccccccccc
Confidence            46899999999999988765444 33332222   259999999 88888899998888654567766666652332222


Q ss_pred             HhcCCCcEEEeChHHHH
Q psy9277         146 KLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       146 ~~~~~~~IlV~TP~~l~  162 (178)
                      ......+|+|+|.+.+.
T Consensus       103 ~~~~~~~vvi~ty~~~~  119 (299)
T PF00176_consen  103 NQLPKYDVVITTYETLR  119 (299)
T ss_dssp             SSCCCSSEEEEEHHHHH
T ss_pred             cccccceeeeccccccc
Confidence            22345789999999887

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.

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

Probab=98.20  E-value=1.3e-05  Score=70.35  Aligned_cols=106  Identities=21%  Similarity=0.180  Sum_probs=78.5

Q ss_pred             CCCcHHHHHHHHHHHc----C-CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          53 EKPSAIQQRSIKPIVK----G-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~----g-~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      ..++.+|..||..+.+    | +-+++.+.||+|||..+ +.++.+|.+...-.++|+|+-.++|+.|.+..+..+...-
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~  242 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG  242 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCc
Confidence            3588999999987664    3 45999999999999886 4677777777677799999999999999999988875432


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                       -.+..+. +...       ..+++|.|+|-+.+..-+...
T Consensus       243 -~~~n~i~-~~~~-------~~s~~i~lsTyqt~~~~~~~~  274 (875)
T COG4096         243 -TKMNKIE-DKKG-------DTSSEIYLSTYQTMTGRIEQK  274 (875)
T ss_pred             -cceeeee-cccC-------CcceeEEEeehHHHHhhhhcc
Confidence             2211111 1111       125789999999998776554

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.18  E-value=1e-05  Score=71.86  Aligned_cols=77  Identities=21%  Similarity=0.288  Sum_probs=64.6

Q ss_pred             CCcHHHHHHHHHHHc---CC-cEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPIVK---GR-DVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~---g~-~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      ...+.|..++..+.+   .. .+++.||||.|||.+.+.++...+.. .....+.+++.|+++++.++++.++.+....+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~  274 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFS  274 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccc
Confidence            358899999988877   24 78999999999999999999887765 44677999999999999999999988765544


Q ss_pred             ce
Q psy9277         129 VQ  130 (178)
Q Consensus       129 ~~  130 (178)
                      +.
T Consensus       275 ~~  276 (733)
T COG1203         275 VI  276 (733)
T ss_pred             cc
Confidence            43

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

Probab=98.17  E-value=2.2e-05  Score=62.85  Aligned_cols=101  Identities=18%  Similarity=0.203  Sum_probs=77.6

Q ss_pred             CCcHHHHHHHHHH----HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPI----VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i----~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      ++++.|..+-..+    .+.++.++.|-||+|||....-.+-+.+.   .|.++.|.+|....+.+++.+++.-..  +.
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~---~G~~vciASPRvDVclEl~~Rlk~aF~--~~  171 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALN---QGGRVCIASPRVDVCLELYPRLKQAFS--NC  171 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHh---cCCeEEEecCcccchHHHHHHHHHhhc--cC
Confidence            6899998876554    45789999999999999875444433333   577999999999999999999977655  45


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      .+.+++|+++..-+       .+++|+|-..|+.+-+
T Consensus       172 ~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk~  201 (441)
T COG4098         172 DIDLLYGDSDSYFR-------APLVVATTHQLLRFKQ  201 (441)
T ss_pred             CeeeEecCCchhcc-------ccEEEEehHHHHHHHh
Confidence            67788888765532       5699999988887754

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.16  E-value=1.6e-05  Score=73.57  Aligned_cols=112  Identities=13%  Similarity=0.113  Sum_probs=65.9

Q ss_pred             CCCCCCcHHHH---HHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH-HHhcc
Q psy9277          50 YGFEKPSAIQQ---RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV-LALGD  125 (178)
Q Consensus        50 ~g~~~~~~~Q~---~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~-~~~~~  125 (178)
                      ..|....|+..   +.+..+..+..++++|+||||||.-  +|.+-.-.......++++.-|.|--|..++..+ ..+..
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~~~~~~~I~~tQPRRlAA~svA~RvA~elg~  137 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGT  137 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcCCCCCceEecCCccHHHHHHHHHHHHHHhCC
Confidence            34554455544   4555666678899999999999983  454332111111224444557777777777655 33433


Q ss_pred             CCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         126 FMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       126 ~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      ..|-.++..+...+.      ...+..|.++|||.|++.+.+..
T Consensus       138 ~lG~~VGY~vR~~~~------~s~~T~I~~~TdGiLLr~l~~d~  175 (1283)
T TIGR01967       138 PLGEKVGYKVRFHDQ------VSSNTLVKLMTDGILLAETQQDR  175 (1283)
T ss_pred             CcceEEeeEEcCCcc------cCCCceeeeccccHHHHHhhhCc
Confidence            344444332222111      12357899999999999987643

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.

>KOG0950|consensus

Probab=98.15  E-value=7.7e-06  Score=72.46  Aligned_cols=121  Identities=14%  Similarity=0.131  Sum_probs=96.9

Q ss_pred             CCHHHHHH-HHhCCCCCCcHHHHHHH--HHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHH
Q psy9277          39 LREDLLRG-IYAYGFEKPSAIQQRSI--KPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ  115 (178)
Q Consensus        39 l~~~i~~~-l~~~g~~~~~~~Q~~~i--~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q  115 (178)
                      +++...+. .+..|+..++.||.+|+  +.++.++|.+..+||+.|||++.-+-++......  ...++.+.|-.+-++.
T Consensus       207 ~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~--rr~~llilp~vsiv~E  284 (1008)
T KOG0950|consen  207 LPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR--RRNVLLILPYVSIVQE  284 (1008)
T ss_pred             CchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH--hhceeEecceeehhHH
Confidence            33333333 46778999999999998  6788899999999999999999998888877663  3468999999999999


Q ss_pred             HHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHH
Q psy9277         116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI  165 (178)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l  165 (178)
                      -...+..+...+|+.+-.++|.......    .+.-++-|+|-++=..++
T Consensus       285 k~~~l~~~~~~~G~~ve~y~g~~~p~~~----~k~~sv~i~tiEkansli  330 (1008)
T KOG0950|consen  285 KISALSPFSIDLGFPVEEYAGRFPPEKR----RKRESVAIATIEKANSLI  330 (1008)
T ss_pred             HHhhhhhhccccCCcchhhcccCCCCCc----ccceeeeeeehHhhHhHH
Confidence            9999999999999999888877655432    234579999998865444

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.10  E-value=3.7e-05  Score=68.28  Aligned_cols=112  Identities=16%  Similarity=0.178  Sum_probs=88.5

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      -+|. +|+++|...--.+..|  -+..+.||-|||+++.+|+.-...   .|..+-|++..--||..=...+..+...+|
T Consensus        74 ~lG~-r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL---~GkgVhVVTvNdYLA~RDae~mg~vy~fLG  147 (925)
T PRK12903         74 VLGK-RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNAL---TGKGVIVSTVNEYLAERDAEEMGKVFNFLG  147 (925)
T ss_pred             HhCC-CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHh---cCCceEEEecchhhhhhhHHHHHHHHHHhC
Confidence            3465 6888888776555555  479999999999999988854333   355788889999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      +.+.+...+.+..+....  ..|||..||...| .|+|+.+
T Consensus       148 LsvG~i~~~~~~~~rr~a--Y~~DItYgTn~E~gFDYLRDn  186 (925)
T PRK12903        148 LSVGINKANMDPNLKREA--YACDITYSVHSELGFDYLRDN  186 (925)
T ss_pred             CceeeeCCCCChHHHHHh--ccCCCeeecCcccchhhhhhc
Confidence            999999888777765444  3599999999887 5566654

>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=98.09  E-value=1.9e-05  Score=62.44  Aligned_cols=69  Identities=23%  Similarity=0.276  Sum_probs=53.8

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      +++-|.+++..  ...+++|.|+.|||||.+.+--++..+... ....+.+++++|++.+.++...+.....
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~aa~e~~~ri~~~l~   70 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAAAQEMRERIRELLE   70 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHHHHHHHHHHHHhcC
Confidence            47789998877  788999999999999998877666665543 3446899999999999999999877543

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 ....

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

Probab=98.04  E-value=0.00011  Score=66.28  Aligned_cols=50  Identities=14%  Similarity=0.260  Sum_probs=39.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      .++.+.++||+|||.+|+-.++... ......+.||+||+.+.-..+...+
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~-~~~~~~~fii~vp~~aI~egv~~~l  109 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELH-QKYGLFKFIIVVPTPAIKEGTRNFI  109 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHH-HHcCCcEEEEEeCCHHHHHHHHHHh
Confidence            4899999999999999988776643 3334468999999999888777654

>PRK14873 primosome assembly protein PriA; Provisional

Probab=97.99  E-value=3.8e-05  Score=67.34  Aligned_cols=81  Identities=17%  Similarity=0.168  Sum_probs=60.7

Q ss_pred             EcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---cC-C
Q psy9277          75 QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---DY-G  150 (178)
Q Consensus        75 ~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~-~  150 (178)
                      .+-+|||||.+|+-.+-..+.   .+.++|+++|..+|+.|+.+.++..+.  +..++.++++.+..++...+   .. .
T Consensus       166 ~~~~GSGKTevyl~~i~~~l~---~Gk~vLvLvPEi~lt~q~~~rl~~~f~--~~~v~~lhS~l~~~~R~~~w~~~~~G~  240 (665)
T PRK14873        166 QALPGEDWARRLAAAAAATLR---AGRGALVVVPDQRDVDRLEAALRALLG--AGDVAVLSAGLGPADRYRRWLAVLRGQ  240 (665)
T ss_pred             hcCCCCcHHHHHHHHHHHHHH---cCCeEEEEecchhhHHHHHHHHHHHcC--CCcEEEECCCCCHHHHHHHHHHHhCCC
Confidence            334699999999877766555   456899999999999999999976653  25577888887766544433   23 4


Q ss_pred             CcEEEeChHH
Q psy9277         151 QHVVSGTPGR  160 (178)
Q Consensus       151 ~~IlV~TP~~  160 (178)
                      ..|+|||-.-
T Consensus       241 ~~IViGtRSA  250 (665)
T PRK14873        241 ARVVVGTRSA  250 (665)
T ss_pred             CcEEEEccee
Confidence            7899999543

>TIGR00376 DNA helicase, putative

Probab=97.86  E-value=0.00015  Score=63.59  Aligned_cols=74  Identities=18%  Similarity=0.174  Sum_probs=57.0

Q ss_pred             CCcHHHHHHHHHHHcC-CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEE
Q psy9277          54 KPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCH  132 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g-~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  132 (178)
                      .++..|..|+..++.. ..++|.||+|+|||....-.+.+.+.   .+.++++++||..-+.++.+.+...    +++++
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~---~g~~VLv~a~sn~Avd~l~e~l~~~----~~~vv  229 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVK---RGLRVLVTAPSNIAVDNLLERLALC----DQKIV  229 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHH---cCCCEEEEcCcHHHHHHHHHHHHhC----CCcEE
Confidence            4689999999998875 68899999999999766544444333   3458999999999999999988654    45544


Q ss_pred             EE
Q psy9277         133 AC  134 (178)
Q Consensus       133 ~~  134 (178)
                      .+
T Consensus       230 Rl  231 (637)
T TIGR00376       230 RL  231 (637)
T ss_pred             Ee
Confidence            44

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.

>KOG1802|consensus

Probab=97.84  E-value=6.5e-05  Score=64.72  Aligned_cols=86  Identities=21%  Similarity=0.230  Sum_probs=69.6

Q ss_pred             HHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          46 GIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        46 ~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+...|+.+++.-|..|...++...=.++++|+|+|||.... .|+.++.+. ....+|+++|+.--+.|+.+.+.+.  
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa-~IVyhl~~~-~~~~VLvcApSNiAVDqLaeKIh~t--  477 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-HAGPVLVCAPSNIAVDQLAEKIHKT--  477 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhH-HHHHHHHHh-cCCceEEEcccchhHHHHHHHHHhc--
Confidence            344557888999999999999999999999999999998754 444444443 4568999999999999999998655  


Q ss_pred             CCCceEEEEEcC
Q psy9277         126 FMNVQCHACIGG  137 (178)
Q Consensus       126 ~~~~~~~~~~g~  137 (178)
                        |++++.+...
T Consensus       478 --gLKVvRl~ak  487 (935)
T KOG1802|consen  478 --GLKVVRLCAK  487 (935)
T ss_pred             --CceEeeeehh
Confidence              6888777643

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

Probab=97.78  E-value=0.0002  Score=53.62  Aligned_cols=64  Identities=23%  Similarity=0.420  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      ++++-|.+++..++.+  +-+++.|+.|+|||.+. -.+...+..  .+.++++++||...+..+.+..
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~--~g~~v~~~apT~~Aa~~L~~~~   66 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEA--AGKRVIGLAPTNKAAKELREKT   66 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHH--TT--EEEEESSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHh--CCCeEEEECCcHHHHHHHHHhh
Confidence            3688999999999754  35788899999999653 334444443  3579999999999999888774

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

Probab=97.74  E-value=9.6e-05  Score=62.30  Aligned_cols=72  Identities=25%  Similarity=0.295  Sum_probs=55.0

Q ss_pred             CCcHHHHHHHHHHHcC-----CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPIVKG-----RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g-----~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .|.--|-+||..+..|     +.-.+.|-||||||+...-.|-.      -..-+||++|.+.||.|+|..++.|.....
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI~~------~~rPtLV~AhNKTLAaQLy~Efk~fFP~Na   85 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIAK------VQRPTLVLAHNKTLAAQLYSEFKEFFPENA   85 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHHHH------hCCCeEEEecchhHHHHHHHHHHHhCcCcc
Confidence            4777788888777663     57889999999999775433322      123589999999999999999999987765


Q ss_pred             ceE
Q psy9277         129 VQC  131 (178)
Q Consensus       129 ~~~  131 (178)
                      +..
T Consensus        86 VEY   88 (663)
T COG0556          86 VEY   88 (663)
T ss_pred             eEE
Confidence            543

>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=97.73  E-value=8.6e-05  Score=55.95  Aligned_cols=59  Identities=19%  Similarity=0.240  Sum_probs=41.7

Q ss_pred             CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          52 FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        52 ~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      ++-.+..|..++..+....-+++.||.|||||+.++...++.+.. ..-.+.+|.-|..+
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~-g~~~kiii~Rp~v~   60 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKE-GEYDKIIITRPPVE   60 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHT-TS-SEEEEEE-S--
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCcEEEEEecCCC
Confidence            345689999999999998999999999999999999988888765 34447777777765

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

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.70  E-value=0.00086  Score=61.45  Aligned_cols=106  Identities=13%  Similarity=0.052  Sum_probs=71.8

Q ss_pred             CCcHHHHHHHHHHH----cCCcEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPIV----KGRDVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~----~g~~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+.++|.+.+.-+.    +|.+.++.-..|.|||+-.+.. +..+.. .......|||||. ++..+..+.+.+++.  .
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIal-L~~L~~~~~~~gp~LIVvP~-SlL~nW~~Ei~kw~p--~  244 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISL-LGYLHEYRGITGPHMVVAPK-STLGNWMNEIRRFCP--V  244 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHH-HHHHHHhcCCCCCEEEEeCh-HHHHHHHHHHHHHCC--C
Confidence            58999999987654    5788999999999999875433 333332 2233478999996 556677777887764  4


Q ss_pred             ceEEEEEcCccHHHHHH--H-hcCCCcEEEeChHHHHH
Q psy9277         129 VQCHACIGGTNLSEDLR--K-LDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~--~-~~~~~~IlV~TP~~l~~  163 (178)
                      ++++.++|.........  . .....+|+|+|.+.+..
T Consensus       245 l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~  282 (1033)
T PLN03142        245 LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIK  282 (1033)
T ss_pred             CceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHH
Confidence            56666776654322211  1 12357999999988754

>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=97.61  E-value=0.0031  Score=48.20  Aligned_cols=128  Identities=18%  Similarity=0.247  Sum_probs=81.3

Q ss_pred             ccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc---CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK---GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        33 ~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~---g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      .|+-...+.+++=.+.. ++ -.++.|.+....+.+   |.|.+.+.-.|.|||.+. +|++..+..++. ..+.+++| 
T Consensus         4 ~w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg~-~LvrviVp-   78 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADGS-RLVRVIVP-   78 (229)
T ss_pred             CCCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCCC-cEEEEEcC-
Confidence            45556666777766643 45 589999999988876   689999999999999774 567666655333 34555555 


Q ss_pred             HHHHHHHHHHHHHhcc-CCCceEEEE--EcCcc--HH--HHHH----HhcCCCcEEEeChHHHHHHH
Q psy9277         110 RELAVQIQKVVLALGD-FMNVQCHAC--IGGTN--LS--EDLR----KLDYGQHVVSGTPGRVFDMI  165 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~-~~~~~~~~~--~g~~~--~~--~~~~----~~~~~~~IlV~TP~~l~~~l  165 (178)
                      ++|..|.+..++.-.. -.+-++..+  .-...  ..  ....    .......|+++||+.++.+.
T Consensus        79 k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~  145 (229)
T PF12340_consen   79 KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFK  145 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHH
Confidence            5699999888844433 234444333  11111  11  1111    11234469999999997663

There are two conserved sequence motifs: LLE and NMG.

>KOG1123|consensus

Probab=97.55  E-value=5.5e-05  Score=63.38  Aligned_cols=96  Identities=17%  Similarity=0.108  Sum_probs=74.4

Q ss_pred             CCcHHHHHHHHHHHc---CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce
Q psy9277          54 KPSAIQQRSIKPIVK---GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ  130 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~---g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (178)
                      .++|+|..++.....   .++-+|..|.|+|||++-+-+++.      -+.+||++|.+---+.|....++.++...+-.
T Consensus       302 ~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t------ikK~clvLcts~VSVeQWkqQfk~wsti~d~~  375 (776)
T KOG1123|consen  302 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT------IKKSCLVLCTSAVSVEQWKQQFKQWSTIQDDQ  375 (776)
T ss_pred             ccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee------ecccEEEEecCccCHHHHHHHHHhhcccCccc
Confidence            478999999998876   368899999999999887655543      23589999999999999999998887766667


Q ss_pred             EEEEEcCccHHHHHHHhcCCCcEEEeChHH
Q psy9277         131 CHACIGGTNLSEDLRKLDYGQHVVSGTPGR  160 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~  160 (178)
                      ++.++.+....     ...++.|+|+|-..
T Consensus       376 i~rFTsd~Ke~-----~~~~~gvvvsTYsM  400 (776)
T KOG1123|consen  376 ICRFTSDAKER-----FPSGAGVVVTTYSM  400 (776)
T ss_pred             eEEeecccccc-----CCCCCcEEEEeeeh
Confidence            77776655332     23578899999643

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.53  E-value=0.0015  Score=57.54  Aligned_cols=67  Identities=21%  Similarity=0.315  Sum_probs=52.3

Q ss_pred             CCcHHHHHHHHHHHcC-----CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          54 KPSAIQQRSIKPIVKG-----RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g-----~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      .|+-.|..+|..+.++     ++.++.|-||||||+...- +++.     .+..+|||+|++.+|.|+++.++.|...
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~-----~~~p~Lvi~~n~~~A~ql~~el~~f~p~   80 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQ-----VNRPTLVIAHNKTLAAQLYNEFKEFFPE   80 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHH-----hCCCEEEEECCHHHHHHHHHHHHHhCCC
Confidence            5889999999887653     3677999999999977542 2221     1235899999999999999999999754

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

>COG4889 Predicted helicase [General function prediction only]

Probab=97.52  E-value=0.00075  Score=60.23  Aligned_cols=99  Identities=23%  Similarity=0.209  Sum_probs=64.5

Q ss_pred             ccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCC----cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR----DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        33 ~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~----~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      .|+.+.. .++...+.-..-++|+|+|+.|+....+|-    .-=+.+.+|+|||+..+- +...+.    ..++|+++|
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk-isEala----~~~iL~LvP  214 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK-ISEALA----AARILFLVP  214 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH-HHHHHh----hhheEeecc
Confidence            3444332 234444433345689999999999988731    122445578999988753 333333    268999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEEcCc
Q psy9277         109 TRELAVQIQKVVLALGDFMNVQCHACIGGT  138 (178)
Q Consensus       109 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~  138 (178)
                      +.+|..|..+.+..- +.+.++...++++.
T Consensus       215 SIsLLsQTlrew~~~-~~l~~~a~aVcSD~  243 (1518)
T COG4889         215 SISLLSQTLREWTAQ-KELDFRASAVCSDD  243 (1518)
T ss_pred             hHHHHHHHHHHHhhc-cCccceeEEEecCc
Confidence            999999999888544 23456665555443

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

Probab=97.40  E-value=0.00022  Score=50.60  Aligned_cols=87  Identities=21%  Similarity=0.234  Sum_probs=54.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL  147 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  147 (178)
                      +|+-.++-..+|+|||--.+.-++..-..  ++.++|+|.|||.++..+++.++..    .+++..   .....    ..
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~--~~~rvLvL~PTRvva~em~~aL~~~----~~~~~t---~~~~~----~~   69 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK--RRLRVLVLAPTRVVAEEMYEALKGL----PVRFHT---NARMR----TH   69 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH--TT--EEEEESSHHHHHHHHHHTTTS----SEEEES---TTSS-------
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH--ccCeEEEecccHHHHHHHHHHHhcC----CcccCc---eeeec----cc
Confidence            45667889999999999877766664443  4579999999999999999888533    333321   11111    11


Q ss_pred             cCCCcEEEeChHHHHHHHHc
Q psy9277         148 DYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       148 ~~~~~IlV~TP~~l~~~l~~  167 (178)
                      ..+.-|-|.|-+.+..++-+
T Consensus        70 ~g~~~i~vMc~at~~~~~~~   89 (148)
T PF07652_consen   70 FGSSIIDVMCHATYGHFLLN   89 (148)
T ss_dssp             -SSSSEEEEEHHHHHHHHHT
T ss_pred             cCCCcccccccHHHHHHhcC
Confidence            12345667777777766654

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 ....

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.33  E-value=0.00038  Score=62.85  Aligned_cols=107  Identities=19%  Similarity=0.216  Sum_probs=81.8

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      |+++|..  ..+.-...-+..+.||-|||+++.+|+.-...   .+.-+-+|+-.--||..=.+++..+...+|+.+.+.
T Consensus       139 ~ydVQLi--GgivLh~G~IAEM~TGEGKTLvatlp~yLnAL---~G~gVHvVTvNDYLA~RDaewm~p~y~flGLtVg~i  213 (1025)
T PRK12900        139 PYDVQLI--GGIVLHSGKISEMATGEGKTLVSTLPTFLNAL---TGRGVHVVTVNDYLAQRDKEWMNPVFEFHGLSVGVI  213 (1025)
T ss_pred             ccchHHh--hhHHhhcCCccccCCCCCcchHhHHHHHHHHH---cCCCcEEEeechHhhhhhHHHHHHHHHHhCCeeeee
Confidence            5556554  44444556689999999999999998865444   344678888899999999999999999999999999


Q ss_pred             EcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         135 IGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       135 ~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      ..+.+..++...  ..|||..||..-| .|+|+.+
T Consensus       214 ~~~~~~~~Rr~a--Y~~DItYgTn~EfGFDYLRDn  246 (1025)
T PRK12900        214 LNTMRPEERREQ--YLCDITYGTNNEFGFDYLRDN  246 (1025)
T ss_pred             CCCCCHHHHHHh--CCCcceecCCCccccccchhc
Confidence            777776665433  4699999998877 4555544

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.33  E-value=0.00057  Score=53.07  Aligned_cols=74  Identities=18%  Similarity=0.274  Sum_probs=58.2

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcC-ccHHHHHHHhcC-CCcEEEeChHHHHHHHHcCCCCCc
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGG-TNLSEDLRKLDY-GQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~-~~~~~~~~~~~~-~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      ..|.+|||+..---|.++.+.++.+- .-+..++.++.- ...+++...+.. ..+|.||||+||.+++.++.+.+.
T Consensus       125 gsP~~lvvs~SalRa~dl~R~l~~~~-~k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~  200 (252)
T PF14617_consen  125 GSPHVLVVSSSALRAADLIRALRSFK-GKDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLS  200 (252)
T ss_pred             CCCEEEEEcchHHHHHHHHHHHHhhc-cCCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcc
Confidence            35799999999999999999998873 113445555544 488888888875 579999999999999998887763

>KOG1803|consensus

Probab=97.32  E-value=0.00082  Score=57.48  Aligned_cols=64  Identities=22%  Similarity=0.275  Sum_probs=52.7

Q ss_pred             CCcHHHHHHHHHHHcC-CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g-~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      .+.+-|..|+....+. .=.+++||+|+|||.....-+.+.+.   .+.++|+.+||..-+.-+.+.+
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk---~~k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVK---QKKRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHH---cCCeEEEEcCchHHHHHHHHHh
Confidence            5788999999888886 45688999999999887766666555   3469999999999999888864

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.24  E-value=0.004  Score=56.85  Aligned_cols=104  Identities=18%  Similarity=0.053  Sum_probs=66.1

Q ss_pred             CCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceE
Q psy9277          54 KPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC  131 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  131 (178)
                      .|.|+|.+....++.  ...+++.-..|.|||+-+.+.+-+.+. .....++|||||. .|..|-...+.+..   ++..
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~-~g~~~rvLIVvP~-sL~~QW~~El~~kF---~l~~  226 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLL-TGRAERVLILVPE-TLQHQWLVEMLRRF---NLRF  226 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHH-cCCCCcEEEEcCH-HHHHHHHHHHHHHh---CCCe
Confidence            499999999877765  357899999999999888655544433 3334589999997 78888877774332   4444


Q ss_pred             EEEEcCccHHHHHH--HhcCCCcEEEeChHHHH
Q psy9277         132 HACIGGTNLSEDLR--KLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       132 ~~~~g~~~~~~~~~--~~~~~~~IlV~TP~~l~  162 (178)
                      .++.++........  ......+++|++-+.+.
T Consensus       227 ~i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~  259 (956)
T PRK04914        227 SLFDEERYAEAQHDADNPFETEQLVICSLDFLR  259 (956)
T ss_pred             EEEcCcchhhhcccccCccccCcEEEEEHHHhh
Confidence            43332221110000  01123578888877654

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.23  E-value=0.0016  Score=53.45  Aligned_cols=89  Identities=22%  Similarity=0.240  Sum_probs=50.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC-c-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP-T-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      |..+++.||||+|||.....-+....... ...++.++.. + +.=+.+   .++.+++..++.+..+............
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~-G~~~V~lit~D~~R~ga~E---qL~~~a~~~gv~~~~~~~~~~l~~~l~~  212 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRF-GASKVALLTTDSYRIGGHE---QLRIFGKILGVPVHAVKDGGDLQLALAE  212 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhc-CCCeEEEEecccccccHHH---HHHHHHHHcCCceEecCCcccHHHHHHH
Confidence            67899999999999988654433322221 1124444432 1 222333   3344444456666666555555555555


Q ss_pred             hcCCCcEEEeChHHH
Q psy9277         147 LDYGQHVVSGTPGRV  161 (178)
Q Consensus       147 ~~~~~~IlV~TP~~l  161 (178)
                      +.+.--|+|=|||+.
T Consensus       213 l~~~DlVLIDTaG~~  227 (374)
T PRK14722        213 LRNKHMVLIDTIGMS  227 (374)
T ss_pred             hcCCCEEEEcCCCCC
Confidence            554445788888865

>PRK10536 hypothetical protein; Provisional

Probab=97.22  E-value=0.0016  Score=50.72  Aligned_cols=60  Identities=17%  Similarity=0.183  Sum_probs=45.0

Q ss_pred             CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      .++...+..|...+..+.++..+++.||+|+|||+..+...++.+... .-.+++|.-|+.
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-~~~kIiI~RP~v  114 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-DVDRIIVTRPVL  114 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-CeeEEEEeCCCC
Confidence            355667899999999999989999999999999999887777665432 223445544553

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=97.22  E-value=0.0058  Score=53.89  Aligned_cols=69  Identities=23%  Similarity=0.355  Sum_probs=53.7

Q ss_pred             CCCCCcHHHHHHHHHHHcC-----CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          51 GFEKPSAIQQRSIKPIVKG-----RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~g-----~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .| .|+..|..++..+.++     +..++.|.+||||++... .++..     .+..+|||+|+...|.|+++.+..+..
T Consensus        10 ~~-~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~-----~~r~vLIVt~~~~~A~~l~~dL~~~~~   82 (652)
T PRK05298         10 PY-KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIAR-----LQRPTLVLAHNKTLAAQLYSEFKEFFP   82 (652)
T ss_pred             CC-CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHH-----hCCCEEEEECCHHHHHHHHHHHHHhcC
Confidence            45 6999999999988652     267799999999997743 22221     134699999999999999999988865


Q ss_pred             C
Q psy9277         126 F  126 (178)
Q Consensus       126 ~  126 (178)
                      .
T Consensus        83 ~   83 (652)
T PRK05298         83 E   83 (652)
T ss_pred             C
Confidence            3

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=97.20  E-value=0.0019  Score=52.01  Aligned_cols=68  Identities=24%  Similarity=0.313  Sum_probs=42.7

Q ss_pred             HHHHHHHhCCCCCCcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          42 DLLRGIYAYGFEKPSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        42 ~i~~~l~~~g~~~~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      .-++.+.+.|.  +++.|.+.+.. +..+.+++++|+|||||| .++-.++..+.......+++++-.+.++
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            34455555665  56778877765 455889999999999999 4445555543221223355555555554

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=97.18  E-value=0.0015  Score=57.72  Aligned_cols=69  Identities=16%  Similarity=0.167  Sum_probs=54.4

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .+++-|.+++..  ....++|.|..|||||.+.+.-+.+.+... -...++++++-|+.-|.++.+++..+.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            478999998764  356789999999999999776666655432 234589999999999999999887664

>PRK11054 helD DNA helicase IV; Provisional

Probab=97.08  E-value=0.0053  Score=54.35  Aligned_cols=78  Identities=17%  Similarity=0.165  Sum_probs=56.3

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceE
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC  131 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  131 (178)
                      ..+++-|.+++-.  ...+++|.|..|||||.+.+--+...+... ..+.++++++.|+..|..+.+++.......++.+
T Consensus       195 ~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~AA~em~eRL~~~lg~~~v~v  272 (684)
T PRK11054        195 SPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQAAEEMDERIRERLGTEDITA  272 (684)
T ss_pred             CCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHHHHHHHHHHHHhcCCCCcEE
Confidence            3689999998743  345789999999999988765554444332 2345899999999999999998866543323444


Q ss_pred             E
Q psy9277         132 H  132 (178)
Q Consensus       132 ~  132 (178)
                      .
T Consensus       273 ~  273 (684)
T PRK11054        273 R  273 (684)
T ss_pred             E
Confidence            3

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.07  E-value=0.0011  Score=60.26  Aligned_cols=107  Identities=20%  Similarity=0.232  Sum_probs=79.9

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      ++++|  .+..+.-...-+..+.||-|||+++.+|+.-...   .+.-+-+|+.+--||..=.+++..+...+|+.+.+.
T Consensus       170 ~yDVQ--liGgivLh~G~IAEM~TGEGKTLvAtlp~yLnAL---~GkgVHvVTVNDYLA~RDaewmgply~fLGLsvg~i  244 (1112)
T PRK12901        170 HYDVQ--LIGGVVLHQGKIAEMATGEGKTLVATLPVYLNAL---TGNGVHVVTVNDYLAKRDSEWMGPLYEFHGLSVDCI  244 (1112)
T ss_pred             ccchH--HhhhhhhcCCceeeecCCCCchhHHHHHHHHHHH---cCCCcEEEEechhhhhccHHHHHHHHHHhCCceeec
Confidence            44454  4455555667799999999999999998865544   344578888999999999999999999999999987


Q ss_pred             Ec-CccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         135 IG-GTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       135 ~g-~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      .. +.+..++..  ...|||..||..-| .|+|+.+
T Consensus       245 ~~~~~~~~~rr~--aY~~DItYgTn~EfGFDYLRDn  278 (1112)
T PRK12901        245 DKHQPNSEARRK--AYNADITYGTNNEFGFDYLRDN  278 (1112)
T ss_pred             CCCCCCHHHHHH--hCCCcceecCCCccccccchhc
Confidence            65 444444433  34699999998777 5555544

>KOG0920|consensus

Probab=97.04  E-value=0.0088  Score=54.07  Aligned_cols=108  Identities=16%  Similarity=0.230  Sum_probs=77.4

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH-HHhccCCCceEEE
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV-LALGDFMNVQCHA  133 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~-~~~~~~~~~~~~~  133 (178)
                      .+..+...+..+.+..-++++|.||+|||.=.---++.....+......++=-|.|--|..+++++ .+.+...|-.|+.
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            477888888999999999999999999998877777777665554445555558888888888876 4445555544444


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      -....+..      .....++++|-|.|++.|...
T Consensus       254 qvrl~~~~------s~~t~L~fcTtGvLLr~L~~~  282 (924)
T KOG0920|consen  254 QVRLESKR------SRETRLLFCTTGVLLRRLQSD  282 (924)
T ss_pred             EEeeeccc------CCceeEEEecHHHHHHHhccC
Confidence            33333222      123579999999999999763

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

Probab=97.04  E-value=0.0047  Score=49.05  Aligned_cols=111  Identities=16%  Similarity=0.191  Sum_probs=57.5

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCC-------
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE-------  100 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~-------  100 (178)
                      +..+.+|+++++++-+.+.+..-                  .-=++|.+|||||||.. +.+++..+......       
T Consensus       102 p~~i~~~e~LglP~i~~~~~~~~------------------~GLILVTGpTGSGKSTT-lAamId~iN~~~~~HIlTIED  162 (353)
T COG2805         102 PSKIPTLEELGLPPIVRELAESP------------------RGLILVTGPTGSGKSTT-LAAMIDYINKHKAKHILTIED  162 (353)
T ss_pred             CccCCCHHHcCCCHHHHHHHhCC------------------CceEEEeCCCCCcHHHH-HHHHHHHHhccCCcceEEecC
Confidence            34566677777666655533210                  12389999999999976 34566666554322       


Q ss_pred             ceEEEEcCcHHHHHHHHH--HHHHhccCC-----CceEEEEEcCccHHHHHHH-h--cCCCcEEEeC
Q psy9277         101 TQVLCLSPTRELAVQIQK--VVLALGDFM-----NVQCHACIGGTNLSEDLRK-L--DYGQHVVSGT  157 (178)
Q Consensus       101 ~~~lil~Pt~~L~~q~~~--~~~~~~~~~-----~~~~~~~~g~~~~~~~~~~-~--~~~~~IlV~T  157 (178)
                      |.-.+-.+-++|++|-.-  ....|...+     .-.-+.++|.+...+-+.. +  .+..|.+++|
T Consensus       163 PIE~vh~skkslI~QREvG~dT~sF~~aLraALReDPDVIlvGEmRD~ETi~~ALtAAETGHLV~~T  229 (353)
T COG2805         163 PIEYVHESKKSLINQREVGRDTLSFANALRAALREDPDVILVGEMRDLETIRLALTAAETGHLVFGT  229 (353)
T ss_pred             chHhhhcchHhhhhHHHhcccHHHHHHHHHHHhhcCCCEEEEeccccHHHHHHHHHHHhcCCEEEEe
Confidence            111222344666665321  223332211     1112355677655443332 1  2456888886

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.04  E-value=0.0038  Score=50.33  Aligned_cols=65  Identities=15%  Similarity=0.263  Sum_probs=41.1

Q ss_pred             HHHHhCCCCCCcHHHHHHHHHHH-cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          45 RGIYAYGFEKPSAIQQRSIKPIV-KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        45 ~~l~~~g~~~~~~~Q~~~i~~i~-~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      +.+.+.|.  +++.|...+..+. .+.+++++|+||||||... -.++..+......-+.+.+=.+.||
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~~~~rivtiEd~~El  186 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASAPEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCCCCceEEEecCCccc
Confidence            34545554  5677877776544 4789999999999999653 4555554322223355555555554

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.04  E-value=0.0033  Score=50.17  Aligned_cols=68  Identities=21%  Similarity=0.314  Sum_probs=41.3

Q ss_pred             HHHHHHHhCCCCCCcHHHHHHHHHH-HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          42 DLLRGIYAYGFEKPSAIQQRSIKPI-VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        42 ~i~~~l~~~g~~~~~~~Q~~~i~~i-~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      .-++.+.+.|.  +++-|...+..+ ..+.+++++|+||||||... -.++..+.......+++++=.+.|+
T Consensus       106 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~~~~ri~tiEd~~El  174 (299)
T TIGR02782       106 FTLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKNDPTDRVVIIEDTREL  174 (299)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccCCCceEEEECCchhh
Confidence            34555555564  456666666554 45789999999999999653 4455544332123355555555554

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.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.95  E-value=0.0039  Score=55.00  Aligned_cols=69  Identities=16%  Similarity=0.167  Sum_probs=54.2

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      +++-|.+++..  ...+++|.|..|||||.+.+--+.+.+... ....++++|+.|+.-+.++.+.+.+...
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            68889988754  356899999999999988777666666432 2345889999999999999999876543

Designed to identify rep members of the uvrD/rep subfamily.

>KOG4150|consensus

Probab=96.86  E-value=0.00077  Score=57.59  Aligned_cols=117  Identities=12%  Similarity=-0.058  Sum_probs=84.8

Q ss_pred             HHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          46 GIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        46 ~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .++.+--+....+|.+++..+.+|+++.+...+.+||.++|.+.....+... .....+++.|++++++...+.+.....
T Consensus       278 ~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~-~~s~~~~~~~~~~~~~~~~~~~~V~~~  356 (1034)
T KOG4150|consen  278 LLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLC-HATNSLLPSEMVEHLRNGSKGQVVHVE  356 (1034)
T ss_pred             HHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcC-cccceecchhHHHHhhccCCceEEEEE
Confidence            3455555678899999999999999999999999999999998877655543 334779999999999887765432221


Q ss_pred             C---CCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHH
Q psy9277         126 F---MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       126 ~---~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~  163 (178)
                      .   ..--++-.+++.+........+.+.+++.+.|..+..
T Consensus       357 ~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s  397 (1034)
T KOG4150|consen  357 VIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAIS  397 (1034)
T ss_pred             ehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHH
Confidence            1   1112333456666666656667788999999976643

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=96.83  E-value=0.0075  Score=52.50  Aligned_cols=67  Identities=18%  Similarity=0.231  Sum_probs=48.8

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH--HHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHH
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS--ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLA  122 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l--l~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  122 (178)
                      ..+|+.++..++.+.-+++.|++|+|||....  +..+..........++++.+||..-|..+.+.+..
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkAA~rL~e~~~~  215 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKAAARLAESLRK  215 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHHHHHHHHHHHh
Confidence            37999999999999999999999999997643  22222222111235799999998888877766543

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.83  E-value=0.013  Score=52.26  Aligned_cols=68  Identities=21%  Similarity=0.175  Sum_probs=50.8

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ..++ .+++-|.+|+..+..++-+++.|++|+|||.+. -.++..+........+++++||..-|..+.+
T Consensus       319 ~~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e  386 (720)
T TIGR01448       319 KLRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGGLLPVGLAAPTGRAAKRLGE  386 (720)
T ss_pred             hcCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCCCceEEEEeCchHHHHHHHH
Confidence            3454 689999999999999999999999999999654 2344433332212578889999888777665

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.

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

Probab=96.82  E-value=0.016  Score=52.18  Aligned_cols=106  Identities=20%  Similarity=0.223  Sum_probs=68.6

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH-HHhccCCCceEEEE
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV-LALGDFMNVQCHAC  134 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~-~~~~~~~~~~~~~~  134 (178)
                      +....+.+..+.++.-++++|+||||||.-.=.-+++...  ..+....+.=|.|--|..++..+ .++....|-.|++.
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            4555666777778899999999999999765444444332  23345666668887777777766 44544445444443


Q ss_pred             EcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       135 ~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +-..+..      .....|-+.|-|.|+..+.+..
T Consensus       130 iRfe~~~------s~~Trik~mTdGiLlrei~~D~  158 (845)
T COG1643         130 IRFESKV------SPRTRIKVMTDGILLREIQNDP  158 (845)
T ss_pred             EEeeccC------CCCceeEEeccHHHHHHHhhCc
Confidence            3221111      1245788999999999987543

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.81  E-value=0.0048  Score=55.02  Aligned_cols=70  Identities=14%  Similarity=0.188  Sum_probs=54.9

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+++-|.+++..  ....++|.|..|||||.+..-=+.+.+.. .-...++++|+-|+..|.++.+++.++..
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            589999998764  35689999999999998876655555432 22345899999999999999999977754

>TIGR01075 uvrD DNA helicase II

Probab=96.81  E-value=0.0051  Score=54.78  Aligned_cols=71  Identities=17%  Similarity=0.234  Sum_probs=55.5

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      ..+++-|.+++..  ....++|.|..|||||.+..-=+.+.+.. .-...++++|+-|+.-|.++.+++..+..
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            4589999998854  35689999999999998876655555443 22345899999999999999999987754

Designed to identify uvrD members of the uvrD/rep subfamily.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=96.80  E-value=0.0043  Score=55.19  Aligned_cols=50  Identities=16%  Similarity=0.250  Sum_probs=36.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      .-|+=|.+.||+|||.||+=.+.. |.+.-.-.+-|||||+.+.-.-++..
T Consensus        74 ~lNiDI~METGTGKTy~Ylrtmfe-Lhk~YG~~KFIivVPs~AIkeGv~~~  123 (985)
T COG3587          74 KLNIDILMETGTGKTYTYLRTMFE-LHKKYGLFKFIIVVPSLAIKEGVFLT  123 (985)
T ss_pred             cceeeEEEecCCCceeeHHHHHHH-HHHHhCceeEEEEeccHHHHhhhHHH
Confidence            358899999999999999865543 33332446889999998876654443

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.73  E-value=0.0066  Score=57.18  Aligned_cols=68  Identities=19%  Similarity=0.271  Sum_probs=54.4

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|+-|.++|.  ..+.+++|.|..|||||.+.+--++..+.......+.++|+=|++-|.++..++..-.
T Consensus         2 ~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~~~~~~il~~tFt~~aa~e~~~ri~~~l   69 (1232)
T TIGR02785         2 WTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRGVDIDRLLVVTFTNAAAREMKERIEEAL   69 (1232)
T ss_pred             CCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCHhhEEEEeccHHHHHHHHHHHHHHH
Confidence            5889999986  4689999999999999998877777766543233479999999999999888875543

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.

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

Probab=96.68  E-value=0.012  Score=54.03  Aligned_cols=94  Identities=17%  Similarity=0.147  Sum_probs=68.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcC
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY  149 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  149 (178)
                      +.-+|-=-+|||||+.-+..+ +.+......+.+++|+-.++|-.|..+.+..+........    ...+.++..+.+..
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A-~~l~~~~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~----~~~s~~~Lk~~l~~  348 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLA-RLLLELPKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP----KAESTSELKELLED  348 (962)
T ss_pred             CceEEEeecCCchHHHHHHHH-HHHHhccCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc----cccCHHHHHHHHhc
Confidence            457777789999998855433 3334445678999999999999999999998865433221    34556666566664


Q ss_pred             C-CcEEEeChHHHHHHHHcC
Q psy9277         150 G-QHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       150 ~-~~IlV~TP~~l~~~l~~~  168 (178)
                      + ..|+|||-++|-..+...
T Consensus       349 ~~~~ii~TTIQKf~~~~~~~  368 (962)
T COG0610         349 GKGKIIVTTIQKFNKAVKED  368 (962)
T ss_pred             CCCcEEEEEecccchhhhcc
Confidence            4 489999999998877654

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.64  E-value=0.011  Score=48.89  Aligned_cols=91  Identities=20%  Similarity=0.149  Sum_probs=49.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR  145 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  145 (178)
                      +..+++.||||+|||.+..--+...... ...+..+.+++  +.|.-+..+   ++.+++.+++.+..............
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~lgvpv~~~~~~~~l~~~L~  250 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQ---IQTYGDIMGIPVKAIESFKDLKEEIT  250 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHH---HHHHhhcCCcceEeeCcHHHHHHHHH
Confidence            3578999999999998875433222211 12334555544  334545444   45555556666544433233333223


Q ss_pred             HhcCCCcEEEeChHHHH
Q psy9277         146 KLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       146 ~~~~~~~IlV~TP~~l~  162 (178)
                      ...+.-.|+|=|||+..
T Consensus       251 ~~~~~DlVLIDTaGr~~  267 (388)
T PRK12723        251 QSKDFDLVLVDTIGKSP  267 (388)
T ss_pred             HhCCCCEEEEcCCCCCc
Confidence            33332357888998864

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=96.62  E-value=0.017  Score=50.51  Aligned_cols=65  Identities=20%  Similarity=0.205  Sum_probs=48.3

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc--CCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~--~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      .++|+.|+-..+.++-.++.|++|+|||.+..- ++..+...  ....++++.+||..-|..+.+.+.
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~~-ll~~l~~~~~~~~~~i~l~APTgkAA~rL~e~~~  220 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTVAK-LLAALIQLADGERCRIRLAAPTGKAAARLTESLG  220 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHHH-HHHHHHHhcCCCCcEEEEECCcHHHHHHHHHHHH
Confidence            589999999999999999999999999977432 22222221  123578888999888888776553

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.54  E-value=0.011  Score=46.86  Aligned_cols=86  Identities=20%  Similarity=0.264  Sum_probs=40.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      ++.++++||||+|||....--+.. +.....+.++.++.  |-+.-+.++...   +....++.+...............
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~-~~~~~g~~~V~li~~D~~r~~a~eql~~---~~~~~~~p~~~~~~~~~l~~~l~~  269 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAAR-FVLEHGNKKVALITTDTYRIGAVEQLKT---YAKILGVPVKVARDPKELRKALDR  269 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHHcCCCeEEEEECCccchhHHHHHHH---HHHHhCCceeccCCHHHHHHHHHH
Confidence            457899999999999776533322 22211123444444  223333333333   333345544333332233333333


Q ss_pred             hcCCCc-EEEeChH
Q psy9277         147 LDYGQH-VVSGTPG  159 (178)
Q Consensus       147 ~~~~~~-IlV~TP~  159 (178)
                      +. .++ |+|=|||
T Consensus       270 ~~-~~d~vliDt~G  282 (282)
T TIGR03499       270 LR-DKDLILIDTAG  282 (282)
T ss_pred             cc-CCCEEEEeCCC
Confidence            33 344 5566654

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.47  E-value=0.034  Score=49.82  Aligned_cols=76  Identities=13%  Similarity=0.234  Sum_probs=53.3

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      .++..+...-..++ .+++-|..|+..++. ++-+++.|+.|+|||...- .+...+..  .+..++.++||..-+..+.
T Consensus       338 ~~~~~~~~~l~~~~-~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll~-~i~~~~~~--~g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       338 VSPPIVDAAIDQHY-RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTMLK-AAREAWEA--AGYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCHHHHHHHHhccC-CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHHH-HHHHHHHh--CCCeEEEEeCcHHHHHHHH
Confidence            44444444333344 589999999999987 4678999999999996532 33333332  3568999999988877765


Q ss_pred             H
Q psy9277         118 K  118 (178)
Q Consensus       118 ~  118 (178)
                      +
T Consensus       414 ~  414 (744)
T TIGR02768       414 A  414 (744)
T ss_pred             h
Confidence            4

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.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.45  E-value=0.033  Score=46.06  Aligned_cols=89  Identities=21%  Similarity=0.251  Sum_probs=57.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL  147 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  147 (178)
                      ++-+.+.||||.|||....--+........+..-++|=.-| |-=|..+   ++.|++-+++.+.++.......+....+
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYRIGA~EQ---Lk~Ya~im~vp~~vv~~~~el~~ai~~l  279 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQ---LKTYADIMGVPLEVVYSPKELAEAIEAL  279 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcceEEEEeccchhhHHHH---HHHHHHHhCCceEEecCHHHHHHHHHHh
Confidence            67899999999999988654333333222233345554444 4444433   3344455588888888888887777777


Q ss_pred             cCCCcEEEeChHH
Q psy9277         148 DYGQHVVSGTPGR  160 (178)
Q Consensus       148 ~~~~~IlV~TP~~  160 (178)
                      .+.-.|+|=|-|+
T Consensus       280 ~~~d~ILVDTaGr  292 (407)
T COG1419         280 RDCDVILVDTAGR  292 (407)
T ss_pred             hcCCEEEEeCCCC
Confidence            6555678888765

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.39  E-value=0.035  Score=51.10  Aligned_cols=65  Identities=18%  Similarity=0.156  Sum_probs=49.0

Q ss_pred             CCCCCCcHHHHHHHHHHHcCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .|+ .+++-|.+++..++.+. -+++.|+.|+|||.. +-.+...+..  .+.+++.++||-.-|..+.+
T Consensus       343 ~g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~--~G~~V~~~ApTGkAA~~L~e  408 (988)
T PRK13889        343 RGL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA--AGYEVRGAALSGIAAENLEG  408 (988)
T ss_pred             cCC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH--cCCeEEEecCcHHHHHHHhh
Confidence            454 58999999999999865 478999999999975 3334443332  46789999999887766643

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=96.37  E-value=0.013  Score=52.22  Aligned_cols=71  Identities=18%  Similarity=0.248  Sum_probs=55.3

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      ..+++-|.+++..  ....++|.|..|||||.+..-=+.+.+... -...+++.++-|+.-|..+.+.+.++..
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            3589999998864  356899999999999988776666655432 2334899999999999999998877643

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK05973 replicative DNA helicase; Provisional

Probab=96.35  E-value=0.02  Score=44.24  Aligned_cols=85  Identities=20%  Similarity=0.219  Sum_probs=53.9

Q ss_pred             ccCCCCHHHHHHHHhCCCCC----------CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEE
Q psy9277          35 DNMGLREDLLRGIYAYGFEK----------PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVL  104 (178)
Q Consensus        35 ~~~~l~~~i~~~l~~~g~~~----------~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~l  104 (178)
                      ..+++|+.+-+.-.+-||..          ++|. .+...-+..|.-++|.|++|+|||...+--+.+...   ++..++
T Consensus        21 ~~~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~-~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~---~Ge~vl   96 (237)
T PRK05973         21 QNIPLHEALDRIAAEEGFSSWSLLAAKAAATTPA-EELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMK---SGRTGV   96 (237)
T ss_pred             cCCcHHHHHHHHHHHhccchHHHHHHhccCCCCH-HHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHh---cCCeEE
Confidence            45567777777777778853          3332 223344555788999999999999877655544332   345677


Q ss_pred             EEcCcHHHHHHHHHHHHHhc
Q psy9277         105 CLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus       105 il~Pt~~L~~q~~~~~~~~~  124 (178)
                      |++- .+-..|+.+.+..+.
T Consensus        97 yfSl-Ees~~~i~~R~~s~g  115 (237)
T PRK05973         97 FFTL-EYTEQDVRDRLRALG  115 (237)
T ss_pred             EEEE-eCCHHHHHHHHHHcC
Confidence            7753 333566666666553

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.31  E-value=0.017  Score=47.49  Aligned_cols=26  Identities=23%  Similarity=0.238  Sum_probs=19.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      +..++++||||||||... -.++..+.
T Consensus       149 ~GlilI~G~TGSGKTT~l-~al~~~i~  174 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLA-ASIYQHCG  174 (372)
T ss_pred             CCEEEEECCCCCCHHHHH-HHHHHHHH
Confidence            457899999999999664 45555553

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).

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.31  E-value=0.062  Score=46.20  Aligned_cols=90  Identities=19%  Similarity=0.213  Sum_probs=45.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR  145 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  145 (178)
                      .|..+.++||+|+|||.....-+.. +.....+.++.++.  +.+.-+.   ..++.+....++.+..............
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~-la~~~~gkkVaLIdtDtyRigA~---EQLk~ya~iLgv~v~~a~d~~~L~~aL~  424 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQR-FAAQHAPRDVALVTTDTQRVGGR---EQLHSYGRQLGIAVHEADSAESLLDLLE  424 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH-HHHhcCCCceEEEecccccccHH---HHHHHhhcccCceeEecCcHHHHHHHHH
Confidence            3678999999999999776432222 11111122444443  2233332   2234444445555444333333333333


Q ss_pred             HhcCCCcEEEeChHHH
Q psy9277         146 KLDYGQHVVSGTPGRV  161 (178)
Q Consensus       146 ~~~~~~~IlV~TP~~l  161 (178)
                      .+.+.--|||=|||+.
T Consensus       425 ~l~~~DLVLIDTaG~s  440 (559)
T PRK12727        425 RLRDYKLVLIDTAGMG  440 (559)
T ss_pred             HhccCCEEEecCCCcc
Confidence            3333334778888753

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.28  E-value=0.024  Score=47.36  Aligned_cols=91  Identities=18%  Similarity=0.117  Sum_probs=49.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL  147 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  147 (178)
                      |.-+.+.||||+|||.....-.-..+.......-.++.+.+ +.=+.++   +..+++..|+.+...............+
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~~~~v~~i~~d~~rigalEQ---L~~~a~ilGvp~~~v~~~~dl~~al~~l  267 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQ---LRIYGKLLGVSVRSIKDIADLQLMLHEL  267 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecCCcchhHHHH---HHHHHHHcCCceecCCCHHHHHHHHHHh
Confidence            56799999999999987654332222222222234555555 3323333   3334444466555444444433333344


Q ss_pred             cCCCcEEEeChHHHH
Q psy9277         148 DYGQHVVSGTPGRVF  162 (178)
Q Consensus       148 ~~~~~IlV~TP~~l~  162 (178)
                      .+.-.|+|-|+|+..
T Consensus       268 ~~~d~VLIDTaGrsq  282 (420)
T PRK14721        268 RGKHMVLIDTVGMSQ  282 (420)
T ss_pred             cCCCEEEecCCCCCc
Confidence            444468898987653

>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=43.02  Aligned_cols=47  Identities=23%  Similarity=0.326  Sum_probs=29.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      +++++++.||+|+|||..+.. +...+..  .+..++ .++..+|+..+..
T Consensus        46 ~~~~l~l~G~~G~GKThLa~a-i~~~~~~--~g~~v~-f~~~~~L~~~l~~   92 (178)
T PF01695_consen   46 NGENLILYGPPGTGKTHLAVA-IANEAIR--KGYSVL-FITASDLLDELKQ   92 (178)
T ss_dssp             C--EEEEEESTTSSHHHHHHH-HHHHHHH--TT--EE-EEEHHHHHHHHHC
T ss_pred             cCeEEEEEhhHhHHHHHHHHH-HHHHhcc--CCccee-EeecCceeccccc
Confidence            478999999999999987643 3444443  343444 4566777776654

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.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.17  E-value=0.031  Score=47.53  Aligned_cols=89  Identities=21%  Similarity=0.222  Sum_probs=46.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc-Cc-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS-PT-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~-Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      |.-+.+.||||+|||.+...-.-...... ...++.++. -+ +.=+.++   ++.|++..++.+...............
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~-G~~kV~LI~~Dt~RigA~EQ---Lr~~AeilGVpv~~~~~~~Dl~~aL~~  331 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRH-GASKVALLTTDSYRIGGHEQ---LRIYGKILGVPVHAVKDAADLRLALSE  331 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhc-CCCeEEEEeCCccchhHHHH---HHHHHHHhCCCeeccCCchhHHHHHHh
Confidence            45688999999999988654332222221 122343333 22 3333333   333344445554444333333334444


Q ss_pred             hcCCCcEEEeChHHH
Q psy9277         147 LDYGQHVVSGTPGRV  161 (178)
Q Consensus       147 ~~~~~~IlV~TP~~l  161 (178)
                      +.+.-.++|-|+|+.
T Consensus       332 L~d~d~VLIDTaGr~  346 (484)
T PRK06995        332 LRNKHIVLIDTIGMS  346 (484)
T ss_pred             ccCCCeEEeCCCCcC
Confidence            444457889999944

>KOG1132|consensus

Probab=96.17  E-value=0.023  Score=50.81  Aligned_cols=73  Identities=16%  Similarity=0.195  Sum_probs=53.9

Q ss_pred             CCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHh---hh---------cC-------------------
Q psy9277          54 KPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSL---DT---------QL-------------------   98 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l---~~---------~~-------------------   98 (178)
                      +|++.|...+..++.    ..+.++.+|||+|||++.+=..+...   ..         +.                   
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            589999988877765    67899999999999999875555433   10         01                   


Q ss_pred             --------CCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          99 --------RETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        99 --------~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                              ..++..|-+-|.+-..|+.+.+++..-.
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~Y~  136 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTGYR  136 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcCCC
Confidence                    0246677778888899999999877544

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.14  E-value=0.036  Score=46.47  Aligned_cols=87  Identities=21%  Similarity=0.240  Sum_probs=45.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      ++.+++.+|||+|||....--+...... ..+.++.++.-  -+.-+.   ..++.+....++.+...............
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~-~~g~~V~li~~D~~r~~a~---eqL~~~a~~~~vp~~~~~~~~~l~~~l~~  296 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALL-YGKKKVALITLDTYRIGAV---EQLKTYAKIMGIPVEVVYDPKELAKALEQ  296 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHh-cCCCeEEEEECCccHHHHH---HHHHHHHHHhCCceEccCCHHhHHHHHHH
Confidence            5678999999999997765333222111 12345555542  233232   23333334445555444443333333333


Q ss_pred             hcCCCc-EEEeChHH
Q psy9277         147 LDYGQH-VVSGTPGR  160 (178)
Q Consensus       147 ~~~~~~-IlV~TP~~  160 (178)
                      +. +++ |+|=|||+
T Consensus       297 ~~-~~DlVlIDt~G~  310 (424)
T PRK05703        297 LR-DCDVILIDTAGR  310 (424)
T ss_pred             hC-CCCEEEEeCCCC
Confidence            33 354 88889965

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

Probab=96.10  E-value=0.023  Score=46.59  Aligned_cols=59  Identities=24%  Similarity=0.321  Sum_probs=43.9

Q ss_pred             CcHHHHHHHHHH------HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          55 PSAIQQRSIKPI------VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        55 ~~~~Q~~~i~~i------~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +++-|..++..+      ..+.++++.|+-|+|||..+  -.+...... .+..+++++||-.-|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~--~~i~~~~~~-~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI--KAIIDYLRS-RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH--HHHHHHhcc-ccceEEEecchHHHHHhc
Confidence            677899998888      56889999999999999654  233322222 345788999998877776

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

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

Probab=96.02  E-value=0.014  Score=43.17  Aligned_cols=38  Identities=24%  Similarity=0.350  Sum_probs=28.6

Q ss_pred             HHhCCCCCCcHHHHHHHHHHH-cCCcEEEEcCCCChHHHHH
Q psy9277          47 IYAYGFEKPSAIQQRSIKPIV-KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        47 l~~~g~~~~~~~Q~~~i~~i~-~g~~v~v~aptGsGKTl~~   86 (178)
                      |.+.|+  +++-|...+.... .|.++++++|||||||...
T Consensus         4 l~~~g~--~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130           4 LIAQGT--FSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             HHHcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            444454  5677777776654 4899999999999999764

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.

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

Probab=96.00  E-value=0.038  Score=49.49  Aligned_cols=106  Identities=20%  Similarity=0.229  Sum_probs=83.1

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA  133 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  133 (178)
                      +++.+|  .+..+.-...-+.-+.||-|||++..+|+--...   .+..+.+++-.--||..-...+..+...+|+.+++
T Consensus        80 ~~~dVQ--liG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL---~gkgVhvVTvNdYLA~RDae~m~~l~~~LGlsvG~  154 (822)
T COG0653          80 RHFDVQ--LLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNAL---AGKGVHVVTVNDYLARRDAEWMGPLYEFLGLSVGV  154 (822)
T ss_pred             ChhhHH--HhhhhhhcCCceeeeecCCchHHHHHHHHHHHhc---CCCCcEEeeehHHhhhhCHHHHHHHHHHcCCceee
Confidence            345554  4456666777889999999999999988754333   34568888899999999999999999999999999


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHH
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIR  166 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~  166 (178)
                      ...+++..++....  .|||.-+|-..| .|+++
T Consensus       155 ~~~~m~~~ek~~aY--~~DItY~TnnElGFDYLR  186 (822)
T COG0653         155 ILAGMSPEEKRAAY--ACDITYGTNNELGFDYLR  186 (822)
T ss_pred             ccCCCChHHHHHHH--hcCceeccccccCcchhh
Confidence            99999887775554  589999998877 44444

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.99  E-value=0.048  Score=45.31  Aligned_cols=86  Identities=16%  Similarity=0.190  Sum_probs=46.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL  147 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  147 (178)
                      +.+++.||+|+|||.....-... +..  .+.++.++..  -|.-+.++   ++.+....++.+...............+
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~-L~~--~GkkVglI~aDt~RiaAvEQ---Lk~yae~lgipv~v~~d~~~L~~aL~~l  315 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQ-FHG--KKKTVGFITTDHSRIGTVQQ---LQDYVKTIGFEVIAVRDEAAMTRALTYF  315 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH-HHH--cCCcEEEEecCCcchHHHHH---HHHHhhhcCCcEEecCCHHHHHHHHHHH
Confidence            57899999999999876544433 322  3345554443  34223222   3334344466655443333333333333


Q ss_pred             cC--CC-cEEEeChHHH
Q psy9277         148 DY--GQ-HVVSGTPGRV  161 (178)
Q Consensus       148 ~~--~~-~IlV~TP~~l  161 (178)
                      ..  ++ -|+|=|||+.
T Consensus       316 k~~~~~DvVLIDTaGRs  332 (436)
T PRK11889        316 KEEARVDYILIDTAGKN  332 (436)
T ss_pred             HhccCCCEEEEeCcccc
Confidence            32  34 4788999885

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.98  E-value=0.02  Score=44.01  Aligned_cols=53  Identities=19%  Similarity=0.260  Sum_probs=38.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|..+++.||+|+|||...+--+...+.   ++..++|++ +.+-..++.+.+..+.
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            4689999999999999876655555442   355788887 4566667777676654

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.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=95.93  E-value=0.025  Score=44.13  Aligned_cols=66  Identities=17%  Similarity=0.281  Sum_probs=44.2

Q ss_pred             CCCCcHHHHHHHHHHH-------cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          52 FEKPSAIQQRSIKPIV-------KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        52 ~~~~~~~Q~~~i~~i~-------~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      |......+..++..+.       ++.++++.||+|+|||..+. ++.+.+..  . +..++++++.+++.++...+.
T Consensus        81 ~~~~~~~~~~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~-Ai~~~l~~--~-g~sv~f~~~~el~~~Lk~~~~  153 (254)
T COG1484          81 FEFQPGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAI-AIGNELLK--A-GISVLFITAPDLLSKLKAAFD  153 (254)
T ss_pred             ccCCcchhHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHH-HHHHHHHH--c-CCeEEEEEHHHHHHHHHHHHh
Confidence            3334445555444333       57899999999999997654 34444442  3 356677789999999888664

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

Probab=95.87  E-value=0.025  Score=46.07  Aligned_cols=52  Identities=19%  Similarity=0.245  Sum_probs=38.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      -++|.|.+|||||+..+- ++..+.....+..+++++++.+|...+...+..-
T Consensus         3 v~~I~G~aGTGKTvla~~-l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~~   54 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALN-LAKELQNSEEGKKVLYLCGNHPLRNKLREQLAKK   54 (352)
T ss_pred             EEEEEecCCcCHHHHHHH-HHHHhhccccCCceEEEEecchHHHHHHHHHhhh
Confidence            478999999999988653 3333422335668999999999999888777433

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=95.84  E-value=0.042  Score=50.46  Aligned_cols=84  Identities=19%  Similarity=0.179  Sum_probs=61.4

Q ss_pred             CCcHHHHHHHHHHHc--------CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVK--------GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~--------g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .-..+|-.|+..+..        |-.++--|.||+|||++=. =|++.+.....+.|..|-.-.|.|-.|..+.+++-..
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNA-RImyaLsd~~~g~RfsiALGLRTLTLQTGda~r~rL~  486 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANA-RAMYALRDDKQGARFAIALGLRSLTLQTGHALKTRLN  486 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHH-HHHHHhCCCCCCceEEEEccccceeccchHHHHHhcC
Confidence            446799999988765        4466777899999998742 3445555556677888888999999999999977654


Q ss_pred             CCCceEEEEEcCc
Q psy9277         126 FMNVQCHACIGGT  138 (178)
Q Consensus       126 ~~~~~~~~~~g~~  138 (178)
                      --+-..++++|+.
T Consensus       487 L~~ddLAVlIGs~  499 (1110)
T TIGR02562       487 LSDDDLAVLIGGT  499 (1110)
T ss_pred             CCccceEEEECHH
Confidence            4344566666663

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.

>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=95.80  E-value=0.03  Score=40.89  Aligned_cols=50  Identities=22%  Similarity=0.237  Sum_probs=33.0

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .+++.||+|+|||...+--+...+.   .+..++|++. .+-..++.+.+..++
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~---~g~~v~~~s~-e~~~~~~~~~~~~~g   50 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLA---RGEPGLYVTL-EESPEELIENAESLG   50 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH---CCCcEEEEEC-CCCHHHHHHHHHHcC
Confidence            3789999999999876544444332   4556777754 455666666666553

A related protein is found in archaea.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.74  E-value=0.023  Score=46.25  Aligned_cols=44  Identities=18%  Similarity=0.344  Sum_probs=27.4

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      .+..+.+++++||||||||... -.++..+..   ..+.+.+=.+.||
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll-~aLl~~i~~---~~rivtiEd~~El  201 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMS-KTLISAIPP---QERLITIEDTLEL  201 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHH-HHHHcccCC---CCCEEEECCCccc
Confidence            4456899999999999999653 445544422   2244444444444

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

Probab=95.74  E-value=0.045  Score=44.33  Aligned_cols=58  Identities=21%  Similarity=0.326  Sum_probs=39.6

Q ss_pred             CCCCCcHHHHHHHHHHHcCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          51 GFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      .|..+++-|...+..+..++ |+++++.||||||... -.++..+..   .-++|.+=-|.+|
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlL-Nal~~~i~~---~eRvItiEDtaEL  212 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLL-NALSGFIDS---DERVITIEDTAEL  212 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHH-HHHHhcCCC---cccEEEEeehhhh
Confidence            35578999999998888755 9999999999999542 222222221   1266666666655

>KOG1133|consensus

Probab=95.68  E-value=0.018  Score=50.31  Aligned_cols=42  Identities=26%  Similarity=0.422  Sum_probs=35.9

Q ss_pred             CCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          54 KPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      +|+.+|.+.+..+.+    |+=-+..+|||+|||++.+=..+..+.
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~   60 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLR   60 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHH
Confidence            699999998887765    888899999999999998877777663

>PRK08181 transposase; Validated

Probab=95.64  E-value=0.064  Score=42.21  Aligned_cols=60  Identities=23%  Similarity=0.269  Sum_probs=36.5

Q ss_pred             CcHHHHHHHHH----HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          55 PSAIQQRSIKP----IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        55 ~~~~Q~~~i~~----i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      +...|..++..    +..++++++.||+|+|||.... .+...+..  .+..+ +..+..+|+.++..
T Consensus        88 ~~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~-Aia~~a~~--~g~~v-~f~~~~~L~~~l~~  151 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAA-AIGLALIE--NGWRV-LFTRTTDLVQKLQV  151 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHH-HHHHHHHH--cCCce-eeeeHHHHHHHHHH
Confidence            34555555532    3358899999999999996654 33333332  33344 44456777776643

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.64  E-value=0.086  Score=42.71  Aligned_cols=46  Identities=24%  Similarity=0.330  Sum_probs=30.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      +.++++.|++|+|||.... ++...+..  .+..+++ .+..+|..++..
T Consensus       183 ~~~Lll~G~~GtGKThLa~-aIa~~l~~--~g~~V~y-~t~~~l~~~l~~  228 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSN-CIAKELLD--RGKSVIY-RTADELIEILRE  228 (329)
T ss_pred             CCcEEEECCCCCcHHHHHH-HHHHHHHH--CCCeEEE-EEHHHHHHHHHH
Confidence            6899999999999997543 45555543  3445555 455667666543

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.63  E-value=0.12  Score=40.64  Aligned_cols=87  Identities=18%  Similarity=0.199  Sum_probs=45.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHH----
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSED----  143 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~----  143 (178)
                      +-+++++|+|+|||....--+.. +..  .+.+++++.  +.|.-+.++...   +....++.+.....+.+....    
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~-l~~--~g~~V~li~~D~~r~~a~~ql~~---~~~~~~i~~~~~~~~~dp~~~~~~~  146 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANK-LKK--QGKSVLLAAGDTFRAAAIEQLEE---WAKRLGVDVIKQKEGADPAAVAFDA  146 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHh--cCCEEEEEeCCCCCHHHHHHHHH---HHHhCCeEEEeCCCCCCHHHHHHHH
Confidence            56788899999999876544433 222  345666665  334444333333   333335443322222222111    


Q ss_pred             H-HHhcCCCc-EEEeChHHHH
Q psy9277         144 L-RKLDYGQH-VVSGTPGRVF  162 (178)
Q Consensus       144 ~-~~~~~~~~-IlV~TP~~l~  162 (178)
                      . ....+++| |+|=||+++.
T Consensus       147 l~~~~~~~~D~ViIDT~G~~~  167 (272)
T TIGR00064       147 IQKAKARNIDVVLIDTAGRLQ  167 (272)
T ss_pred             HHHHHHCCCCEEEEeCCCCCc
Confidence            1 11234565 8899999873

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.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=95.61  E-value=0.019  Score=48.47  Aligned_cols=56  Identities=20%  Similarity=0.236  Sum_probs=41.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      .++++.||||||||..+++|.+-.     ...-+|+.=|-.+|........++.    |.+|.++
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~-----~~~s~iV~D~KgEl~~~t~~~r~~~----G~~V~vl  100 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN-----YPGSMIVTDPKGELYEKTAGYRKKR----GYKVYVL  100 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh-----ccCCEEEEECCCcHHHHHHHHHHHC----CCEEEEe
Confidence            479999999999999999987632     1236778889999888777766555    4445444

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

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=95.57  E-value=0.012  Score=48.45  Aligned_cols=48  Identities=27%  Similarity=0.257  Sum_probs=37.3

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ++++.||||||||.++++|-+-.     ....+++.=|--++........+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~-----~~~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT-----WPGSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc-----CCCCEEEEccchhHHHHHHHHHHHc
Confidence            57899999999999998887653     2357888889999987766665543

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.55  E-value=0.13  Score=43.19  Aligned_cols=85  Identities=15%  Similarity=0.134  Sum_probs=45.9

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccH-H---HHH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNL-S---EDL  144 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~-~---~~~  144 (178)
                      -++++|++|+|||....--+.. +..  .+.++++++.  -|.-+.++.+   .+....++.+....++.+. .   +..
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~~-l~~--~G~kV~lV~~D~~R~aA~eQLk---~~a~~~~vp~~~~~~~~dp~~i~~~~l  175 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAYY-YQR--KGFKPCLVCADTFRAGAFDQLK---QNATKARIPFYGSYTESDPVKIASEGV  175 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH-HHH--CCCCEEEEcCcccchhHHHHHH---HHhhccCCeEEeecCCCCHHHHHHHHH
Confidence            5789999999998765432222 222  3446666653  3544444333   3344446665544443332 1   122


Q ss_pred             HHhc-CCCc-EEEeChHHH
Q psy9277         145 RKLD-YGQH-VVSGTPGRV  161 (178)
Q Consensus       145 ~~~~-~~~~-IlV~TP~~l  161 (178)
                      .... .++| |+|=|||++
T Consensus       176 ~~~~~~~~DvViIDTaGr~  194 (429)
T TIGR01425       176 EKFKKENFDIIIVDTSGRH  194 (429)
T ss_pred             HHHHhCCCCEEEEECCCCC
Confidence            2222 3454 789999987

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.54  E-value=0.073  Score=43.17  Aligned_cols=29  Identities=21%  Similarity=0.407  Sum_probs=21.7

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .+..+.+++++|+||||||... -+++..+
T Consensus       156 ~v~~~~nili~G~tgSGKTTll-~aL~~~i  184 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTTFT-NAALREI  184 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHHHH-HHHHhhC
Confidence            3445899999999999999653 4555544

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.53  E-value=0.049  Score=48.72  Aligned_cols=89  Identities=22%  Similarity=0.223  Sum_probs=44.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc--HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT--RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt--~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      ++-+.++||||+|||.+...-........ .+.++.++.-.  +.=+   .+.++.+.+..++.+....+.....+....
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~-G~kkV~lit~Dt~RigA---~eQL~~~a~~~gvpv~~~~~~~~l~~al~~  260 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVARE-GADQLALLTTDSFRIGA---LEQLRIYGRILGVPVHAVKDAADLRFALAA  260 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHc-CCCeEEEecCcccchHH---HHHHHHHHHhCCCCccccCCHHHHHHHHHH
Confidence            34578999999999987654332221221 12244444432  2112   233444444456554433322222223333


Q ss_pred             hcCCCcEEEeChHHH
Q psy9277         147 LDYGQHVVSGTPGRV  161 (178)
Q Consensus       147 ~~~~~~IlV~TP~~l  161 (178)
                      +.+.-.|+|=|||+.
T Consensus       261 ~~~~D~VLIDTAGRs  275 (767)
T PRK14723        261 LGDKHLVLIDTVGMS  275 (767)
T ss_pred             hcCCCEEEEeCCCCC
Confidence            333235789999954

>KOG0390|consensus

Probab=95.48  E-value=0.26  Score=44.16  Aligned_cols=84  Identities=19%  Similarity=0.182  Sum_probs=58.7

Q ss_pred             CCcHHHHHHHHHHHc---C-------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCC-----ceEEEEcCcHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVK---G-------RDVIAQAQSGTGKTATFSISILQSLDTQLRE-----TQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~---g-------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~-----~~~lil~Pt~~L~~q~~~  118 (178)
                      .+.|+|.+.+.-+..   |       ..+++.=..|+|||+-. ++.+..+.+....     .++|||+|. .|+.-..+
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~-IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQC-ISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHH-HHHHHHHHHhCcCccccccccEEEccH-HHHHHHHH
Confidence            589999999976654   2       24566666899999774 4555666555555     689999995 67777777


Q ss_pred             HHHHhccCCCceEEEEEcCcc
Q psy9277         119 VVLALGDFMNVQCHACIGGTN  139 (178)
Q Consensus       119 ~~~~~~~~~~~~~~~~~g~~~  139 (178)
                      .+.++.....+....+++...
T Consensus       316 EF~KWl~~~~i~~l~~~~~~~  336 (776)
T KOG0390|consen  316 EFGKWLGNHRINPLDFYSTKK  336 (776)
T ss_pred             HHHHhccccccceeeeecccc
Confidence            777776544555555666555

>KOG4439|consensus

Probab=95.46  E-value=0.079  Score=46.65  Aligned_cols=105  Identities=17%  Similarity=0.115  Sum_probs=69.1

Q ss_pred             CCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHHHHHHHHhh-h---cCCC---ceEEEEcCcHHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFSISILQSLD-T---QLRE---TQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~ll~il~~l~-~---~~~~---~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      .+-++|..++..+.-     +..-++...-|-|||++-+-.+++.-. .   ...+   ...|||||- .|+.|.+..+.
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            356788887755442     456677778899999976655554321 1   1111   148999996 56777777776


Q ss_pred             HhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHH
Q psy9277         122 ALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGR  160 (178)
Q Consensus       122 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~  160 (178)
                      +-.....++|..++|....+-....+. ..||||+|..-
T Consensus       404 ~rl~~n~LsV~~~HG~n~r~i~~~~L~-~YDvViTTY~l  441 (901)
T KOG4439|consen  404 RRLEQNALSVYLYHGPNKREISAKELR-KYDVVITTYNL  441 (901)
T ss_pred             HHHhhcceEEEEecCCccccCCHHHHh-hcceEEEeeec
Confidence            665666788888888775443333433 68999999743

>TIGR00959 ffh signal recognition particle protein

Probab=95.41  E-value=0.13  Score=43.22  Aligned_cols=86  Identities=28%  Similarity=0.312  Sum_probs=45.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHH----HH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE----DL  144 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~----~~  144 (178)
                      -+++++++|+|||....--+.. +.. ..+.+++++.-  .|.-+.++...   ++...++.+.....+.+..+    ..
T Consensus       101 vi~~vG~~GsGKTTtaakLA~~-l~~-~~g~kV~lV~~D~~R~~a~~QL~~---~a~~~gvp~~~~~~~~~P~~i~~~al  175 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGKLAYY-LKK-KQGKKVLLVACDLYRPAAIEQLKV---LGQQVGVPVFALGKGQSPVEIARRAL  175 (428)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHH-hCCCeEEEEeccccchHHHHHHHH---HHHhcCCceEecCCCCCHHHHHHHHH
Confidence            5889999999999886544433 221 13445655552  34444443333   33334555444333222211    11


Q ss_pred             HH-hcCCC-cEEEeChHHH
Q psy9277         145 RK-LDYGQ-HVVSGTPGRV  161 (178)
Q Consensus       145 ~~-~~~~~-~IlV~TP~~l  161 (178)
                      .. ...++ .|+|=||+++
T Consensus       176 ~~~~~~~~DvVIIDTaGr~  194 (428)
T TIGR00959       176 EYAKENGFDVVIVDTAGRL  194 (428)
T ss_pred             HHHHhcCCCEEEEeCCCcc
Confidence            11 13456 4889999976

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.40  E-value=0.036  Score=42.09  Aligned_cols=54  Identities=24%  Similarity=0.311  Sum_probs=34.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|..+++.|++|+|||...+--+.+.+...  +-.++|++ +.+-..++.+.++.+.
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--ge~vlyvs-~ee~~~~l~~~~~s~g   71 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF--GEKVLYVS-FEEPPEELIENMKSFG   71 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--T--EEEEE-SSS-HHHHHHHHHTTT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--CCcEEEEE-ecCCHHHHHHHHHHcC
Confidence            467899999999999987665555544431  44677777 3444466666665553

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 ....

>PRK13764 ATPase; Provisional

Probab=95.39  E-value=0.044  Score=47.83  Aligned_cols=27  Identities=11%  Similarity=0.289  Sum_probs=20.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      .+++++++||||||||... -+++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTll-~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFA-QALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4789999999999999654 45555554

>PRK06921 hypothetical protein; Provisional

Probab=95.36  E-value=0.27  Score=38.65  Aligned_cols=48  Identities=19%  Similarity=0.250  Sum_probs=30.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+.++++.|++|+|||.... ++...+... .+..++|+. ..++..++..
T Consensus       116 ~~~~l~l~G~~G~GKThLa~-aia~~l~~~-~g~~v~y~~-~~~l~~~l~~  163 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLT-AAANELMRK-KGVPVLYFP-FVEGFGDLKD  163 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHH-HHHHHHhhh-cCceEEEEE-HHHHHHHHHH
Confidence            36789999999999996643 445544432 144555554 4555555543

>KOG0953|consensus

Probab=95.27  E-value=0.034  Score=47.60  Aligned_cols=59  Identities=24%  Similarity=0.322  Sum_probs=44.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGT  138 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~  138 (178)
                      .+=++=+|||.||||.-+    ++++...+   ..+|-.|.|-||.++++.++..    |+.+-+++|..
T Consensus       191 RkIi~H~GPTNSGKTy~A----Lqrl~~ak---sGvycGPLrLLA~EV~~r~na~----gipCdL~TGeE  249 (700)
T KOG0953|consen  191 RKIIMHVGPTNSGKTYRA----LQRLKSAK---SGVYCGPLRLLAHEVYDRLNAL----GIPCDLLTGEE  249 (700)
T ss_pred             heEEEEeCCCCCchhHHH----HHHHhhhc---cceecchHHHHHHHHHHHhhhc----CCCccccccce
Confidence            345777899999999765    46665433   5689999999999999999766    56655555554

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.27  E-value=0.088  Score=43.54  Aligned_cols=87  Identities=24%  Similarity=0.234  Sum_probs=46.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      ++.+++.||+|+|||....--+.. +..  .+.++.++.-  -|.=+.   +.++.+.+..++.+...............
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~-l~~--~g~~V~lItaDtyR~gAv---eQLk~yae~lgvpv~~~~dp~dL~~al~~  279 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQ-LLK--QNRTVGFITTDTFRSGAV---EQFQGYADKLDVELIVATSPAELEEAVQY  279 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHH--cCCeEEEEeCCccCccHH---HHHHHHhhcCCCCEEecCCHHHHHHHHHH
Confidence            567899999999999776544333 222  2345555542  233222   23555555566654433221222222222


Q ss_pred             hc--CCC-cEEEeChHHH
Q psy9277         147 LD--YGQ-HVVSGTPGRV  161 (178)
Q Consensus       147 ~~--~~~-~IlV~TP~~l  161 (178)
                      +.  .++ .|+|=|||+.
T Consensus       280 l~~~~~~D~VLIDTAGr~  297 (407)
T PRK12726        280 MTYVNCVDHILIDTVGRN  297 (407)
T ss_pred             HHhcCCCCEEEEECCCCC
Confidence            22  244 4889999983

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=95.19  E-value=0.42  Score=38.60  Aligned_cols=116  Identities=21%  Similarity=0.216  Sum_probs=63.5

Q ss_pred             CCCcHHHHHHHHHHHc----CC---cEEEEcCCCChHHHHHHHHHHHHhhhc----------------CCCceEEEE--c
Q psy9277          53 EKPSAIQQRSIKPIVK----GR---DVIAQAQSGTGKTATFSISILQSLDTQ----------------LRETQVLCL--S  107 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~----g~---~v~v~aptGsGKTl~~ll~il~~l~~~----------------~~~~~~lil--~  107 (178)
                      ..++|+|..+|..+.+    |+   -.++.||.|.||+..+.. +.+.+...                ...|-..++  .
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~-lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~   81 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALA-LAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFI   81 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecC
Confidence            4678899999987764    33   589999999999876543 23333221                123445666  5


Q ss_pred             CcH-------H-HHHHHHHHHHHhcc---CCCceEEEEEcCccHHH--HHH---HhcC---CCc-EEEeC-hHHHHHHHH
Q psy9277         108 PTR-------E-LAVQIQKVVLALGD---FMNVQCHACIGGTNLSE--DLR---KLDY---GQH-VVSGT-PGRVFDMIR  166 (178)
Q Consensus       108 Pt~-------~-L~~q~~~~~~~~~~---~~~~~~~~~~g~~~~~~--~~~---~~~~---~~~-IlV~T-P~~l~~~l~  166 (178)
                      |..       + .+.|+.+....+..   .-+.+++++........  ...   .+++   ++. |+++. |++|+.-++
T Consensus        82 p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIr  161 (319)
T PRK08769         82 PNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIR  161 (319)
T ss_pred             CCcccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHH
Confidence            642       1 24444443333322   22567777765544332  111   2222   233 44444 678877766


Q ss_pred             cCC
Q psy9277         167 SSQ  169 (178)
Q Consensus       167 ~~~  169 (178)
                      ++-
T Consensus       162 SRC  164 (319)
T PRK08769        162 SRC  164 (319)
T ss_pred             hhh
Confidence            653

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.17  E-value=0.24  Score=40.16  Aligned_cols=113  Identities=14%  Similarity=0.108  Sum_probs=62.0

Q ss_pred             CcHHHHHHHHHHHcC----CcEEEEcCCCChHHHHHHHHHHHHhhhc-------------------CCCceEEEEcCcH-
Q psy9277          55 PSAIQQRSIKPIVKG----RDVIAQAQSGTGKTATFSISILQSLDTQ-------------------LRETQVLCLSPTR-  110 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g----~~v~v~aptGsGKTl~~ll~il~~l~~~-------------------~~~~~~lil~Pt~-  110 (178)
                      .+|||...|..+...    ...+++||.|.||+..+.. +...+...                   ...+...++.|.. 
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~-~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~   82 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAER-LAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEA   82 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHH-HHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCC
Confidence            478999999888763    3689999999999976543 22333221                   1234567777742 


Q ss_pred             ---HHHHHHHHHHHHhcc---CCCceEEEEEcCcc--HHHHHH---HhcC---CCcEEEeC--hHHHHHHHHcC
Q psy9277         111 ---ELAVQIQKVVLALGD---FMNVQCHACIGGTN--LSEDLR---KLDY---GQHVVSGT--PGRVFDMIRSS  168 (178)
Q Consensus       111 ---~L~~q~~~~~~~~~~---~~~~~~~~~~g~~~--~~~~~~---~~~~---~~~IlV~T--P~~l~~~l~~~  168 (178)
                         --+.|+.+....+..   ..+.+++++.....  ......   .+++   +.-++++|  |++|+.-++++
T Consensus        83 ~~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI~SR  156 (328)
T PRK05707         83 DKTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSR  156 (328)
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHHHhh
Confidence               234555544433332   23567766643332  222211   2222   33455555  55666555544

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=95.15  E-value=0.29  Score=45.66  Aligned_cols=78  Identities=21%  Similarity=0.268  Sum_probs=56.7

Q ss_pred             CCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          38 GLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        38 ~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +.++..++.....++ .+++-|..++..+.. ++-+++.|+.|+|||...- ++...+..  .+.+++.++||-.-|..+
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-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMMK-AAREAWEA--AGYRVVGGALAGKAAEGL  441 (1102)
T ss_pred             CCCHHHHHHHHhcCC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHHH-HHHHHHHH--cCCeEEEEcCcHHHHHHH
Confidence            455666666544454 699999999998865 6778999999999996532 33333332  466899999998888777


Q ss_pred             HHH
Q psy9277         117 QKV  119 (178)
Q Consensus       117 ~~~  119 (178)
                      .+.
T Consensus       442 ~e~  444 (1102)
T PRK13826        442 EKE  444 (1102)
T ss_pred             HHh
Confidence            653

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.14  E-value=0.079  Score=43.43  Aligned_cols=26  Identities=23%  Similarity=0.447  Sum_probs=19.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .+..++++||||||||... -.++..+
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            4678999999999999764 4455544

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.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.10  E-value=0.057  Score=45.77  Aligned_cols=40  Identities=25%  Similarity=0.376  Sum_probs=29.5

Q ss_pred             cHHHHHHHHHHHcCC--cEEEEcCCCChHHHHHHHHHHHHhhh
Q psy9277          56 SAIQQRSIKPIVKGR--DVIAQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~--~v~v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      ++.|...+..+++..  =+++.||||||||.. +..+++.+..
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~  284 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNT  284 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcC
Confidence            667777777776633  478999999999976 5667776654

>PRK06526 transposase; Provisional

Probab=95.04  E-value=0.069  Score=41.67  Aligned_cols=48  Identities=17%  Similarity=0.122  Sum_probs=29.6

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      +..+.++++.||+|+|||....--. ..+..  .+.++++ ....+++.++.
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~al~-~~a~~--~g~~v~f-~t~~~l~~~l~  142 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAIGLG-IRACQ--AGHRVLF-ATAAQWVARLA  142 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHHHHH-HHHHH--CCCchhh-hhHHHHHHHHH
Confidence            3357899999999999997765333 22222  3334444 44455666554

>KOG0387|consensus

Probab=95.02  E-value=0.14  Score=45.73  Aligned_cols=104  Identities=19%  Similarity=0.128  Sum_probs=65.9

Q ss_pred             CCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+.++|++...-+.+    +..-++.-.=|-|||.-. ++.|..+..+ +-...+|||||. .++.|..+.+..++.  .
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQi-isFLaaL~~S~k~~~paLIVCP~-Tii~qW~~E~~~w~p--~  280 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQI-ISFLAALHHSGKLTKPALIVCPA-TIIHQWMKEFQTWWP--P  280 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhH-HHHHHHHhhcccccCceEEEccH-HHHHHHHHHHHHhCc--c
Confidence            468899998766544    667788888999999643 2233333322 233589999996 466677777777754  4


Q ss_pred             ceEEEEEcCccH--------HHHHHH-h----cCCCcEEEeChHHH
Q psy9277         129 VQCHACIGGTNL--------SEDLRK-L----DYGQHVVSGTPGRV  161 (178)
Q Consensus       129 ~~~~~~~g~~~~--------~~~~~~-~----~~~~~IlV~TP~~l  161 (178)
                      +++..+++..+.        ...... +    ..+.+|+|+|-..+
T Consensus       281 ~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~  326 (923)
T KOG0387|consen  281 FRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGF  326 (923)
T ss_pred             eEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhh
Confidence            677777765542        111111 1    12457999998765

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.00  E-value=0.12  Score=44.84  Aligned_cols=92  Identities=25%  Similarity=0.303  Sum_probs=58.5

Q ss_pred             ccCCCCHHHHHH-HHhCCCCCCcH----HHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEE
Q psy9277          35 DNMGLREDLLRG-IYAYGFEKPSA----IQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVL  104 (178)
Q Consensus        35 ~~~~l~~~i~~~-l~~~g~~~~~~----~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~l  104 (178)
                      .+.+..++++.. |.+.--..+..    +|.+==..|..  +.-++|+|..|||||.+++--+...++.-   .....++
T Consensus       185 sd~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vl  264 (747)
T COG3973         185 SDTGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVL  264 (747)
T ss_pred             cCCchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhccccccccCceE
Confidence            344566665554 54432223322    23332223333  56789999999999999876555544332   2233599


Q ss_pred             EEcCcHHHHHHHHHHHHHhccC
Q psy9277         105 CLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus       105 il~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      ++.|.+-+..-+.+++-+++..
T Consensus       265 vl~PN~vFleYis~VLPeLGe~  286 (747)
T COG3973         265 VLGPNRVFLEYISRVLPELGEE  286 (747)
T ss_pred             EEcCcHHHHHHHHHhchhhccC
Confidence            9999999999999999888654

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.98  E-value=0.65  Score=37.61  Aligned_cols=33  Identities=21%  Similarity=0.235  Sum_probs=26.0

Q ss_pred             cHHHHHHHHHHHc--C---CcEEEEcCCCChHHHHHHH
Q psy9277          56 SAIQQRSIKPIVK--G---RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        56 ~~~Q~~~i~~i~~--g---~~v~v~aptGsGKTl~~ll   88 (178)
                      +|||...|..+..  +   ...++.||.|.|||..+..
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~   40 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARF   40 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHH
Confidence            5788888887774  3   3689999999999977654

>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=94.95  E-value=0.29  Score=36.66  Aligned_cols=84  Identities=24%  Similarity=0.234  Sum_probs=42.2

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHH----HHH
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE----DLR  145 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~----~~~  145 (178)
                      +++.||||+|||....--+.+....   +.++.+++  ..|.=+.++.+.+   ++.+++.+.......+..+    ...
T Consensus         4 i~lvGptGvGKTTt~aKLAa~~~~~---~~~v~lis~D~~R~ga~eQL~~~---a~~l~vp~~~~~~~~~~~~~~~~~l~   77 (196)
T PF00448_consen    4 IALVGPTGVGKTTTIAKLAARLKLK---GKKVALISADTYRIGAVEQLKTY---AEILGVPFYVARTESDPAEIAREALE   77 (196)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEESTSSTHHHHHHHHH---HHHHTEEEEESSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCchHhHHHHHHHHHhhc---cccceeecCCCCCccHHHHHHHH---HHHhccccchhhcchhhHHHHHHHHH
Confidence            6899999999998865433333222   33444444  2354444444433   3334666555443332211    111


Q ss_pred             Hh-cCCC-cEEEeChHHH
Q psy9277         146 KL-DYGQ-HVVSGTPGRV  161 (178)
Q Consensus       146 ~~-~~~~-~IlV~TP~~l  161 (178)
                      .. .+++ -|+|=|||+.
T Consensus        78 ~~~~~~~D~vlIDT~Gr~   95 (196)
T PF00448_consen   78 KFRKKGYDLVLIDTAGRS   95 (196)
T ss_dssp             HHHHTTSSEEEEEE-SSS
T ss_pred             HHhhcCCCEEEEecCCcc
Confidence            11 1333 4778898754

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 ....

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=94.88  E-value=0.11  Score=42.38  Aligned_cols=44  Identities=23%  Similarity=0.238  Sum_probs=31.6

Q ss_pred             HHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHH
Q psy9277          41 EDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        41 ~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~   86 (178)
                      ..-++.|.+.|+  +++.+...+..+.. +.+++++++||||||...
T Consensus       151 ~~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll  195 (340)
T TIGR03819       151 TFTLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL  195 (340)
T ss_pred             cCCHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH
Confidence            334566666675  45667776665544 789999999999998654

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.87  E-value=0.019  Score=46.16  Aligned_cols=19  Identities=21%  Similarity=0.375  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .-|+++.+|||||||+.+.
T Consensus        97 KSNILLiGPTGsGKTlLAq  115 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQ  115 (408)
T ss_pred             eccEEEECCCCCcHHHHHH
Confidence            3589999999999997653

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=94.84  E-value=0.071  Score=43.63  Aligned_cols=64  Identities=20%  Similarity=0.261  Sum_probs=47.5

Q ss_pred             CCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHH
Q psy9277          50 YGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELA  113 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~  113 (178)
                      .|+.--+..|..|+..++..  .=|.+.++-|||||+.++-+.+......+.-.+.|+--|+..+-
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG  289 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVG  289 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcc
Confidence            47776778899999988884  45778899999999999988888776554444555555665443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.83  E-value=0.2  Score=43.69  Aligned_cols=57  Identities=7%  Similarity=0.084  Sum_probs=45.2

Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          98 LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        98 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ..+.++||.|+++..+.++++.+...    ++.+..++|+.+..++...+.    ...+|||+|-
T Consensus       255 ~~~~k~LVF~nt~~~ae~l~~~L~~~----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTd  315 (572)
T PRK04537        255 SEGARTMVFVNTKAFVERVARTLERH----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD  315 (572)
T ss_pred             ccCCcEEEEeCCHHHHHHHHHHHHHc----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEeh
Confidence            34568999999999999999988654    788999999988776655443    3579999993

>PRK04328 hypothetical protein; Provisional

Probab=94.82  E-value=0.083  Score=40.99  Aligned_cols=53  Identities=19%  Similarity=0.248  Sum_probs=35.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|..+++.+++|+|||...+--+.+.+.   ++..++|++ +.+-..++.+.+..+.
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~---~ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQ---MGEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh---cCCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            4678999999999999776554544433   345677776 5555556666666654

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.80  E-value=0.022  Score=44.40  Aligned_cols=65  Identities=22%  Similarity=0.238  Sum_probs=38.9

Q ss_pred             HHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          41 EDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        41 ~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      +++.++|..-|...-.+.--+.+.-+..|.-+++.|++|+|||...+-.+.+....  .+..++|++
T Consensus         2 ~~~~~~~~~~~~~tg~~~Ld~~~gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--~g~~vl~iS   66 (271)
T cd01122           2 EEIREALSNEEVWWPFPVLNKLTKGLRKGELIILTAGTGVGKTTFLREYALDLITQ--HGVRVGTIS   66 (271)
T ss_pred             chhhccccccCCCCCcceeeeeeEEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--cCceEEEEE
Confidence            45666665334333222222233456678899999999999997665444433221  245677776

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

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

Probab=94.80  E-value=0.067  Score=43.03  Aligned_cols=47  Identities=21%  Similarity=0.246  Sum_probs=30.7

Q ss_pred             HHHHhCCCCCCcHHHHH-HHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          45 RGIYAYGFEKPSAIQQR-SIKPIVKGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        45 ~~l~~~g~~~~~~~Q~~-~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      ..|.+.|.  +++.|.. .|-.+.++++++++++||||||.. +.+++..+
T Consensus       120 ~~l~~~gt--~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~I  167 (312)
T COG0630         120 EDLIEYGT--ISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFI  167 (312)
T ss_pred             HHHhhcCC--CCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhC
Confidence            33433444  4555544 445566699999999999999954 44555444

>KOG1131|consensus

Probab=94.79  E-value=0.28  Score=42.05  Aligned_cols=72  Identities=14%  Similarity=0.094  Sum_probs=46.8

Q ss_pred             CCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHHHHHHHhhhcC-CCceEEEEcCcHHHHHHHHHHHHH
Q psy9277          51 GFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSISILQSLDTQL-RETQVLCLSPTRELAVQIQKVVLA  122 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll~il~~l~~~~-~~~~~lil~Pt~~L~~q~~~~~~~  122 (178)
                      -|.+.+|-|.+-+..+.+    +-+.++.+|+|+|||.+.+..++.....-. ...+.+|-+-|..-+......++.
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEieK~l~El~~   89 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEIEKALEELKR   89 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHHHHHHHHHHH
Confidence            455677888776665554    678999999999999987765555433222 334667766665555555444433

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=94.74  E-value=0.11  Score=40.70  Aligned_cols=45  Identities=20%  Similarity=0.364  Sum_probs=29.9

Q ss_pred             HHHhCCCCCCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          46 GIYAYGFEKPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        46 ~l~~~g~~~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .|.++|+   .+.|.+.+..+..  +..+++.++||||||... ..++..+
T Consensus        58 ~l~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i  104 (264)
T cd01129          58 DLEKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSEL  104 (264)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhh
Confidence            3556664   5556666665554  346899999999999764 3444444

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=94.73  E-value=0.088  Score=44.92  Aligned_cols=46  Identities=20%  Similarity=0.388  Sum_probs=30.5

Q ss_pred             HHHhCCCCCCcHHHHHHHHHHHc-CC-cEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          46 GIYAYGFEKPSAIQQRSIKPIVK-GR-DVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        46 ~l~~~g~~~~~~~Q~~~i~~i~~-g~-~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      .|.++|+   .+-|.+.+..+.. .. -++++||||||||... ..++..+.
T Consensus       220 ~l~~Lg~---~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~  267 (486)
T TIGR02533       220 DLETLGM---SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLN  267 (486)
T ss_pred             CHHHcCC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccC
Confidence            3455664   5667777766655 33 3789999999999764 34555553

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.

>PRK10436 hypothetical protein; Provisional

Probab=94.73  E-value=0.091  Score=44.53  Aligned_cols=45  Identities=24%  Similarity=0.434  Sum_probs=29.6

Q ss_pred             HHhCCCCCCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          47 IYAYGFEKPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        47 l~~~g~~~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      |.++|+   .+.|.+.|..+..  +--++++||||||||... ..++..+.
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            445553   4556666665544  456899999999999764 44555543

>KOG1805|consensus

Probab=94.70  E-value=0.2  Score=45.66  Aligned_cols=68  Identities=22%  Similarity=0.185  Sum_probs=51.0

Q ss_pred             CCCcHHHHHHHHHHHcCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          53 EKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..++.-|++|+-.++..+ ..+|.|=+|+|||......+ ..+..  .+.++|+.+-|..-+..+.-.++.+
T Consensus       668 ~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~LI-kiL~~--~gkkVLLtsyThsAVDNILiKL~~~  736 (1100)
T KOG1805|consen  668 LRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISLLI-KILVA--LGKKVLLTSYTHSAVDNILIKLKGF  736 (1100)
T ss_pred             hhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHHHH-HHHHH--cCCeEEEEehhhHHHHHHHHHHhcc
Confidence            478999999999888855 56788889999997754333 22222  4568999999988888888877655

>PRK11823 DNA repair protein RadA; Provisional

Probab=94.67  E-value=0.31  Score=41.17  Aligned_cols=81  Identities=23%  Similarity=0.197  Sum_probs=47.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD  148 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  148 (178)
                      |.-+++.+++|+|||...+.-+.... .  .+.+++|+.- .+-..|+...+..+.....  -..+....+.+.....+.
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a-~--~g~~vlYvs~-Ees~~qi~~ra~rlg~~~~--~l~~~~e~~l~~i~~~i~  153 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLA-A--AGGKVLYVSG-EESASQIKLRAERLGLPSD--NLYLLAETNLEAILATIE  153 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHH-h--cCCeEEEEEc-cccHHHHHHHHHHcCCChh--cEEEeCCCCHHHHHHHHH
Confidence            56889999999999977654443322 2  3457888874 4455677766766643221  123444555554444443


Q ss_pred             C-CCcEEE
Q psy9277         149 Y-GQHVVS  155 (178)
Q Consensus       149 ~-~~~IlV  155 (178)
                      + +++++|
T Consensus       154 ~~~~~lVV  161 (446)
T PRK11823        154 EEKPDLVV  161 (446)
T ss_pred             hhCCCEEE
Confidence            2 455443

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=94.65  E-value=0.051  Score=47.51  Aligned_cols=57  Identities=18%  Similarity=0.050  Sum_probs=43.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      ..++++.||||||||..+++|-+-..     +.-+|++=|--|+........+++    |.+|.++
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~~-----~~S~VV~DpKGEl~~~Ta~~R~~~----G~~V~vf  214 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLFW-----EDSVVVHDIKLENYELTSGWREKQ----GQKVFVW  214 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHhC-----CCCEEEEeCcHHHHHHHHHHHHHC----CCeEEEE
Confidence            35899999999999999999987642     346788889999987777766554    5555544

>KOG1002|consensus

Probab=94.64  E-value=0.4  Score=40.97  Aligned_cols=106  Identities=17%  Similarity=0.160  Sum_probs=68.4

Q ss_pred             CCcHHHHHHHHHHHcCC-----cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPIVKGR-----DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~-----~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+.|+|.+-+--+....     .-++.-.-|.|||.-.+.-++.    ...+...++++|+.+|.+-. +.+..+.. -.
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLlla----e~~ra~tLVvaP~VAlmQW~-nEI~~~T~-gs  257 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLA----EVDRAPTLVVAPTVALMQWK-NEIERHTS-GS  257 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHh----ccccCCeeEEccHHHHHHHH-HHHHHhcc-Cc
Confidence            46789998775544432     3455566899999776554444    33445699999999997644 33444433 13


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      .++..++|.. .+..+..+ .+.|++.+|...+...++.
T Consensus       258 lkv~~YhG~~-R~~nikel-~~YDvVLTty~vvEs~yRk  294 (791)
T KOG1002|consen  258 LKVYIYHGAK-RDKNIKEL-MNYDVVLTTYAVVESVYRK  294 (791)
T ss_pred             eEEEEEeccc-ccCCHHHh-hcCcEEEEecHHHHHHHHh
Confidence            5555555544 33333333 3689999999999877765

>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=94.63  E-value=0.069  Score=44.20  Aligned_cols=52  Identities=17%  Similarity=0.337  Sum_probs=33.8

Q ss_pred             HHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          64 KPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        64 ~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      |.-...+++++.|.||||||. ++..++..+..  ++.++||.=|.-+.....++
T Consensus        10 ~~~~e~~~~li~G~~GsGKT~-~i~~ll~~~~~--~g~~~iI~D~kg~~~~~f~~   61 (386)
T PF10412_consen   10 PKDSENRHILIIGATGSGKTQ-AIRHLLDQIRA--RGDRAIIYDPKGEFTERFYR   61 (386)
T ss_dssp             -GGGGGG-EEEEE-TTSSHHH-HHHHHHHHHHH--TT-EEEEEEETTHHHHHH--
T ss_pred             ccchhhCcEEEECCCCCCHHH-HHHHHHHHHHH--cCCEEEEEECCchHHHHhcC
Confidence            334457899999999999997 44566666654  35578888888877665544

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.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=94.62  E-value=0.44  Score=33.33  Aligned_cols=40  Identities=20%  Similarity=0.271  Sum_probs=25.3

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHH
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAV  114 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~  114 (178)
                      +++.|++|+|||.....-+... ..  .+..++++........
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~-~~--~~~~v~~~~~e~~~~~   41 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNI-AT--KGGKVVYVDIEEEIEE   41 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHH-Hh--cCCEEEEEECCcchHH
Confidence            6899999999997654433332 22  3456777766544433

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.

>PRK12377 putative replication protein; Provisional

Probab=94.61  E-value=0.2  Score=38.95  Aligned_cols=47  Identities=15%  Similarity=0.244  Sum_probs=30.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      ..++++.||+|+|||.... ++.+.+..  .+..+ +.++..+|..++...
T Consensus       101 ~~~l~l~G~~GtGKThLa~-AIa~~l~~--~g~~v-~~i~~~~l~~~l~~~  147 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAA-AIGNRLLA--KGRSV-IVVTVPDVMSRLHES  147 (248)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH--cCCCe-EEEEHHHHHHHHHHH
Confidence            3689999999999996643 44444443  23334 445666777766543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=94.57  E-value=0.81  Score=37.07  Aligned_cols=113  Identities=17%  Similarity=0.139  Sum_probs=59.9

Q ss_pred             CcHHHHHHHHHHHc----C---CcEEEEcCCCChHHHHHHHHHHHHhhhc-------------------CCCceEEEEcC
Q psy9277          55 PSAIQQRSIKPIVK----G---RDVIAQAQSGTGKTATFSISILQSLDTQ-------------------LRETQVLCLSP  108 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~----g---~~v~v~aptGsGKTl~~ll~il~~l~~~-------------------~~~~~~lil~P  108 (178)
                      .+|||...|..+.+    |   .-.++.||.|.||+..+.. +.+.+...                   ...|-..++.|
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~-~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRA-LAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEP   81 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHH-HHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEcc
Confidence            35777777776653    3   4678999999999976543 22333221                   12244667777


Q ss_pred             c--H-HHHHHHHHHHHHh---ccCCCceEEEEEcCccHHH--HHH---HhcCC---CcEEEeC--hHHHHHHHHcC
Q psy9277         109 T--R-ELAVQIQKVVLAL---GDFMNVQCHACIGGTNLSE--DLR---KLDYG---QHVVSGT--PGRVFDMIRSS  168 (178)
Q Consensus       109 t--~-~L~~q~~~~~~~~---~~~~~~~~~~~~g~~~~~~--~~~---~~~~~---~~IlV~T--P~~l~~~l~~~  168 (178)
                      .  + --+.|+.+....+   ...-+.+++.+........  ...   .+++.   .-+++.|  |++|+.-++++
T Consensus        82 ~~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~SR  157 (325)
T PRK06871         82 IDNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSR  157 (325)
T ss_pred             ccCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHHhh
Confidence            3  1 2344444433333   2333577777765544332  212   22222   2333333  77777666654

>PF12846 AAA_10: AAA-like domain

Probab=94.55  E-value=0.092  Score=41.04  Aligned_cols=43  Identities=21%  Similarity=0.435  Sum_probs=29.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAV  114 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~  114 (178)
                      +.++++.|+||+|||.... .++..+..  .+..++++=|..+...
T Consensus         1 n~h~~i~G~tGsGKT~~~~-~l~~~~~~--~g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK-NLLEQLIR--RGPRVVIFDPKGDYSP   43 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHH--cCCCEEEEcCCchHHH
Confidence            3689999999999997766 44444433  3456777766655444

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=94.53  E-value=0.09  Score=41.04  Aligned_cols=52  Identities=13%  Similarity=0.362  Sum_probs=31.7

Q ss_pred             HHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          58 IQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        58 ~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      ...+.+.. +..+.+++++|+||||||... -.++..+...  ..+++++-.+.|+
T Consensus       115 ~~~~~l~~~v~~~~~ili~G~tGSGKTT~l-~all~~i~~~--~~~iv~iEd~~E~  167 (270)
T PF00437_consen  115 EIAEFLRSAVRGRGNILISGPTGSGKTTLL-NALLEEIPPE--DERIVTIEDPPEL  167 (270)
T ss_dssp             HHHHHHHHCHHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--TSEEEEEESSS-S
T ss_pred             HHHHHHhhccccceEEEEECCCccccchHH-HHHhhhcccc--ccceEEeccccce
Confidence            33344433 345789999999999999664 5556655433  2355555544444

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 ....

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=94.53  E-value=0.11  Score=45.26  Aligned_cols=45  Identities=24%  Similarity=0.372  Sum_probs=30.7

Q ss_pred             HHhCCCCCCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          47 IYAYGFEKPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        47 l~~~g~~~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      |.++|+   .+.|...|..+..  +-.++++||||||||... ..++..+.
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            556665   4566666666554  346789999999999774 45555553

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

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

Probab=94.53  E-value=0.29  Score=42.11  Aligned_cols=64  Identities=20%  Similarity=0.197  Sum_probs=49.4

Q ss_pred             HHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          90 ILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        90 il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      .+..+.......++||.+.|+..+..+...+...    |+.+..++|+.+..++.+.+.    ...+|+|+|
T Consensus       263 ~L~~ll~~~~~~~~IVF~~tk~~~~~l~~~l~~~----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaT  330 (513)
T COG0513         263 LLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKR----GFKVAALHGDLPQEERDRALEKFKDGELRVLVAT  330 (513)
T ss_pred             HHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHHC----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEe
Confidence            3344444444458999999999999988877665    789999999998887766654    357999999

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=94.48  E-value=0.13  Score=39.50  Aligned_cols=54  Identities=19%  Similarity=0.185  Sum_probs=34.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      +..|..+++.+++|+|||...+-.+...+ .  ++.+++|++. .+-..+..+.+..+
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~-~--~g~~~~yi~~-e~~~~~~~~~~~~~   74 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFL-Q--NGYSVSYVST-QLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHH-h--CCCcEEEEeC-CCCHHHHHHHHHHh
Confidence            34578999999999999987544443322 2  3457788884 33345555555444

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=94.47  E-value=0.19  Score=44.31  Aligned_cols=55  Identities=20%  Similarity=0.294  Sum_probs=39.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH--HHHHHHHHHHHhccC
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE--LAVQIQKVVLALGDF  126 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~--L~~q~~~~~~~~~~~  126 (178)
                      ..+++|.|+||+|||..+.+-+.+.+.   .+..++++=|-..  |...+...++.++..
T Consensus       176 ~~H~lv~G~TGsGKT~l~~~l~~q~i~---~g~~viv~DpKgD~~l~~~~~~~~~~~G~~  232 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLAELLITQDIR---RGDVVIVIDPKGDADLKRRMRAEAKRAGRP  232 (634)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence            468999999999999887555555444   3446666667754  778888877777543

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.

>PHA02244 ATPase-like protein

Probab=94.47  E-value=0.037  Score=45.44  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=18.8

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+.++++.||||+|||....
T Consensus       115 ~l~~~~PVLL~GppGtGKTtLA~  137 (383)
T PHA02244        115 IVNANIPVFLKGGAGSGKNHIAE  137 (383)
T ss_pred             HHhcCCCEEEECCCCCCHHHHHH
Confidence            34458999999999999996653

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.44  E-value=0.074  Score=43.37  Aligned_cols=72  Identities=18%  Similarity=0.255  Sum_probs=42.4

Q ss_pred             cCCCCCCcccccccccccccccccCC-CCHHHHHHH--HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          13 IPEDLSNVEFETSEDVEVVSTFDNMG-LREDLLRGI--YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~~~f~~~~-l~~~i~~~l--~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ++.+.+..-.....+..|..+|++.| |.+.+.+.=  -++-.+.|--++.-   -|---+.|++.||+|+|||+.+=
T Consensus       129 Lp~~~Dp~V~~M~v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~---GI~PPKGVLLYGPPGTGKTLLAk  203 (406)
T COG1222         129 LPPEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEEL---GIDPPKGVLLYGPPGTGKTLLAK  203 (406)
T ss_pred             CCCccCchhheeeeccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHc---CCCCCCceEeeCCCCCcHHHHHH
Confidence            44444444444445667788999986 655444432  12333333323222   12235899999999999998763

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.40  E-value=0.61  Score=37.62  Aligned_cols=88  Identities=22%  Similarity=0.184  Sum_probs=44.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc-Cc-HHHHHHHHHHHHHhccCCCceEEEEEcCccH-H----
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS-PT-RELAVQIQKVVLALGDFMNVQCHACIGGTNL-S----  141 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~-Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~-~----  141 (178)
                      +.-++++||+|+|||....--+.. +..  .+.+++++. .+ +.-+.++...+..   ..++.+.....+.+. .    
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~-l~~--~g~~V~Li~~D~~r~~a~eql~~~a~---~~~i~~~~~~~~~dpa~~v~~  187 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHK-YKA--QGKKVLLAAGDTFRAAAIEQLQVWGE---RVGVPVIAQKEGADPASVAFD  187 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHH-HHh--cCCeEEEEecCccchhhHHHHHHHHH---HcCceEEEeCCCCCHHHHHHH
Confidence            346789999999999775432222 222  344666655 22 4444333333322   224444333222222 1    


Q ss_pred             HHHHHhcCCC-cEEEeChHHHH
Q psy9277         142 EDLRKLDYGQ-HVVSGTPGRVF  162 (178)
Q Consensus       142 ~~~~~~~~~~-~IlV~TP~~l~  162 (178)
                      ........+. .|+|=||+++.
T Consensus       188 ~l~~~~~~~~D~ViIDTaGr~~  209 (318)
T PRK10416        188 AIQAAKARGIDVLIIDTAGRLH  209 (318)
T ss_pred             HHHHHHhCCCCEEEEeCCCCCc
Confidence            1111223455 48899999863

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=94.38  E-value=0.046  Score=36.99  Aligned_cols=39  Identities=18%  Similarity=0.263  Sum_probs=24.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      +..+++.||+|+|||.....- +..+..  ....++++.+..
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l-~~~~~~--~~~~~~~~~~~~   40 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARAL-ARELGP--PGGGVIYIDGED   40 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHH-HhccCC--CCCCEEEECCEE
Confidence            568999999999999765432 222221  112467776664

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.

>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=94.38  E-value=0.35  Score=32.90  Aligned_cols=38  Identities=24%  Similarity=0.326  Sum_probs=23.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      +..+++.||+|+|||.... .+...+..  .+..++++...
T Consensus        19 ~~~v~i~G~~G~GKT~l~~-~i~~~~~~--~~~~v~~~~~~   56 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLAR-AIANELFR--PGAPFLYLNAS   56 (151)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHhhc--CCCCeEEEehh
Confidence            6789999999999996433 33333321  23345555443

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.

>PHA02533 17 large terminase protein; Provisional

Probab=94.37  E-value=0.36  Score=41.73  Aligned_cols=69  Identities=17%  Similarity=0.159  Sum_probs=54.2

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .+.++|...+..+..++-.++..+-..|||.+....++...... .+..+++++|+.+-|..+++.++.+
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~-~~~~v~i~A~~~~QA~~vF~~ik~~  127 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN-KDKNVGILAHKASMAAEVLDRTKQA  127 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC-CCCEEEEEeCCHHHHHHHHHHHHHH
Confidence            58899999998876677777888889999998775555443332 3569999999999999999888654

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

Probab=94.35  E-value=0.11  Score=46.57  Aligned_cols=52  Identities=21%  Similarity=0.270  Sum_probs=40.3

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .=.+|.+|-|||||.+..-++-+.+.  ....++++|+..++|+.++...++..
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            34689999999999876554444333  24568999999999999999998644

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

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=94.34  E-value=0.054  Score=42.33  Aligned_cols=27  Identities=30%  Similarity=0.414  Sum_probs=21.6

Q ss_pred             HHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          61 RSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        61 ~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .++..+..|.++++.||+|+|||.+..
T Consensus        13 ~~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        13 RALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            344455669999999999999998764

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).

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.33  E-value=0.15  Score=38.78  Aligned_cols=52  Identities=21%  Similarity=0.217  Sum_probs=32.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .|..+++.+++|+|||...+.-+.+.+.   ++..++++.- .+...++.+.+..+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~---~g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLR---DGDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHh---cCCeEEEEEc-cCCHHHHHHHHHHh
Confidence            4789999999999999776544433332   3446677663 33444554444433

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.

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=94.31  E-value=0.33  Score=40.58  Aligned_cols=65  Identities=17%  Similarity=0.154  Sum_probs=48.8

Q ss_pred             HHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        89 ~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      .++..+.......++||.+++++-+..+++.++.    .++.+..++|+.+..++...+.    ...+|||+|
T Consensus       234 ~~l~~l~~~~~~~~~lVF~~s~~~~~~l~~~L~~----~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaT  302 (434)
T PRK11192        234 ALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRK----AGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVAT  302 (434)
T ss_pred             HHHHHHHhcCCCCeEEEEeCChHHHHHHHHHHHh----CCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEc
Confidence            3344444443556899999999999999998875    3788899999988776655443    347899999

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.28  E-value=0.11  Score=40.66  Aligned_cols=38  Identities=18%  Similarity=0.122  Sum_probs=27.6

Q ss_pred             HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          67 VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      ..|.-++|.|++|+|||...+--+.+.+.   ++..++|++
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~~a~---~Ge~vlyis   71 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVTQAS---RGNPVLFVT   71 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHHHHh---CCCcEEEEE
Confidence            34678999999999999876655444332   355778877

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>KOG0385|consensus

Probab=94.28  E-value=0.79  Score=41.07  Aligned_cols=105  Identities=16%  Similarity=0.092  Sum_probs=67.7

Q ss_pred             CCcHHHHHHHHHH----HcCCcEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          54 KPSAIQQRSIKPI----VKGRDVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        54 ~~~~~Q~~~i~~i----~~g~~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+.++|.+-+.-+    .+|-|.++.-.-|-|||+--+ +.+..+.. ....+--+|++|...|.+- .+.+++|..  +
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtI-s~l~yl~~~~~~~GPfLVi~P~StL~NW-~~Ef~rf~P--~  242 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTI-SLLGYLKGRKGIPGPFLVIAPKSTLDNW-MNEFKRFTP--S  242 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHH-HHHHHHHHhcCCCCCeEEEeeHhhHHHH-HHHHHHhCC--C
Confidence            4788888766543    348899999999999997643 33333322 2223456888998887654 344566643  6


Q ss_pred             ceEEEEEcCccHHHHHH--Hhc-CCCcEEEeChHHHH
Q psy9277         129 VQCHACIGGTNLSEDLR--KLD-YGQHVVSGTPGRVF  162 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~--~~~-~~~~IlV~TP~~l~  162 (178)
                      +++++++|+........  .+. ...+|+|||-+..+
T Consensus       243 l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i  279 (971)
T KOG0385|consen  243 LNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAI  279 (971)
T ss_pred             cceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHH
Confidence            78888898874332211  112 25699999987763

>KOG0389|consensus

Probab=94.21  E-value=0.36  Score=43.20  Aligned_cols=103  Identities=17%  Similarity=0.134  Sum_probs=67.6

Q ss_pred             CcHHHHHHHHHH---H-cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce
Q psy9277          55 PSAIQQRSIKPI---V-KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ  130 (178)
Q Consensus        55 ~~~~Q~~~i~~i---~-~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~  130 (178)
                      +-++|..-+.-+   . .+.+.++.-.-|-|||.- +++.+..+......+--|||||.-.|-+.. +.+.+|+.  .++
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQ-vIaFlayLkq~g~~gpHLVVvPsSTleNWl-rEf~kwCP--sl~  475 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQ-VIAFLAYLKQIGNPGPHLVVVPSSTLENWL-REFAKWCP--SLK  475 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchhH-HHHHHHHHHHcCCCCCcEEEecchhHHHHH-HHHHHhCC--ceE
Confidence            677777655433   2 266778888899999954 445555555544455679999988775433 33445543  478


Q ss_pred             EEEEEcCccHHHHHHHhc----CCCcEEEeChHHH
Q psy9277         131 CHACIGGTNLSEDLRKLD----YGQHVVSGTPGRV  161 (178)
Q Consensus       131 ~~~~~g~~~~~~~~~~~~----~~~~IlV~TP~~l  161 (178)
                      +..++|......+.+..-    .+.+|+|+|..-.
T Consensus       476 Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la  510 (941)
T KOG0389|consen  476 VEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLA  510 (941)
T ss_pred             EEeccCcHHHHHHHHHHHhccCCCccEEEEEeecc
Confidence            888898886655444332    2579999997543

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.20  E-value=0.34  Score=40.44  Aligned_cols=56  Identities=14%  Similarity=0.119  Sum_probs=44.1

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ...++||.++++..|..+++.+...    ++.+..++|+....++...+.    ...+|||+|-
T Consensus       254 ~~~~~lVF~~t~~~~~~l~~~L~~~----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd  313 (423)
T PRK04837        254 WPDRAIIFANTKHRCEEIWGHLAAD----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD  313 (423)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhC----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec
Confidence            4568999999999999888887643    788999999987766655443    3579999993

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.16  E-value=0.36  Score=40.69  Aligned_cols=87  Identities=18%  Similarity=0.206  Sum_probs=44.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc--HHHHHHHHHHHHHhccCCCceEEEEEcCccHH----HH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT--RELAVQIQKVVLALGDFMNVQCHACIGGTNLS----ED  143 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt--~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~----~~  143 (178)
                      ..++++|++|+|||.+..--+. .+..  .+.+++++...  +.-+.   +.++.++...++.+..........    +.
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~-~L~~--~g~kV~lV~~D~~R~aa~---eQL~~la~~~gvp~~~~~~~~d~~~i~~~a  169 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLAR-YFKK--KGLKVGLVAADTYRPAAY---DQLKQLAEKIGVPFYGDPDNKDAVEIAKEG  169 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHH-HHHH--cCCeEEEecCCCCCHHHH---HHHHHHHHHcCCcEEecCCccCHHHHHHHH
Confidence            4689999999999987654332 2332  33455555532  33333   333334444455543222122211    11


Q ss_pred             HHHhcCCCcEEEeChHHHH
Q psy9277         144 LRKLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       144 ~~~~~~~~~IlV~TP~~l~  162 (178)
                      .......--|||=||+++.
T Consensus       170 l~~~~~~DvVIIDTAGr~~  188 (437)
T PRK00771        170 LEKFKKADVIIVDTAGRHA  188 (437)
T ss_pred             HHHhhcCCEEEEECCCccc
Confidence            1222222348888998874

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=94.14  E-value=0.064  Score=44.70  Aligned_cols=51  Identities=18%  Similarity=0.300  Sum_probs=34.8

Q ss_pred             HHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          63 IKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        63 i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      ++.-...+++++.|+||||||.+ +..++..+..  .+.+++|+=|..++....
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~~--~~~~~vi~D~kg~~~~~~   86 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIRA--RGDRAIIYDPNGGFVSKF   86 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHHh--cCCCEEEEeCCcchhHhh
Confidence            44445578999999999999976 3344444433  345788888887775543

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.

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=94.09  E-value=0.21  Score=39.07  Aligned_cols=89  Identities=20%  Similarity=0.198  Sum_probs=44.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCC-CceEEEEcCc----HHHHHHHHHHHHHhccC-----------------
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLR-ETQVLCLSPT----RELAVQIQKVVLALGDF-----------------  126 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~-~~~~lil~Pt----~~L~~q~~~~~~~~~~~-----------------  126 (178)
                      .+-+.+.|+.|+|||..+.-.. +....... ...+++-+..    ..+..++...+..-...                 
T Consensus        19 ~~~v~I~G~~G~GKT~LA~~~~-~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~   97 (287)
T PF00931_consen   19 VRVVAIVGMGGIGKTTLARQVA-RDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLREL   97 (287)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHH-CHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHH
T ss_pred             eEEEEEEcCCcCCcceeeeecc-cccccccccccccccccccccccccccccccccccccccccccccccccccccchhh
Confidence            3568999999999998775433 32211111 2223333222    33444444333111000                 


Q ss_pred             -CCceEEEEEcCccHHHHHHHh-------cCCCcEEEeCh
Q psy9277         127 -MNVQCHACIGGTNLSEDLRKL-------DYGQHVVSGTP  158 (178)
Q Consensus       127 -~~~~~~~~~g~~~~~~~~~~~-------~~~~~IlV~TP  158 (178)
                       .+-++.++.++.........+       ..++.|||||=
T Consensus        98 L~~~~~LlVlDdv~~~~~~~~l~~~~~~~~~~~kilvTTR  137 (287)
T PF00931_consen   98 LKDKRCLLVLDDVWDEEDLEELREPLPSFSSGSKILVTTR  137 (287)
T ss_dssp             HCCTSEEEEEEEE-SHHHH-------HCHHSS-EEEEEES
T ss_pred             hccccceeeeeeeccccccccccccccccccccccccccc
Confidence             023777777776655544222       24789999983

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=94.04  E-value=0.33  Score=42.74  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=42.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH--HHHHHHHHHHHHhccC
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR--ELAVQIQKVVLALGDF  126 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~--~L~~q~~~~~~~~~~~  126 (178)
                      ..+.+|.|+||+|||..+.+.+.+.+.   .+..++++=|-.  ++...++..++.+++.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~---~g~~vi~fDpkgD~el~~~~~~~~~~~GR~  236 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIR---RGDVVIVFDPKGDADLLKRMYAEAKRAGRL  236 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHH---cCCeEEEEeCCCCHHHHHHHHHHHHHhCCC
Confidence            468999999999999998877766654   345677777774  6788888888887664

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.

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=93.99  E-value=0.2  Score=47.10  Aligned_cols=56  Identities=23%  Similarity=0.376  Sum_probs=45.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .++++|.|+-|||||...+--++..+........+++|+-|+.-|.++..++....
T Consensus        10 ~~~~~~~a~agsgkt~~l~~~~~~~~~~~~~~~~i~~~t~t~~aa~em~~Ri~~~L   65 (1141)
T TIGR02784        10 KTSAWVSANAGSGKTHVLTQRVIRLLLNGVPPSKILCLTYTKAAAAEMQNRVFDRL   65 (1141)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHcCCCCCeEEEEecCHHHHHHHHHHHHHHH
Confidence            57999999999999998877777766554444589999999999999888775544

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=93.94  E-value=0.46  Score=36.88  Aligned_cols=44  Identities=23%  Similarity=0.335  Sum_probs=28.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      ..+++.|++|+|||.... .+...+..  .+..++++ +..++...+.
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~--~g~~v~~i-t~~~l~~~l~  143 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLL--RGKSVLII-TVADIMSAMK  143 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHh--cCCeEEEE-EHHHHHHHHH
Confidence            479999999999997654 44444443  23345444 5566665443

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=93.94  E-value=0.32  Score=47.06  Aligned_cols=64  Identities=25%  Similarity=0.378  Sum_probs=47.3

Q ss_pred             CCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHH--HHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATF--SISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~--ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+++-|.+++..++.  ++-+++.|..|+|||...  ++.++..+. ...+..++.++||..-+..+.+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~-e~~g~~V~glAPTgkAa~~L~e  902 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLP-ESERPRVVGLGPTHRAVGEMRS  902 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHh-hccCceEEEEechHHHHHHHHH
Confidence            689999999999986  488999999999999764  223333222 2245678889999887776543

>PRK08116 hypothetical protein; Validated

Probab=93.94  E-value=0.58  Score=36.77  Aligned_cols=46  Identities=22%  Similarity=0.207  Sum_probs=30.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      ..+++.|++|+|||.... ++.+.+...  +..+ +..+..++..++...
T Consensus       115 ~gl~l~G~~GtGKThLa~-aia~~l~~~--~~~v-~~~~~~~ll~~i~~~  160 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAA-CIANELIEK--GVPV-IFVNFPQLLNRIKST  160 (268)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHHc--CCeE-EEEEHHHHHHHHHHH
Confidence            459999999999997654 455655543  3344 444566666666443

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.93  E-value=0.097  Score=46.36  Aligned_cols=57  Identities=18%  Similarity=0.142  Sum_probs=42.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      ..++++.||||||||..+++|-+-..     ...+|++=|--++........++.    |.+|.++
T Consensus       139 ~~hvlviApTgSGKgvg~VIPnLL~~-----~gS~VV~DpKGE~~~~Ta~~R~~~----G~~V~~F  195 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPTLLTF-----KGSVIALDVKGELFELTSRARKAS----GDAVFKF  195 (670)
T ss_pred             CceEEEEecCCCCceeeehHhHHhcC-----CCCEEEEeCCchHHHHHHHHHHhC----CCEEEEe
Confidence            35899999999999999999886532     236788889888887766655443    5555544

>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=93.91  E-value=0.12  Score=39.23  Aligned_cols=46  Identities=24%  Similarity=0.262  Sum_probs=30.6

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+++.||+|+|||-. +.++.+.+.....+.+++|+.. .+.......
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~~~~~v~y~~~-~~f~~~~~~   81 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQHPGKRVVYLSA-EEFIREFAD   81 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHCTTS-EEEEEH-HHHHHHHHH
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhccccccceeecH-HHHHHHHHH
Confidence            489999999999973 5567776666545667777654 344444433

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.

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=93.84  E-value=0.47  Score=40.03  Aligned_cols=55  Identities=13%  Similarity=0.102  Sum_probs=44.0

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ...++||.|+++.-+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|
T Consensus       241 ~~~~~lVF~~t~~~~~~l~~~L~~~----~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaT  299 (460)
T PRK11776        241 QPESCVVFCNTKKECQEVADALNAQ----GFSALALHGDLEQRDRDQVLVRFANRSCSVLVAT  299 (460)
T ss_pred             CCCceEEEECCHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEe
Confidence            4458999999999999999988655    788899999998776655443    246899999

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=93.84  E-value=0.24  Score=40.89  Aligned_cols=53  Identities=17%  Similarity=0.345  Sum_probs=40.3

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH-HHHHHHHHHHHh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE-LAVQIQKVVLAL  123 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~-L~~q~~~~~~~~  123 (178)
                      -.++.|+.|||||.+...-++..+.....+.+++++.++.. +-..++..+...
T Consensus         3 ~~i~~GgrgSGKS~~~~~~~~~~~~~~~~~~~~~~~r~~~~sl~~sv~~~l~~~   56 (396)
T TIGR01547         3 EIIAKGGRRSGKTFAIALKLVEKLAINKKQQNILAARKVQNSIRDSVFKDIENL   56 (396)
T ss_pred             eEEEeCCCCcccHHHHHHHHHHHHHhcCCCcEEEEEehhhhHHHHHHHHHHHHH
Confidence            46789999999999998888877766434568899999865 666666666544

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.

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=93.82  E-value=0.44  Score=40.22  Aligned_cols=58  Identities=19%  Similarity=0.134  Sum_probs=44.7

Q ss_pred             cCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          97 QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        97 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .....++||.++++.-+..+++.+...    ++.+..++|+.+..++...+.    ...+|||+|-
T Consensus       242 ~~~~~~~lVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd  303 (456)
T PRK10590        242 KGNWQQVLVFTRTKHGANHLAEQLNKD----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD  303 (456)
T ss_pred             cCCCCcEEEEcCcHHHHHHHHHHHHHC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc
Confidence            334468999999999999998888654    788899999988766655443    3468999993

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.72  E-value=0.17  Score=43.13  Aligned_cols=53  Identities=19%  Similarity=0.235  Sum_probs=38.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      |..+++.+|+|+|||...+.-+...+.   ++-+++|++ ..+-..|+.+.+..+..
T Consensus       263 gs~~li~G~~G~GKt~l~~~f~~~~~~---~ge~~~y~s-~eEs~~~i~~~~~~lg~  315 (484)
T TIGR02655       263 DSIILATGATGTGKTLLVSKFLENACA---NKERAILFA-YEESRAQLLRNAYSWGI  315 (484)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEE-eeCCHHHHHHHHHHcCC
Confidence            578999999999999876554443322   455788876 66777788888877753

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.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=93.70  E-value=0.44  Score=34.78  Aligned_cols=43  Identities=7%  Similarity=0.127  Sum_probs=29.9

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      ++|.|++|||||....--+..      .+.+++|++..+..-....+.+
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~------~~~~~~y~at~~~~d~em~~rI   44 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAE------LGGPVTYIATAEAFDDEMAERI   44 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHh------cCCCeEEEEccCcCCHHHHHHH
Confidence            589999999999776543322      3457888887777655555554

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.

>KOG0744|consensus

Probab=93.69  E-value=0.64  Score=37.74  Aligned_cols=67  Identities=21%  Similarity=0.191  Sum_probs=43.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhh--cCCCceE-EEE-----------cCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDT--QLRETQV-LCL-----------SPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~--~~~~~~~-lil-----------~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      ++=++++||+|+|||-. .-++.|++.-  +.+.... +|=           .-+-.|+.++++.+.++.+.-+.-+.++
T Consensus       177 NRliLlhGPPGTGKTSL-CKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvL  255 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSL-CKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVL  255 (423)
T ss_pred             eeEEEEeCCCCCChhHH-HHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEE
Confidence            45689999999999943 4566676632  1111222 222           2445678888888888888777666665


Q ss_pred             Ec
Q psy9277         135 IG  136 (178)
Q Consensus       135 ~g  136 (178)
                      .+
T Consensus       256 ID  257 (423)
T KOG0744|consen  256 ID  257 (423)
T ss_pred             eH
Confidence            53

>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=93.65  E-value=0.059  Score=42.48  Aligned_cols=22  Identities=41%  Similarity=0.631  Sum_probs=18.3

Q ss_pred             HHcCCcEEEEcCCCChHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.+++.++++||+|+|||...-
T Consensus        30 ~~~~~pvLl~G~~GtGKT~li~   51 (272)
T PF12775_consen   30 LSNGRPVLLVGPSGTGKTSLIQ   51 (272)
T ss_dssp             HHCTEEEEEESSTTSSHHHHHH
T ss_pred             HHcCCcEEEECCCCCchhHHHH
Confidence            3458999999999999997643

>PRK14974 cell division protein FtsY; Provisional

Probab=93.61  E-value=0.99  Score=36.74  Aligned_cols=85  Identities=20%  Similarity=0.190  Sum_probs=43.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc--H-HHHHHHHHHHHHhccCCCceEEEEEcCccHHH----
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT--R-ELAVQIQKVVLALGDFMNVQCHACIGGTNLSE----  142 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt--~-~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~----  142 (178)
                      .-+++.|++|+|||....-.+ ..+..  .+.+++++...  | .-..|......    .+++.+.....+.+...    
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA-~~l~~--~g~~V~li~~Dt~R~~a~eqL~~~a~----~lgv~v~~~~~g~dp~~v~~~  213 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLA-YYLKK--NGFSVVIAAGDTFRAGAIEQLEEHAE----RLGVKVIKHKYGADPAAVAYD  213 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHH-HHHHH--cCCeEEEecCCcCcHHHHHHHHHHHH----HcCCceecccCCCCHHHHHHH
Confidence            358899999999998654333 22332  34466666543  2 33344433333    34555443322222111    


Q ss_pred             HHHH-hcCCC-cEEEeChHHH
Q psy9277         143 DLRK-LDYGQ-HVVSGTPGRV  161 (178)
Q Consensus       143 ~~~~-~~~~~-~IlV~TP~~l  161 (178)
                      .... ...+. -|+|=|+|++
T Consensus       214 ai~~~~~~~~DvVLIDTaGr~  234 (336)
T PRK14974        214 AIEHAKARGIDVVLIDTAGRM  234 (336)
T ss_pred             HHHHHHhCCCCEEEEECCCcc
Confidence            1111 12344 4788899987

>PRK09183 transposase/IS protein; Provisional

Probab=93.59  E-value=0.17  Score=39.52  Aligned_cols=47  Identities=19%  Similarity=0.177  Sum_probs=29.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +..+.++++.||+|+|||.....-. ..+..  .+..++++ +..++..++
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~-~~a~~--~G~~v~~~-~~~~l~~~l  145 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALG-YEAVR--AGIKVRFT-TAADLLLQL  145 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHH-HHHHH--cCCeEEEE-eHHHHHHHH
Confidence            4568999999999999997654332 22222  34455554 445565443

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=93.56  E-value=0.19  Score=37.52  Aligned_cols=27  Identities=15%  Similarity=0.283  Sum_probs=17.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      ..++++.|.||||||.+....+.+.+.
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            458999999999999876554444433

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.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=93.52  E-value=0.27  Score=37.52  Aligned_cols=48  Identities=23%  Similarity=0.198  Sum_probs=31.1

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc---CcHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS---PTRELAVQ  115 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~---Pt~~L~~q  115 (178)
                      +..|.-+++.|++|+|||...+--+.+....  .+..++|++   |..+++.+
T Consensus        10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~--~g~~vly~s~E~~~~~~~~r   60 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTAFALNIAENIAKK--QGKPVLFFSLEMSKEQLLQR   60 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCceEEEeCCCCHHHHHHH
Confidence            3457789999999999997665444443332  245777777   33444443

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.

>KOG0331|consensus

Probab=93.49  E-value=0.45  Score=40.77  Aligned_cols=64  Identities=17%  Similarity=0.147  Sum_probs=49.8

Q ss_pred             HHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          89 SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        89 ~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      .++.... ...+.++||.|-|+.-|.++.+.++..    ++.+..++|+.+..++...+.    ..+.|||+|
T Consensus       331 ~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVAT  398 (519)
T KOG0331|consen  331 KLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRK----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVAT  398 (519)
T ss_pred             HHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhc----CcceeeecccccHHHHHHHHHhcccCCcceEEEc
Confidence            3444333 345679999999999999999988765    578889999999888777665    247899999

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.49  E-value=0.37  Score=35.31  Aligned_cols=57  Identities=23%  Similarity=0.195  Sum_probs=33.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhh-------cCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDT-------QLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~-------~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .|.-+++.||+|+|||...+-.+...+..       ...+.+++|+..-.. ..++.+.+..+..
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            57789999999999998765544444321       113457777765544 5556666655443

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=93.40  E-value=0.41  Score=47.47  Aligned_cols=63  Identities=30%  Similarity=0.457  Sum_probs=47.0

Q ss_pred             CCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHH---HHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          53 EKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS---ISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~l---l~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      ..+++.|..++..++.+  +-++|.|+.|+|||...-   -++.+.+..  .+..++.++||..-+..+.
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--EQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--cCCeEEEEeChHHHHHHHH
Confidence            36899999999998874  677889999999996651   233333322  4568899999988877664

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.

>PRK10867 signal recognition particle protein; Provisional

Probab=93.37  E-value=0.87  Score=38.37  Aligned_cols=86  Identities=23%  Similarity=0.320  Sum_probs=45.4

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH---
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR---  145 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---  145 (178)
                      -+++++++|+|||.+..--+.. +... .+.+++++.  +.|.-+.++..   .++...++.+.....+.+..+...   
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~-l~~~-~G~kV~lV~~D~~R~aa~eQL~---~~a~~~gv~v~~~~~~~dp~~i~~~a~  176 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKY-LKKK-KKKKVLLVAADVYRPAAIEQLK---TLGEQIGVPVFPSGDGQDPVDIAKAAL  176 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHH-HHHh-cCCcEEEEEccccchHHHHHHH---HHHhhcCCeEEecCCCCCHHHHHHHHH
Confidence            4789999999999876544433 2222 244565555  33554443333   333444665443322222222111   


Q ss_pred             -H-hcCCC-cEEEeChHHH
Q psy9277         146 -K-LDYGQ-HVVSGTPGRV  161 (178)
Q Consensus       146 -~-~~~~~-~IlV~TP~~l  161 (178)
                       . ...++ -|+|=|||++
T Consensus       177 ~~a~~~~~DvVIIDTaGrl  195 (433)
T PRK10867        177 EEAKENGYDVVIVDTAGRL  195 (433)
T ss_pred             HHHHhcCCCEEEEeCCCCc
Confidence             1 12345 4889999987

>KOG0729|consensus

Probab=93.36  E-value=0.15  Score=40.30  Aligned_cols=96  Identities=16%  Similarity=0.142  Sum_probs=50.6

Q ss_pred             CCCCCCcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHH-HHHcCCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          14 PEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIK-PIVKGRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~-~i~~g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      +..++..-+-..-+..+..+|.+.|=-.+.++.+++. .+.|--+-..... -|---+.+++.+|+|+|||+|+-..+  
T Consensus       156 ppkidpsvtmm~veekpdvty~dvggckeqieklrev-ve~pll~perfv~lgidppkgvllygppgtgktl~arava--  232 (435)
T KOG0729|consen  156 PPKIDPSVTMMQVEEKPDVTYSDVGGCKEQIEKLREV-VELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVA--  232 (435)
T ss_pred             CCCCCCceeEEEeecCCCcccccccchHHHHHHHHHH-HhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHh--
Confidence            3344433333334556677888887555555555432 1111111111111 12225789999999999999874322  


Q ss_pred             HhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          93 SLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        93 ~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                          ++. .-+.|=+=..+|++...
T Consensus       233 ----nrt-dacfirvigselvqkyv  252 (435)
T KOG0729|consen  233 ----NRT-DACFIRVIGSELVQKYV  252 (435)
T ss_pred             ----ccc-CceEEeehhHHHHHHHh
Confidence                112 23444455667877643

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=93.35  E-value=0.31  Score=36.94  Aligned_cols=53  Identities=23%  Similarity=0.263  Sum_probs=33.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|..+++.+++|+|||...+--+...+.   ++..++|++-. +-..++.+.+..+.
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~---~g~~~~y~s~e-~~~~~l~~~~~~~~   67 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLK---NGEKAMYISLE-EREERILGYAKSKG   67 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEECC-CCHHHHHHHHHHcC
Confidence            3678999999999998765544443332   34467776543 34566666665554

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=93.26  E-value=0.53  Score=39.96  Aligned_cols=56  Identities=18%  Similarity=0.179  Sum_probs=44.6

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+..+||.|+++..+.+++..++..    ++.+..++++.+..++.....    ...+|||+|-
T Consensus       225 ~~~~~IIF~~s~~~~e~la~~L~~~----g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~  284 (470)
T TIGR00614       225 KGKSGIIYCPSRKKSEQVTASLQNL----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATV  284 (470)
T ss_pred             CCCceEEEECcHHHHHHHHHHHHhc----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEec
Confidence            4557799999999999999988754    788899999988776654432    4579999994

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

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=93.25  E-value=0.23  Score=42.42  Aligned_cols=55  Identities=22%  Similarity=0.186  Sum_probs=38.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .|..+++.+++|+|||...+--+.+-+..  .+-.++|++- .+-..++.+.+..+..
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~--~ge~~lyvs~-eE~~~~l~~~~~~~G~   74 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIH--FDEPGVFVTF-EESPQDIIKNARSFGW   74 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEEEE-ecCHHHHHHHHHHcCC
Confidence            47899999999999998876555544332  2346777774 4666777777766654

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.

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=93.24  E-value=0.088  Score=44.31  Aligned_cols=20  Identities=35%  Similarity=0.376  Sum_probs=17.2

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+.+++.||+|+|||+.+-
T Consensus       216 ~p~gVLL~GPPGTGKT~LAr  235 (438)
T PTZ00361        216 PPKGVILYGPPGTGKTLLAK  235 (438)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            46789999999999997763

>KOG0922|consensus

Probab=93.23  E-value=1.2  Score=39.22  Aligned_cols=101  Identities=15%  Similarity=0.218  Sum_probs=58.7

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH-HHhccCCCceEEEE
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV-LALGDFMNVQCHAC  134 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~-~~~~~~~~~~~~~~  134 (178)
                      +..-.+.+..+.+.+-++|.|.||||||.=.--.+.. ......+ ++.+--|.|--|..++++. .++.-..|-.|+..
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKSTQipQyL~e-aG~~~~g-~I~~TQPRRVAavslA~RVAeE~~~~lG~~VGY~  130 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKSTQIPQYLAE-AGFASSG-KIACTQPRRVAAVSLAKRVAEEMGCQLGEEVGYT  130 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccccHhHHHHh-cccccCC-cEEeecCchHHHHHHHHHHHHHhCCCcCceeeeE
Confidence            4455566777778899999999999999542222221 1122222 4555558887777777665 44444444444332


Q ss_pred             --EcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         135 --IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       135 --~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                        +.+....        ...|...|-|.|++-+-
T Consensus       131 IRFed~ts~--------~TrikymTDG~LLRE~l  156 (674)
T KOG0922|consen  131 IRFEDSTSK--------DTRIKYMTDGMLLREIL  156 (674)
T ss_pred             EEecccCCC--------ceeEEEecchHHHHHHh
Confidence              2222111        24688888888876554

>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=93.21  E-value=0.17  Score=39.19  Aligned_cols=24  Identities=33%  Similarity=0.389  Sum_probs=17.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      -++++.|++|||||.. ++.++..+
T Consensus        14 fr~viIG~sGSGKT~l-i~~lL~~~   37 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTL-IKSLLYYL   37 (241)
T ss_pred             ceEEEECCCCCCHHHH-HHHHHHhh
Confidence            3789999999999954 44555443

This is thought to be an ATPase involved in viral DNA packaging [].

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=93.13  E-value=0.23  Score=46.80  Aligned_cols=55  Identities=25%  Similarity=0.395  Sum_probs=44.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhc--CCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~--~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      +.+++|.|..|||||.+...-++..+...  -.-.+.++|+-|++-+..+..++.+-
T Consensus        16 ~~~~lveASAGSGKT~vL~~r~lrlLl~~~~~~v~~ILvvTFT~aAa~Emk~RI~~~   72 (1139)
T COG1074          16 GQSVLVEASAGTGKTFVLAERVLRLLLEGGPLDVDEILVVTFTKAAAAEMKERIRDR   72 (1139)
T ss_pred             CCcEEEEEcCCCCchhHHHHHHHHHHhhcCCCChhHeeeeeccHHHHHHHHHHHHHH
Confidence            77999999999999999887777777663  24458999999999988888876443

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=93.06  E-value=0.23  Score=38.60  Aligned_cols=58  Identities=22%  Similarity=0.238  Sum_probs=38.3

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +-.|..+++.+++|||||...+--+.+.+..   +-.++|++ +.+...++.+.+..+....
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~---ge~vlyvs-~~e~~~~l~~~~~~~g~d~   77 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIFALQFLYEGARE---GEPVLYVS-TEESPEELLENARSFGWDL   77 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHHHHHHHHHHHhc---CCcEEEEE-ecCCHHHHHHHHHHcCCCH
Confidence            3457899999999999997765555544332   44566654 5566666777776554433

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=92.99  E-value=0.1  Score=31.60  Aligned_cols=18  Identities=22%  Similarity=0.506  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      |..+++.+++|||||..+
T Consensus        23 g~~tli~G~nGsGKSTll   40 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTLL   40 (62)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            457999999999999664

>TIGR00416 sms DNA repair protein RadA

Probab=92.98  E-value=0.68  Score=39.27  Aligned_cols=81  Identities=20%  Similarity=0.195  Sum_probs=46.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD  148 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  148 (178)
                      |.-+++.+++|+|||...+..+.+ +..  ++.+++|+... +-..|+...+..+....  .-..+....+.+.....+.
T Consensus        94 GsvilI~G~pGsGKTTL~lq~a~~-~a~--~g~kvlYvs~E-Es~~qi~~ra~rlg~~~--~~l~~~~e~~~~~I~~~i~  167 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQVACQ-LAK--NQMKVLYVSGE-ESLQQIKMRAIRLGLPE--PNLYVLSETNWEQICANIE  167 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH-HHh--cCCcEEEEECc-CCHHHHHHHHHHcCCCh--HHeEEcCCCCHHHHHHHHH
Confidence            678899999999999876654333 322  33478888754 44567766666653221  1223334445544444433


Q ss_pred             -CCCcEEE
Q psy9277         149 -YGQHVVS  155 (178)
Q Consensus       149 -~~~~IlV  155 (178)
                       .+++++|
T Consensus       168 ~~~~~~vV  175 (454)
T TIGR00416       168 EENPQACV  175 (454)
T ss_pred             hcCCcEEE
Confidence             2455443

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)).

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=92.96  E-value=0.33  Score=36.25  Aligned_cols=39  Identities=18%  Similarity=0.279  Sum_probs=27.2

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      .|.-+.+.||+|+|||...+-.+.+...   .+..++|+.-.
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            4677899999999999887655444332   34567777654

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.95  E-value=0.22  Score=40.51  Aligned_cols=42  Identities=14%  Similarity=0.369  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      +..++++||||||||... ..++..+... .+.+++.+--..+.
T Consensus       122 ~g~ili~G~tGSGKTT~l-~al~~~i~~~-~~~~i~tiEdp~E~  163 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTL-ASMIDYINKN-AAGHIITIEDPIEY  163 (343)
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHhhCcC-CCCEEEEEcCChhh
Confidence            678999999999999764 3445444322 22355555444443

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.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.90  E-value=0.97  Score=35.64  Aligned_cols=86  Identities=15%  Similarity=0.181  Sum_probs=45.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC-c-H-HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP-T-R-ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR  145 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P-t-~-~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  145 (178)
                      +..+.+++++|+|||..+..-... +..  .+..+.++.- + + +.+.|.    +.+....++.+..........+...
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l~~~-l~~--~~~~v~~i~~D~~ri~~~~ql----~~~~~~~~~~~~~~~~~~~l~~~l~  147 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKMAWQ-FHG--KKKTVGFITTDHSRIGTVQQL----QDYVKTIGFEVIAVRDEAAMTRALT  147 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHH-HHH--cCCeEEEEecCCCCHHHHHHH----HHHhhhcCceEEecCCHHHHHHHHH
Confidence            468999999999999877543332 222  2334444443 2 2 333333    3344444665544333323333323


Q ss_pred             Hhc--CCC-cEEEeChHHH
Q psy9277         146 KLD--YGQ-HVVSGTPGRV  161 (178)
Q Consensus       146 ~~~--~~~-~IlV~TP~~l  161 (178)
                      .+.  .++ .|+|=|||+.
T Consensus       148 ~l~~~~~~D~ViIDt~Gr~  166 (270)
T PRK06731        148 YFKEEARVDYILIDTAGKN  166 (270)
T ss_pred             HHHhcCCCCEEEEECCCCC
Confidence            232  234 3778888876

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=92.90  E-value=0.57  Score=45.85  Aligned_cols=64  Identities=20%  Similarity=0.383  Sum_probs=46.9

Q ss_pred             CCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhh--hcCCCceEEEEcCcHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLD--TQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~--~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+++-|.+++..++.+  +-++|.|..|+|||...- .++..+.  ....+..++.++||..-|..+.+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l~-~v~~~~~~l~~~~~~~V~glAPTgrAAk~L~e 1034 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQFR-AVMSAVNTLPESERPRVVGLGPTHRAVGEMRS 1034 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHHH-HHHHHHHHhhcccCceEEEECCcHHHHHHHHh
Confidence            6899999999999984  689999999999996642 2333222  12234678889999877776543

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.89  E-value=0.47  Score=39.80  Aligned_cols=84  Identities=18%  Similarity=0.175  Sum_probs=42.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL  147 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  147 (178)
                      .-+++++|+|+|||....--+......  .+.++.++.  +-|..+..+..   .++...++......   ........+
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~--~G~~V~Lit~Dt~R~aA~eQLk---~yAe~lgvp~~~~~---~~~~l~~~l  295 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLH--MGKSVSLYTTDNYRIAAIEQLK---RYADTMGMPFYPVK---DIKKFKETL  295 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHh--cCCeEEEecccchhhhHHHHHH---HHHHhcCCCeeehH---HHHHHHHHH
Confidence            348899999999998876544433222  333554444  33455544333   33333344332211   111111122


Q ss_pred             -cCCCc-EEEeChHHH
Q psy9277         148 -DYGQH-VVSGTPGRV  161 (178)
Q Consensus       148 -~~~~~-IlV~TP~~l  161 (178)
                       ..+++ |+|=|||+.
T Consensus       296 ~~~~~D~VLIDTaGr~  311 (432)
T PRK12724        296 ARDGSELILIDTAGYS  311 (432)
T ss_pred             HhCCCCEEEEeCCCCC
Confidence             23454 778888764

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=92.84  E-value=0.2  Score=42.03  Aligned_cols=50  Identities=24%  Similarity=0.218  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHhCCCCC--CcHHH-HH----HHHHHHcCCcEEEEcCCCChHHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEK--PSAIQ-QR----SIKPIVKGRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~--~~~~Q-~~----~i~~i~~g~~v~v~aptGsGKTl~~ll   88 (178)
                      ..+|+--.|++.|++-  ++.-| ..    +++-+.++.|++..||+|+|||..|.-
T Consensus       172 ~dEWid~LlrSiG~~P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~  228 (449)
T TIGR02688       172 LEEWIDVLIRSIGYEPEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNN  228 (449)
T ss_pred             HHHHHHHHHHhcCCCcccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHH
Confidence            3456666778888852  22211 11    124555689999999999999977653

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=92.83  E-value=0.22  Score=37.23  Aligned_cols=23  Identities=22%  Similarity=0.612  Sum_probs=17.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      ++++||||||||... ..++..+.
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~~   26 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYIN   26 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHhh
Confidence            689999999999774 34455443

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.

>KOG0333|consensus

Probab=92.82  E-value=0.59  Score=40.13  Aligned_cols=56  Identities=13%  Similarity=0.157  Sum_probs=45.9

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc---C-CCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~IlV~TP  158 (178)
                      ..+.+||.+.++.=|.-+++.+.+.    ++++..++|+.+.+++...+.   . ..+|+|+|-
T Consensus       516 ~~ppiIIFvN~kk~~d~lAk~LeK~----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD  575 (673)
T KOG0333|consen  516 FDPPIIIFVNTKKGADALAKILEKA----GYKVTTLHGGKSQEQRENALADFREGTGDILVATD  575 (673)
T ss_pred             CCCCEEEEEechhhHHHHHHHHhhc----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec
Confidence            3578999999999988888888766    799999999999888766654   3 579999994

>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=92.77  E-value=0.096  Score=38.75  Aligned_cols=22  Identities=41%  Similarity=0.514  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISI   90 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~i   90 (178)
                      ...+++.||.|||||..|..-.
T Consensus         3 ~~~vlL~Gps~SGKTaLf~~L~   24 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQLV   24 (181)
T ss_dssp             --EEEEE-STTSSHHHHHHHHH
T ss_pred             CceEEEEcCCCCCHHHHHHHHh
Confidence            4679999999999998876433

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.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=92.72  E-value=1.6  Score=35.57  Aligned_cols=33  Identities=15%  Similarity=0.162  Sum_probs=25.9

Q ss_pred             CcHHHHHHHHHHHc--C---CcEEEEcCCCChHHHHHH
Q psy9277          55 PSAIQQRSIKPIVK--G---RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~--g---~~v~v~aptGsGKTl~~l   87 (178)
                      ++|||...|..+.+  +   ...++.||.|.||+..+.
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~   39 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQ   39 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHH
Confidence            36788888887765  2   478899999999997764

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=92.68  E-value=2.7  Score=33.98  Aligned_cols=113  Identities=12%  Similarity=0.146  Sum_probs=63.4

Q ss_pred             CcHHHHHHHHHHHc----C---CcEEEEcCCCChHHHHHHHHHHHHhhh------------------cCCCceEEEEcCc
Q psy9277          55 PSAIQQRSIKPIVK----G---RDVIAQAQSGTGKTATFSISILQSLDT------------------QLRETQVLCLSPT  109 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~----g---~~v~v~aptGsGKTl~~ll~il~~l~~------------------~~~~~~~lil~Pt  109 (178)
                      .+|+|...|..+.+    +   .-.++.||.|.||+..+.. +.+.+..                  ....|-..++.|.
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~-~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~   82 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVEL-FSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPE   82 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecC
Confidence            56788888876654    3   3799999999999966543 2233321                  1123556778885


Q ss_pred             H---HH-HHHHHHHHHHhcc----CCCceEEEEEcCccHHHHH-----HHhcCCC----cEEEeC-hHHHHHHHHcCC
Q psy9277         110 R---EL-AVQIQKVVLALGD----FMNVQCHACIGGTNLSEDL-----RKLDYGQ----HVVSGT-PGRVFDMIRSSQ  169 (178)
Q Consensus       110 ~---~L-~~q~~~~~~~~~~----~~~~~~~~~~g~~~~~~~~-----~~~~~~~----~IlV~T-P~~l~~~l~~~~  169 (178)
                      .   .. +.|+ +.+.++..    .-+.+|+++..........     ..+++.+    =|++++ |++|+.-++++-
T Consensus        83 ~~~~~I~vdqi-R~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI~SRC  159 (319)
T PRK06090         83 KEGKSITVEQI-RQCNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRC  159 (319)
T ss_pred             cCCCcCCHHHH-HHHHHHHhhCcccCCceEEEecchhhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhcc
Confidence            3   23 3444 34433322    2357877776555443221     1222322    244544 678887777653

>PRK05642 DNA replication initiation factor; Validated

Probab=92.63  E-value=0.49  Score=36.30  Aligned_cols=43  Identities=14%  Similarity=0.140  Sum_probs=27.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      ..++++||+|+|||.. +.++.+.+..  .+.+++|+. ..++....
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            5689999999999976 3344544433  244666655 45666543

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=92.61  E-value=0.13  Score=43.40  Aligned_cols=26  Identities=27%  Similarity=0.443  Sum_probs=19.8

Q ss_pred             HHHHHHH-cCCcEEEEcCCCChHHHHH
Q psy9277          61 RSIKPIV-KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        61 ~~i~~i~-~g~~v~v~aptGsGKTl~~   86 (178)
                      .++.... .|+|+++.+|+|||||+..
T Consensus       189 rAleiAAAGgHnLl~~GpPGtGKTmla  215 (490)
T COG0606         189 RALEIAAAGGHNLLLVGPPGTGKTMLA  215 (490)
T ss_pred             HHHHHHHhcCCcEEEecCCCCchHHhh
Confidence            3444333 3899999999999999875

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=92.57  E-value=0.091  Score=35.92  Aligned_cols=21  Identities=24%  Similarity=0.373  Sum_probs=13.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll   88 (178)
                      +++.+++.|++|+|||...-.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~   23 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKR   23 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHH
Confidence            356789999999999977543

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=92.55  E-value=0.21  Score=44.12  Aligned_cols=58  Identities=16%  Similarity=0.097  Sum_probs=41.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI  135 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~  135 (178)
                      ..++++.||||+|||..+++|-+-.     .+.-++++=|..|+........++.    |.+|.++.
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnLL~-----~~gS~VV~DpKgEl~~~Ta~~R~~~----G~~V~vfd  281 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTALK-----WGGPLVVLDPSTEVAPMVSEHRRDA----GREVIVLD  281 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhhhc-----CCCCEEEEeCcHHHHHHHHHHHHHC----CCeEEEEe
Confidence            3689999999999999999997642     2335777778888877666655443    44554443

>PRK13531 regulatory ATPase RavA; Provisional

Probab=92.51  E-value=0.31  Score=41.59  Aligned_cols=44  Identities=16%  Similarity=0.191  Sum_probs=29.1

Q ss_pred             HHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          43 LLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        43 i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.+.+.+ ++..=-.+=..++-.++.|.++++.||+|+|||..+-
T Consensus        14 l~~~l~~-~i~gre~vI~lll~aalag~hVLL~GpPGTGKT~LAr   57 (498)
T PRK13531         14 LSSALEK-GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIAR   57 (498)
T ss_pred             HHHHHhh-hccCcHHHHHHHHHHHccCCCEEEECCCChhHHHHHH
Confidence            3444433 3333333334455567789999999999999998763

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=92.51  E-value=0.094  Score=43.62  Aligned_cols=56  Identities=23%  Similarity=0.186  Sum_probs=33.9

Q ss_pred             cccccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|..+|++++--+...+.+++.   -+..|..++..   -+...+.+++.||+|+|||+..
T Consensus       138 ~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~---Gl~~pkgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQI---GIDPPRGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             CCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhc---CCCCCceEEEECCCCCCHHHHH
Confidence            35567888887665555555432   12222211111   1234689999999999999875

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=92.46  E-value=1.6  Score=36.10  Aligned_cols=81  Identities=23%  Similarity=0.250  Sum_probs=46.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD  148 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~  148 (178)
                      |.-+++.+++|+|||...+..+.. +..  .+.+++|+.-. +-..|+.....++....  .-..+......+.....+.
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~-~a~--~g~~VlYvs~E-Es~~qi~~Ra~rlg~~~--~~l~l~~e~~le~I~~~i~  155 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAAR-LAK--RGGKVLYVSGE-ESPEQIKLRADRLGIST--ENLYLLAETNLEDILASIE  155 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHH-HHh--cCCeEEEEECC-cCHHHHHHHHHHcCCCc--ccEEEEccCcHHHHHHHHH
Confidence            578999999999999776543333 222  33578888754 34556666666554321  1223344555554444443


Q ss_pred             -CCCcEEE
Q psy9277         149 -YGQHVVS  155 (178)
Q Consensus       149 -~~~~IlV  155 (178)
                       .+++++|
T Consensus       156 ~~~~~lVV  163 (372)
T cd01121         156 ELKPDLVI  163 (372)
T ss_pred             hcCCcEEE
Confidence             2566554

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.

>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=92.46  E-value=0.1  Score=35.25  Aligned_cols=16  Identities=25%  Similarity=0.495  Sum_probs=13.6

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      ++|.|++|||||...-
T Consensus         2 I~I~G~~gsGKST~a~   17 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAK   17 (121)
T ss_dssp             EEEEESTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6899999999997653

...

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=92.43  E-value=0.19  Score=40.20  Aligned_cols=21  Identities=29%  Similarity=0.578  Sum_probs=17.9

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+.+++++||||||||...
T Consensus       141 v~~~~~ili~G~tGsGKTTll  161 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFL  161 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHH
Confidence            446899999999999999754

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.

>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=92.35  E-value=0.099  Score=36.38  Aligned_cols=17  Identities=35%  Similarity=0.427  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      ++++.||+|+|||...-
T Consensus         1 ~vlL~G~~G~GKt~l~~   17 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLAR   17 (139)
T ss_dssp             EEEEEESSSSSHHHHHH
T ss_pred             CEEEECCCCCCHHHHHH
Confidence            58999999999997653

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.

>KOG0925|consensus

Probab=92.34  E-value=0.89  Score=38.82  Aligned_cols=90  Identities=16%  Similarity=0.213  Sum_probs=59.5

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      ..+..|+..+.++.-.+.|++..=---|..+.+.+..+.+++-+++.|.||||||.-.=-..+.....  ....+..--|
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 KAINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELS--HLTGVACTQP   99 (699)
T ss_pred             hhcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHh--hccceeecCc
Confidence            33888999999999888886543333466666777777789999999999999996422222222121  1234444557


Q ss_pred             cHHHHHHHHHHH
Q psy9277         109 TRELAVQIQKVV  120 (178)
Q Consensus       109 t~~L~~q~~~~~  120 (178)
                      .|--|.++..+.
T Consensus       100 rrvaamsva~RV  111 (699)
T KOG0925|consen  100 RRVAAMSVAQRV  111 (699)
T ss_pred             hHHHHHHHHHHH
Confidence            777777666554

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=92.33  E-value=0.11  Score=43.07  Aligned_cols=54  Identities=24%  Similarity=0.347  Sum_probs=29.8

Q ss_pred             cccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+|++++--+...+.+.+.   .+..+..++..   -+...+++++.||+|+|||+..
T Consensus       126 p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~---g~~~p~gvLL~GppGtGKT~lA  182 (389)
T PRK03992        126 PNVTYEDIGGLEEQIREVREAVELPLKKPELFEEV---GIEPPKGVLLYGPPGTGKTLLA  182 (389)
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCCceEEECCCCCChHHHH
Confidence            456677776555555554331   11111111100   1122468999999999999765

>PTZ00110 helicase; Provisional

Probab=92.30  E-value=1.2  Score=38.69  Aligned_cols=56  Identities=14%  Similarity=0.063  Sum_probs=43.5

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc---C-CCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~IlV~TP  158 (178)
                      .+.++||.|+++.-|..+++.++..    ++.+..++|+.+..++...+.   + ...|||+|-
T Consensus       376 ~~~k~LIF~~t~~~a~~l~~~L~~~----g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTd  435 (545)
T PTZ00110        376 DGDKILIFVETKKGADFLTKELRLD----GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATD  435 (545)
T ss_pred             cCCeEEEEecChHHHHHHHHHHHHc----CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcc
Confidence            4569999999999999998888643    678888999988776654443   3 468999993

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=92.29  E-value=0.78  Score=37.45  Aligned_cols=28  Identities=11%  Similarity=0.160  Sum_probs=22.3

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCC
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEK   54 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~   54 (178)
                      .+.++....+.|+++...+.|++.||..
T Consensus        27 ~~~~~~~l~~~g~~~~~~~kL~~~g~~t   54 (344)
T PLN03187         27 LFESIDKLISQGINAGDVKKLQDAGIYT   54 (344)
T ss_pred             cccCHHHHhhCCCCHHHHHHHHHcCCCc
Confidence            4566667777889999999999999864

>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=92.25  E-value=1.4  Score=31.76  Aligned_cols=84  Identities=24%  Similarity=0.311  Sum_probs=41.4

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc-Cc-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHH----HH-
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS-PT-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSE----DL-  144 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~-Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~----~~-  144 (178)
                      +++.+++|+|||.....-+. .+..  .+.+++++. .+ +.-..   +.+..+....++.+..........+    .. 
T Consensus         3 ~~~~G~~G~GKTt~~~~la~-~~~~--~g~~v~~i~~D~~~~~~~---~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   76 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLAL-YLKK--KGKKVLLVAADTYRPAAI---EQLRVLGEQVGVPVFEEGEGKDPVSIAKRAIE   76 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHH--CCCcEEEEEcCCCChHHH---HHHHHhcccCCeEEEecCCCCCHHHHHHHHHH
Confidence            57899999999987644332 2222  234555444 33 32222   2233334444555433322222221    11 


Q ss_pred             HHhcCCC-cEEEeChHHH
Q psy9277         145 RKLDYGQ-HVVSGTPGRV  161 (178)
Q Consensus       145 ~~~~~~~-~IlV~TP~~l  161 (178)
                      .....+. -|+|=||+..
T Consensus        77 ~~~~~~~d~viiDt~g~~   94 (173)
T cd03115          77 HAREENFDVVIVDTAGRL   94 (173)
T ss_pred             HHHhCCCCEEEEECcccc
Confidence            1223355 4788899875

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.

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=92.24  E-value=0.31  Score=36.94  Aligned_cols=42  Identities=24%  Similarity=0.441  Sum_probs=28.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      ++++.|.|.||||||...- .+++.+.. ..+..++|+=|.-+=
T Consensus        23 ~~H~~I~G~TGsGKS~~~~-~ll~~l~~-~~~~~~ii~D~~GEY   64 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVK-VLLEELLK-KKGAKVIIFDPHGEY   64 (229)
T ss_pred             cceEEEECCCCCCHHHHHH-HHHHHHHh-cCCCCEEEEcCCCcc
Confidence            5789999999999997654 34444442 244466666665443

It contains several conserved aspartates and histidines that could be metal ligands.

>PRK04296 thymidine kinase; Provisional

Probab=92.18  E-value=0.34  Score=35.93  Aligned_cols=37  Identities=16%  Similarity=0.260  Sum_probs=24.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      |.-.++.||.|+|||...+-- +.++..  .+.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~~-~~~~~~--~g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQR-AYNYEE--RGMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHH-HHHHHH--cCCeEEEEec
Confidence            344788999999999765543 333332  3457777766

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=92.18  E-value=0.65  Score=39.33  Aligned_cols=47  Identities=19%  Similarity=0.281  Sum_probs=31.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ..+++.|++|+|||... -++.+.+.....+.+++|+.. .++..++..
T Consensus       142 npl~i~G~~G~GKTHLl-~Ai~~~l~~~~~~~~v~yv~~-~~f~~~~~~  188 (450)
T PRK14087        142 NPLFIYGESGMGKTHLL-KAAKNYIESNFSDLKVSYMSG-DEFARKAVD  188 (450)
T ss_pred             CceEEECCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHH
Confidence            35899999999999543 455565554445567777655 555555443

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=92.17  E-value=1.7  Score=35.51  Aligned_cols=56  Identities=7%  Similarity=0.017  Sum_probs=43.0

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP  158 (178)
                      .+.+++|+++|+.-++.++..+++.  ..++.+..++|..+..++.+..  ..+|+|+|.
T Consensus       271 ~~~k~LIf~nt~~~~~~l~~~L~~~--~~~~~~~~l~g~~~~~~R~~~~--~~~iLVaTd  326 (357)
T TIGR03158       271 PGERGAIILDSLDEVNRLSDLLQQQ--GLGDDIGRITGFAPKKDRERAM--QFDILLGTS  326 (357)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHhhh--CCCceEEeeecCCCHHHHHHhc--cCCEEEEec
Confidence            4568999999999999999999764  2345677788888877664432  478999995

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.

>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=92.17  E-value=0.12  Score=35.11  Aligned_cols=16  Identities=31%  Similarity=0.517  Sum_probs=13.5

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      +++.||+|+|||...-
T Consensus         1 ill~G~~G~GKT~l~~   16 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLAR   16 (132)
T ss_dssp             EEEESSTTSSHHHHHH
T ss_pred             CEEECcCCCCeeHHHH
Confidence            6899999999996653

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 ....

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=92.13  E-value=0.58  Score=35.67  Aligned_cols=52  Identities=13%  Similarity=0.183  Sum_probs=33.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .|.-+++.+++|+|||.....-+...+.   ++.+++|+.-.. -..++.+.+..+
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~~---~g~~~~y~~~e~-~~~~~~~~~~~~   75 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGALK---QGKKVYVITTEN-TSKSYLKQMESV   75 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHHh---CCCEEEEEEcCC-CHHHHHHHHHHC
Confidence            3678999999999999776554443332   355777776543 334555555554

>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=92.07  E-value=0.17  Score=38.27  Aligned_cols=19  Identities=32%  Similarity=0.454  Sum_probs=14.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+.++++.+|+|+|||+..
T Consensus        21 G~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   21 GGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             CC--EEEES-CCCTHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH
Confidence            4789999999999999775

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.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=92.05  E-value=0.61  Score=38.75  Aligned_cols=47  Identities=15%  Similarity=0.187  Sum_probs=29.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ..+++.||+|+|||... ..+.+.+.....+..++++.. ..+..+...
T Consensus       137 n~l~l~G~~G~GKThL~-~ai~~~l~~~~~~~~v~yi~~-~~~~~~~~~  183 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLL-HAIGNEILENNPNAKVVYVSS-EKFTNDFVN  183 (405)
T ss_pred             CeEEEECCCCCcHHHHH-HHHHHHHHHhCCCCcEEEEEH-HHHHHHHHH
Confidence            35899999999999765 355555544333456777643 445444433

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).

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=92.03  E-value=0.18  Score=41.32  Aligned_cols=56  Identities=21%  Similarity=0.335  Sum_probs=31.0

Q ss_pred             ccccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|++++-.+...+.+.+.   .+..+...  ..+ -+...+.+++.||+|+|||...-
T Consensus       116 ~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~--~~~-g~~~p~gvLL~GppGtGKT~lak  174 (364)
T TIGR01242       116 RPNVSYEDIGGLEEQIREIREAVELPLKHPELF--EEV-GIEPPKGVLLYGPPGTGKTLLAK  174 (364)
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHH--Hhc-CCCCCceEEEECCCCCCHHHHHH
Confidence            3455677776555555555432   11111111  111 12235679999999999997653

Many proteins may score above the trusted cutoff because an internal

>KOG0926|consensus

Probab=92.01  E-value=1  Score=40.67  Aligned_cols=98  Identities=22%  Similarity=0.254  Sum_probs=52.2

Q ss_pred             HHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh---c-CCCceEEEEcCcHHHHHHHHHHH-HHhccCCCceE--EE
Q psy9277          61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT---Q-LRETQVLCLSPTRELAVQIQKVV-LALGDFMNVQC--HA  133 (178)
Q Consensus        61 ~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~---~-~~~~~~lil~Pt~~L~~q~~~~~-~~~~~~~~~~~--~~  133 (178)
                      +.+.+|..+--++|||.||||||.-. .-.|.....   + ..+.-+=|--|.|--|..+..+. .+++. ++-.+  .+
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTTQv-PQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~-~~~eVsYqI  340 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTTQV-PQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGV-LGSEVSYQI  340 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCccccc-hHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhcc-CccceeEEE
Confidence            34456666778999999999999642 111221111   1 11223334447776666655544 33433 23222  22


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      -+.+.-        .....|-+.|-|.|+.-|.+.
T Consensus       341 Rfd~ti--------~e~T~IkFMTDGVLLrEi~~D  367 (1172)
T KOG0926|consen  341 RFDGTI--------GEDTSIKFMTDGVLLREIEND  367 (1172)
T ss_pred             Eecccc--------CCCceeEEecchHHHHHHHHh
Confidence            233321        123568888888887766543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=92.00  E-value=1.2  Score=37.83  Aligned_cols=56  Identities=11%  Similarity=0.157  Sum_probs=42.8

Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          98 LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        98 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ....++||.|++++-+..+++.+...    ++.+..++|+.+.+++...+.    ....|||+|
T Consensus       333 ~~~~~~IVF~~s~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT  392 (475)
T PRK01297        333 NPWERVMVFANRKDEVRRIEERLVKD----GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVAT  392 (475)
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEc
Confidence            34468999999999999988877544    678888899988776644433    246899998

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=91.99  E-value=0.25  Score=41.72  Aligned_cols=33  Identities=24%  Similarity=0.391  Sum_probs=26.4

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +-......+..+..++++++.+|+|+|||..+-
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            444556667777789999999999999997764

>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=91.99  E-value=0.12  Score=35.87  Aligned_cols=15  Identities=27%  Similarity=0.459  Sum_probs=13.2

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      ++++|++|||||...
T Consensus         2 ii~~G~pgsGKSt~a   16 (143)
T PF13671_consen    2 IILCGPPGSGKSTLA   16 (143)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            689999999999764

...

>PRK08727 hypothetical protein; Validated

Probab=91.97  E-value=0.68  Score=35.47  Aligned_cols=50  Identities=18%  Similarity=0.175  Sum_probs=30.7

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..+++.||+|+|||.... ++.+.+..  .+.+++|+. ..++.....+.+..+
T Consensus        42 ~~l~l~G~~G~GKThL~~-a~~~~~~~--~~~~~~y~~-~~~~~~~~~~~~~~l   91 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLAL-ALCAAAEQ--AGRSSAYLP-LQAAAGRLRDALEAL   91 (233)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHH--cCCcEEEEe-HHHhhhhHHHHHHHH
Confidence            459999999999996644 33443333  345666654 455555555545444

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=91.96  E-value=0.61  Score=42.87  Aligned_cols=41  Identities=15%  Similarity=0.351  Sum_probs=30.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      ..|.+|.|+||||||...-.-+.+.+..  .+++++|+=|-++
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q~~~~--~~~~v~IiD~g~s  515 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQVMAV--HRPRLFIVEAGNS  515 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHHHHh--cCCEEEEEcCCCC
Confidence            4589999999999998765555554432  3568899888876

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=91.96  E-value=3.1  Score=33.82  Aligned_cols=115  Identities=16%  Similarity=0.152  Sum_probs=63.6

Q ss_pred             CcHHHHHHHHHHHc----C---CcEEEEcCCCChHHHHHHHHHHHHhhh-------------------cCCCceEEEEcC
Q psy9277          55 PSAIQQRSIKPIVK----G---RDVIAQAQSGTGKTATFSISILQSLDT-------------------QLRETQVLCLSP  108 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~----g---~~v~v~aptGsGKTl~~ll~il~~l~~-------------------~~~~~~~lil~P  108 (178)
                      .+|||...|..+.+    |   .-.++.||.|.||+..+.. +.+.+..                   ....|-..++.|
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~-~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p   81 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYA-LSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTP   81 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHH-HHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEec
Confidence            46778888877653    3   3788999999999977543 2333322                   122355677877


Q ss_pred             cH----HHHHHHHHHHHHhcc---CCCceEEEEEcCccHHHHH--H---HhcCC---Cc-EEEeC-hHHHHHHHHcCCC
Q psy9277         109 TR----ELAVQIQKVVLALGD---FMNVQCHACIGGTNLSEDL--R---KLDYG---QH-VVSGT-PGRVFDMIRSSQG  170 (178)
Q Consensus       109 t~----~L~~q~~~~~~~~~~---~~~~~~~~~~g~~~~~~~~--~---~~~~~---~~-IlV~T-P~~l~~~l~~~~~  170 (178)
                      ..    --+.|+.+..+.+..   .-+.+|+.+..-.......  .   .+++.   .- |+++. |++|+.-++++--
T Consensus        82 ~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTIrSRCq  160 (334)
T PRK07993         82 EKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATLRSRCR  160 (334)
T ss_pred             ccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHHHhccc
Confidence            63    235555554444432   2356777776544433221  1   22222   23 33433 6777766665433

>KOG1806|consensus

Probab=91.88  E-value=0.37  Score=44.29  Aligned_cols=71  Identities=21%  Similarity=0.179  Sum_probs=55.6

Q ss_pred             CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          52 FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        52 ~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      +-..|+-|-+++-.-.....+++.+|+|+|||-...- ++..+..+....+++|++.+..-.+|.++.....
T Consensus       736 ~v~ft~~qveai~sg~qpgltmvvgppgtgktd~avq-il~~lyhn~p~qrTlivthsnqaln~lfeKi~~~  806 (1320)
T KOG1806|consen  736 QVKFTPTQVEAILSGMQPGLTMVVGPPGTGKTDVAVQ-ILSVLYHNSPNQRTLIVTHSNQALNQLFEKIMAL  806 (1320)
T ss_pred             hhccCHHHHHHHHhcCCCCceeeecCCCCCCcchhhh-hhhhhhhcCCCcceEEEEecccchhHHHHHHHhc
Confidence            4457899999888877788999999999999977643 3344444556679999999999989988877444

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=91.86  E-value=0.44  Score=37.76  Aligned_cols=19  Identities=26%  Similarity=0.244  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +.++++.||+|+|||.++.
T Consensus        58 ~~~vll~G~pGTGKT~lA~   76 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVAL   76 (284)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            4589999999999998763

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=91.85  E-value=0.52  Score=38.11  Aligned_cols=40  Identities=15%  Similarity=0.155  Sum_probs=26.3

Q ss_pred             HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          67 VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      -.|+-+.+.+|+|+|||...+..+.+...   .+..++|+...
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~~~~---~g~~v~yId~E   92 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAEAQK---AGGTAAFIDAE   92 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEEccc
Confidence            34678899999999999887655544332   23455555433

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.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=91.78  E-value=1.2  Score=39.36  Aligned_cols=55  Identities=11%  Similarity=0.094  Sum_probs=43.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ...++||.|+|+.-+.++++.+...    ++.+..++|+.+..++...+.    ...+|||+|
T Consensus       244 ~~~~~IVF~~tk~~a~~l~~~L~~~----g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVAT  302 (629)
T PRK11634        244 DFDAAIIFVRTKNATLEVAEALERN----GYNSAALNGDMNQALREQTLERLKDGRLDILIAT  302 (629)
T ss_pred             CCCCEEEEeccHHHHHHHHHHHHhC----CCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEc
Confidence            3458999999999999999888654    778889999988776544432    357999999

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=91.76  E-value=0.75  Score=40.63  Aligned_cols=70  Identities=20%  Similarity=0.263  Sum_probs=54.7

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+++-|.+++...  ...++|.|..|||||-+..-=+.+.+... -...+++.++=|+.-|.++...+..+..
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            5788899987665  67789999999999998877666665542 2234688888999999999998887765

>PTZ00424 helicase 45; Provisional

Probab=91.76  E-value=1.6  Score=35.86  Aligned_cols=57  Identities=16%  Similarity=0.085  Sum_probs=43.5

Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          98 LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        98 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ....++++.|+++.-+..+.+.++..    ++.+..++|+.+..++...+.    ...+|+|+|-
T Consensus       265 ~~~~~~ivF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~  325 (401)
T PTZ00424        265 LTITQAIIYCNTRRKVDYLTKKMHER----DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTD  325 (401)
T ss_pred             cCCCeEEEEecCcHHHHHHHHHHHHC----CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcc
Confidence            34468999999999998888877653    678889999988776655433    2479999993

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=91.74  E-value=1.5  Score=39.42  Aligned_cols=81  Identities=15%  Similarity=0.279  Sum_probs=53.2

Q ss_pred             HHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          47 IYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        47 l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      +.++.......-|.+.+..++..  +-+++.|.-|-|||.+.=+.+....... ...++++.+|+.+-++.++..+.+-.
T Consensus       207 l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~~~~~~-~~~~iiVTAP~~~nv~~Lf~fa~~~l  285 (758)
T COG1444         207 LYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAAAARLA-GSVRIIVTAPTPANVQTLFEFAGKGL  285 (758)
T ss_pred             HhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHHHHHhc-CCceEEEeCCCHHHHHHHHHHHHHhH
Confidence            44443334444555555566653  4789999999999988766663222221 14689999999999999988775544


Q ss_pred             cCCC
Q psy9277         125 DFMN  128 (178)
Q Consensus       125 ~~~~  128 (178)
                      ...|
T Consensus       286 ~~lg  289 (758)
T COG1444         286 EFLG  289 (758)
T ss_pred             HHhC
Confidence            4444

>PRK08939 primosomal protein DnaI; Reviewed

Probab=91.70  E-value=0.47  Score=38.08  Aligned_cols=46  Identities=15%  Similarity=0.220  Sum_probs=27.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ++++++.||+|+|||.... ++.+.+..  .+..+.++ ..-+++.++..
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~~--~g~~v~~~-~~~~l~~~lk~  201 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELAK--KGVSSTLL-HFPEFIRELKN  201 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH--cCCCEEEE-EHHHHHHHHHH
Confidence            4689999999999996644 44444443  33344443 33355555544

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=91.66  E-value=0.71  Score=38.97  Aligned_cols=47  Identities=13%  Similarity=0.185  Sum_probs=29.2

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ..+++.||+|+|||.... .+...+.....+.+++++ +..++..+...
T Consensus       149 ~~l~l~G~~G~GKThL~~-ai~~~~~~~~~~~~v~yi-~~~~~~~~~~~  195 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLH-AIGNYILEKNPNAKVVYV-TSEKFTNDFVN  195 (450)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEE-EHHHHHHHHHH
Confidence            468999999999997643 444555443334566666 44455554433

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=91.63  E-value=1.6  Score=31.77  Aligned_cols=37  Identities=16%  Similarity=0.172  Sum_probs=23.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      +.++|.|++|||||.....-+..      .+...++++.....
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~------~~~~~~~iat~~~~   38 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQ------SGLQVLYIATAQPF   38 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHH------cCCCcEeCcCCCCC
Confidence            45899999999999775433221      12245666654443

>cd01394 radB RadB

Probab=91.61  E-value=0.38  Score=36.16  Aligned_cols=36  Identities=19%  Similarity=0.219  Sum_probs=25.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      |.-+.+.+++|+|||...+.-+.+...   .+..++|+.
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            567899999999999877655444322   345677773

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=91.58  E-value=0.19  Score=44.46  Aligned_cols=50  Identities=12%  Similarity=0.064  Sum_probs=37.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..++++.||||||||..+++|-+-..     ...+||.=|--|+.......-+++
T Consensus       144 ~~hvLviApTrSGKgvg~VIPnLL~~-----~~S~VV~D~KGEl~~~Ta~~R~~~  193 (663)
T PRK13876        144 PEHVLCFAPTRSGKGVGLVVPTLLTW-----PGSAIVHDIKGENWQLTAGFRARF  193 (663)
T ss_pred             CceEEEEecCCCCcceeEehhhHHhC-----CCCEEEEeCcchHHHHHHHHHHhC
Confidence            46999999999999999999987542     236777778888877665554443

>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=91.50  E-value=0.15  Score=34.47  Aligned_cols=16  Identities=25%  Similarity=0.318  Sum_probs=13.8

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      |++.|++|||||.+.-
T Consensus         1 I~i~G~~GsGKtTia~   16 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAK   16 (129)
T ss_dssp             EEEEESTTSSHHHHHH
T ss_pred             CEEECCCCCCHHHHHH
Confidence            6899999999998754

...

>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=91.49  E-value=0.42  Score=34.68  Aligned_cols=45  Identities=27%  Similarity=0.451  Sum_probs=33.9

Q ss_pred             HHHHHHHHhCCCCC-----CcHHHHHHHHHHHcCCcEEEEcCCCChHHHH
Q psy9277          41 EDLLRGIYAYGFEK-----PSAIQQRSIKPIVKGRDVIAQAQSGTGKTAT   85 (178)
Q Consensus        41 ~~i~~~l~~~g~~~-----~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~   85 (178)
                      ++.++..+++||.-     -+....+.+...+.++-+++.+++|.|||..
T Consensus         2 ~~~~~~y~~~gy~v~~~S~~~~~g~~~l~~~l~~k~~vl~G~SGvGKSSL   51 (161)
T PF03193_consen    2 EELLEQYEKLGYPVFFISAKTGEGIEELKELLKGKTSVLLGQSGVGKSSL   51 (161)
T ss_dssp             HHHHHHHHHTTSEEEE-BTTTTTTHHHHHHHHTTSEEEEECSTTSSHHHH
T ss_pred             HHHHHHHHHcCCcEEEEeCCCCcCHHHHHHHhcCCEEEEECCCCCCHHHH
Confidence            35666777888752     2445567777888899999999999999943

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.

>KOG0733|consensus

Probab=91.49  E-value=0.18  Score=43.96  Aligned_cols=55  Identities=20%  Similarity=0.287  Sum_probs=30.5

Q ss_pred             cccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      |..+|++.|--+++...|.-.   -+++|..+  +++. +-.-..+++++|+|+|||+.+=
T Consensus       506 PdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~--k~lG-i~~PsGvLL~GPPGCGKTLlAK  563 (802)
T KOG0733|consen  506 PDVTWDDIGALEEVRLELNMAILAPIKRPDLF--KALG-IDAPSGVLLCGPPGCGKTLLAK  563 (802)
T ss_pred             CCCChhhcccHHHHHHHHHHHHhhhccCHHHH--HHhC-CCCCCceEEeCCCCccHHHHHH
Confidence            355677776544444444211   22222222  2221 1225689999999999998763

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=91.45  E-value=0.54  Score=33.93  Aligned_cols=28  Identities=29%  Similarity=0.555  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQ   97 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~   97 (178)
                      ++.+++.|++|+|||... -.++..+...
T Consensus        24 ~~~~ll~G~~G~GKT~ll-~~~~~~~~~~   51 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSLL-RALLDRLAER   51 (185)
T ss_dssp             ---EEE-B-TTSSHHHHH-HHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHHHHhc
Confidence            578999999999999653 3355554443

>PHA02535 P terminase ATPase subunit; Provisional

Probab=91.44  E-value=1.4  Score=38.33  Aligned_cols=86  Identities=12%  Similarity=0.097  Sum_probs=63.3

Q ss_pred             CCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          38 GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        38 ~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      .+++...+.|.+.-...+.++|...+..=...+.-++.-.--.|||+.|..-++.....  .+...++|+|+++.+....
T Consensus       122 ~~s~~~~~~l~~~~~~~l~~YQ~~W~~~~~~~r~r~ilKSRQiG~T~~fA~EA~~dal~--~G~nqiflSas~~QA~~f~  199 (581)
T PHA02535        122 DISDEQTEKLIEAFLDSLFDYQKHWYRAGLHHRTRNILKSRQIGATYYFAREALEDALL--TGRNQIFLSASKAQAHVFK  199 (581)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHhCccccceeeEeeecccchHHHHHHHHHHHHHh--cCCceEEECCCHHHHHHHH
Confidence            37778888887665678999999988652224555555566689999988766665544  3447799999999999877


Q ss_pred             HHHHHhcc
Q psy9277         118 KVVLALGD  125 (178)
Q Consensus       118 ~~~~~~~~  125 (178)
                      +.+..+.+
T Consensus       200 ~yi~~~a~  207 (581)
T PHA02535        200 QYIIAFAR  207 (581)
T ss_pred             HHHHHHHH
Confidence            77766644

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=91.42  E-value=0.89  Score=37.95  Aligned_cols=55  Identities=15%  Similarity=0.030  Sum_probs=35.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH-------HHHHHHHHHHHHhc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR-------ELAVQIQKVVLALG  124 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~-------~L~~q~~~~~~~~~  124 (178)
                      ..-+++.||+|+|||-.. -++.+.........+++++....       ++-..-.+.+++..
T Consensus       113 ~nplfi~G~~GlGKTHLl-~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y  174 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLL-QAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY  174 (408)
T ss_pred             CCcEEEECCCCCCHHHHH-HHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh
Confidence            356999999999999653 35555555554556788887654       34444444565555

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=91.41  E-value=0.35  Score=42.56  Aligned_cols=49  Identities=22%  Similarity=0.245  Sum_probs=37.3

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .++++.||||||||..+++|-+-.     -+.-++++=|..|+.......-++.
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL~-----~~gS~VV~DpKgE~~~~Ta~~R~~~  260 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTALK-----YGGPLVCLDPSTEVAPMVCEHRRQA  260 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhhc-----CCCCEEEEEChHHHHHHHHHHHHHc
Confidence            689999999999999999997542     2346777788888877666554444

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.

>PRK13700 conjugal transfer protein TraD; Provisional

Probab=91.32  E-value=0.29  Score=43.53  Aligned_cols=75  Identities=15%  Similarity=0.138  Sum_probs=45.8

Q ss_pred             HHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          41 EDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        41 ~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .++.+.+++-|-..+..+----+|.-.+.+++++.|.||||||.+. .-++..+..  ++.++||.=|+-+.+...|+
T Consensus       157 ~~l~k~lk~~~~~s~i~I~gvPip~~~E~~H~li~GttGSGKS~~i-~~LL~~ir~--RGdrAIIyD~~GeFv~~FY~  231 (732)
T PRK13700        157 KDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVI-RRLANYARQ--RGDMVVIYDRSGEFVKSYYD  231 (732)
T ss_pred             HHHHHHHHhcCCCCCeeEccccCCcchhhcceEEeCCCCCCHHHHH-HHHHHHHHH--cCCeEEEEeCCCchHHHhcC
Confidence            3555566665543332222222233345789999999999999864 444554443  45577777787777765554

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=91.23  E-value=0.29  Score=42.58  Aligned_cols=43  Identities=12%  Similarity=0.300  Sum_probs=27.5

Q ss_pred             HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      ...+++++.|+||||||.+ +..++..+..  ++.+++|+=|.-+.
T Consensus       174 ~e~~h~li~G~tGsGKs~~-i~~ll~~~~~--~g~~~ii~D~~g~~  216 (566)
T TIGR02759       174 SETQHILIHGTTGSGKSVA-IRKLLRWIRQ--RGDRAIIYDKGCTF  216 (566)
T ss_pred             ccccceEEEcCCCCCHHHH-HHHHHHHHHh--cCCeEEEEECCCCe
Confidence            3467999999999999964 3445554433  23355555555443

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).

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=91.20  E-value=0.65  Score=37.60  Aligned_cols=39  Identities=18%  Similarity=0.171  Sum_probs=26.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      |+-+.+.+|+|+|||...+..+.+...   .+..++|+....
T Consensus        55 G~iteI~Gp~GsGKTtLal~~~~~~~~---~g~~~vyId~E~   93 (325)
T cd00983          55 GRIIEIYGPESSGKTTLALHAIAEAQK---LGGTVAFIDAEH   93 (325)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCCEEEECccc
Confidence            578899999999999777655544322   344666665533

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=90.98  E-value=0.17  Score=40.43  Aligned_cols=18  Identities=17%  Similarity=0.220  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +=++|.||||||||...+
T Consensus         5 ~ii~I~GpTasGKS~LAl   22 (300)
T PRK14729          5 KIVFIFGPTAVGKSNILF   22 (300)
T ss_pred             cEEEEECCCccCHHHHHH
Confidence            348999999999997665

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=90.96  E-value=0.19  Score=44.41  Aligned_cols=46  Identities=17%  Similarity=0.117  Sum_probs=35.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      ..++++.||||||||..+++|.+-.     .+..+||+=|-.++.......
T Consensus       175 ~~HvlviapTgSGKgvg~ViPnLL~-----~~~S~VV~D~KGE~~~~Tag~  220 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPTLLS-----WGHSSVITDLKGELWALTAGW  220 (636)
T ss_pred             CceEEEEecCCCCCceEEEccchhh-----CCCCEEEEeCcHHHHHHHHHH
Confidence            3689999999999999999888753     234678888888886555443

>CHL00181 cbbX CbbX; Provisional

Probab=90.89  E-value=0.68  Score=36.78  Aligned_cols=21  Identities=29%  Similarity=0.279  Sum_probs=17.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSIS   89 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~   89 (178)
                      +.++++.||+|+|||.++-.-
T Consensus        59 ~~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHH
Confidence            557999999999999887543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=90.89  E-value=0.55  Score=35.31  Aligned_cols=21  Identities=24%  Similarity=0.311  Sum_probs=17.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll   88 (178)
                      .+.++++.||+|+|||.....
T Consensus        37 ~~~~lll~G~~G~GKT~la~~   57 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQA   57 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHHH
Confidence            367899999999999976643

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK08084 DNA replication initiation factor; Provisional

Probab=90.83  E-value=0.74  Score=35.34  Aligned_cols=37  Identities=14%  Similarity=0.189  Sum_probs=24.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +.++++.||+|+|||.... .+.+.+..  .+.+++|+.-
T Consensus        45 ~~~l~l~Gp~G~GKThLl~-a~~~~~~~--~~~~v~y~~~   81 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLH-AACAELSQ--RGRAVGYVPL   81 (235)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHh--CCCeEEEEEH
Confidence            4689999999999996654 33333332  3445666544

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=90.83  E-value=1.4  Score=38.53  Aligned_cols=55  Identities=9%  Similarity=0.075  Sum_probs=43.8

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      +..+||.|+++..+.++++.+...    ++.+..++++.+.+++.....    ...+|||+|-
T Consensus       224 ~~~~IIf~~sr~~~e~la~~L~~~----g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~  282 (591)
T TIGR01389       224 GQSGIIYASSRKKVEELAERLESQ----GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATN  282 (591)
T ss_pred             CCCEEEEECcHHHHHHHHHHHHhC----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEec
Confidence            457899999999999999988653    788889999988776655433    4579999994

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=90.81  E-value=1.5  Score=38.55  Aligned_cols=56  Identities=11%  Similarity=0.055  Sum_probs=44.5

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.|+++.-+.+++..+...    ++.+..++++.+..++.....    ...+|+|+|.
T Consensus       235 ~~~~~IIFc~tr~~~e~la~~L~~~----g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~  294 (607)
T PRK11057        235 RGKSGIIYCNSRAKVEDTAARLQSR----GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATV  294 (607)
T ss_pred             CCCCEEEEECcHHHHHHHHHHHHhC----CCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEec
Confidence            4568899999999999999988754    788899999988776554443    3478999995

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=90.80  E-value=1.4  Score=43.91  Aligned_cols=63  Identities=14%  Similarity=0.191  Sum_probs=48.2

Q ss_pred             CCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      .+++-|.+++..++.+  +-.++.++.|+|||... -.++..+..  .+.+++.++||..-+..+.+.
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~--~G~~V~~lAPTgrAA~~L~e~  493 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE--QGYEIQIITAGSLSAQELRQK  493 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh--cCCeEEEEeCCHHHHHHHHHH
Confidence            5899999999998874  68899999999999653 233333332  467899999998877776665

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.

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=90.79  E-value=1.8  Score=37.00  Aligned_cols=76  Identities=12%  Similarity=0.123  Sum_probs=43.2

Q ss_pred             cHHHHHHHHHHH-------cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEE-----EcCcHHHHHHHHHHHHHh
Q psy9277          56 SAIQQRSIKPIV-------KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLC-----LSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        56 ~~~Q~~~i~~i~-------~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~li-----l~Pt~~L~~q~~~~~~~~  123 (178)
                      +++|.+..+.+.       .|.-+.++||+|||||...-    ..+.....+..+.+     ..|.+.-......++..+
T Consensus        12 r~Ie~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKSTLLr----~~l~~~~sGg~I~ldg~~~~~~~~~ai~~LR~VFQ~f   87 (504)
T TIGR03238        12 RKIQTDLERILVKFNKELPSSSLLFLCGSSGDGKSEILA----ENKRKFSEGYEFFLDATHSFSPNKNAMETLDEIFDGF   87 (504)
T ss_pred             hHHHHHHHHHHhCCceeecCCCEEEEECCCCCCHHHHHh----cCCCCCCCCCEEEECCEECCCCCHHHHHHHHHHHHhh
Confidence            788887766553       38899999999999996654    11111112211211     225555555555566666


Q ss_pred             ccCCCceEEEEE
Q psy9277         124 GDFMNVQCHACI  135 (178)
Q Consensus       124 ~~~~~~~~~~~~  135 (178)
                      -....--++.+.
T Consensus        88 n~~~~~lIvaIN   99 (504)
T TIGR03238        88 NQSNKPLIVGIN   99 (504)
T ss_pred             hcCCCCEEEEEe
Confidence            555443344433

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=90.69  E-value=0.54  Score=35.59  Aligned_cols=38  Identities=16%  Similarity=0.219  Sum_probs=26.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      |.-+.+.+++|+|||...+-.+.+.+.   .+.+++|+.-.
T Consensus        23 g~i~~i~G~~GsGKT~l~~~la~~~~~---~~~~v~yi~~e   60 (225)
T PRK09361         23 GTITQIYGPPGSGKTNICLQLAVEAAK---NGKKVIYIDTE   60 (225)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEECC
Confidence            678899999999999876655544332   24466666543

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=90.67  E-value=0.38  Score=37.27  Aligned_cols=34  Identities=21%  Similarity=0.330  Sum_probs=24.5

Q ss_pred             CCcHHHHHHHHHHH----cCC-cEEEEcCCCChHHHHHH
Q psy9277          54 KPSAIQQRSIKPIV----KGR-DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~----~g~-~v~v~aptGsGKTl~~l   87 (178)
                      .+++.+.+++..+.    .+. .+++.||+|+|||...-
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            46666677776553    233 68999999999997654

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.

>PRK09354 recA recombinase A; Provisional

Probab=90.63  E-value=0.74  Score=37.64  Aligned_cols=39  Identities=18%  Similarity=0.159  Sum_probs=26.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      |+-+.+.+|+|||||...+..+.+...   .+..++|+..-.
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~---~G~~~~yId~E~   98 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQK---AGGTAAFIDAEH   98 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---cCCcEEEECCcc
Confidence            567889999999999887766555432   234555554433

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=90.61  E-value=1  Score=37.99  Aligned_cols=47  Identities=15%  Similarity=0.191  Sum_probs=30.1

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ..+++.||+|+|||... .++.+.+.....+.+++|+.. ..+..+...
T Consensus       131 n~l~lyG~~G~GKTHLl-~ai~~~l~~~~~~~~v~yi~~-~~f~~~~~~  177 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLL-QSIGNYVVQNEPDLRVMYITS-EKFLNDLVD  177 (440)
T ss_pred             CeEEEEcCCCCcHHHHH-HHHHHHHHHhCCCCeEEEEEH-HHHHHHHHH
Confidence            36999999999999664 355555554334456777654 445554443

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=90.41  E-value=0.22  Score=36.45  Aligned_cols=16  Identities=31%  Similarity=0.449  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      ++++.+|||+|||...
T Consensus         5 ~~ll~GpsGvGKT~la   20 (171)
T PF07724_consen    5 NFLLAGPSGVGKTELA   20 (171)
T ss_dssp             EEEEESSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            6899999999999654

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 ATPase AAA-2 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 []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=90.35  E-value=0.23  Score=36.54  Aligned_cols=19  Identities=26%  Similarity=0.487  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |..+++.||+|+|||...-
T Consensus         2 g~~i~l~G~sGsGKsTl~~   20 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSLLA   20 (186)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5678999999999997653

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=90.23  E-value=0.58  Score=34.26  Aligned_cols=18  Identities=28%  Similarity=0.471  Sum_probs=15.2

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      ++-++++||+|+||+...
T Consensus         2 ~r~ivl~Gpsg~GK~~l~   19 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLA   19 (183)
T ss_dssp             SSEEEEESSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            567899999999999554

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 ....

>KOG0738|consensus

Probab=90.18  E-value=0.25  Score=40.90  Aligned_cols=57  Identities=23%  Similarity=0.355  Sum_probs=35.7

Q ss_pred             cccccccCCCCHHHHHHHHhC------CCC-----CCcH---HHHH------HHHHHHcC-----CcEEEEcCCCChHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAY------GFE-----KPSA---IQQR------SIKPIVKG-----RDVIAQAQSGTGKTA   84 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~------g~~-----~~~~---~Q~~------~i~~i~~g-----~~v~v~aptGsGKTl   84 (178)
                      ..+.|+..+....+.++|+.-      +++     .+..   .=.+      .+|.+++|     +.+++.+|+|+|||+
T Consensus       181 ~~~~f~~~~~d~~Lve~lerdIl~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTl  260 (491)
T KOG0738|consen  181 EDKKFDSLGYDADLVEALERDILQRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTL  260 (491)
T ss_pred             ccCCCCcccchHHHHHHHHHHHhccCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHH
Confidence            356688888888888888532      110     0100   1111      12455555     699999999999997


Q ss_pred             HH
Q psy9277          85 TF   86 (178)
Q Consensus        85 ~~   86 (178)
                      .+
T Consensus       261 LA  262 (491)
T KOG0738|consen  261 LA  262 (491)
T ss_pred             HH
Confidence            65

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=90.10  E-value=0.22  Score=38.81  Aligned_cols=20  Identities=35%  Similarity=0.414  Sum_probs=16.7

Q ss_pred             CCcEEEEcCCCChHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll   88 (178)
                      ..++++.||+|+|||..+-.
T Consensus        42 ~~~vll~GppGtGKTtlA~~   61 (261)
T TIGR02881        42 VLHMIFKGNPGTGKTTVARI   61 (261)
T ss_pred             cceEEEEcCCCCCHHHHHHH
Confidence            35899999999999987644

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=90.09  E-value=0.24  Score=40.56  Aligned_cols=27  Identities=37%  Similarity=0.581  Sum_probs=21.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      .|+.+++.+|+|+|||..+ +.+.+.|.
T Consensus        64 aGrgiLi~GppgTGKTAlA-~gIa~eLG   90 (450)
T COG1224          64 AGRGILIVGPPGTGKTALA-MGIARELG   90 (450)
T ss_pred             cccEEEEECCCCCcHHHHH-HHHHHHhC
Confidence            3789999999999999665 45555554

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=90.05  E-value=1.9  Score=29.99  Aligned_cols=50  Identities=14%  Similarity=0.086  Sum_probs=28.8

Q ss_pred             EEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEE-----EcCcHHHHHHHHHHHHHh
Q psy9277          73 IAQAQSGTGKTATFSISILQSLDTQ-LRETQVLC-----LSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        73 ~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~li-----l~Pt~~L~~q~~~~~~~~  123 (178)
                      ...|+||+|||.+.-+-+-+ +..+ .+...+..     =.|....+.+..+.++..
T Consensus        57 SfHG~tGtGKn~v~~liA~~-ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~  112 (127)
T PF06309_consen   57 SFHGWTGTGKNFVSRLIAEH-LYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSW  112 (127)
T ss_pred             EeecCCCCcHHHHHHHHHHH-HHhcccCCCceeeecccccCCCchHHHHHHHHHHHH
Confidence            47899999999887654333 3332 23333332     236666666655555544

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

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=90.00  E-value=0.88  Score=39.02  Aligned_cols=53  Identities=23%  Similarity=0.255  Sum_probs=35.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|..+++.+++|+|||...+-.+...+.   .+-.++|++- .+-..++.+.+..++
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~~~---~g~~~~yis~-e~~~~~i~~~~~~~g  324 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAACR---RGERCLLFAF-EESRAQLIRNARSWG  324 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh---CCCcEEEEEe-cCCHHHHHHHHHHcC
Confidence            3678899999999999876555544332   3457777754 344666666666554

>KOG0745|consensus

Probab=89.86  E-value=0.22  Score=41.83  Aligned_cols=37  Identities=24%  Similarity=0.343  Sum_probs=23.5

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      -|+++.+|||||||+...  .|.++   .+-|.+|.=|.|-.
T Consensus       227 SNvLllGPtGsGKTllaq--TLAr~---ldVPfaIcDcTtLT  263 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQ--TLARV---LDVPFAICDCTTLT  263 (564)
T ss_pred             ccEEEECCCCCchhHHHH--HHHHH---hCCCeEEecccchh
Confidence            489999999999997653  22222   24455555554433

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=89.85  E-value=0.63  Score=42.05  Aligned_cols=40  Identities=23%  Similarity=0.333  Sum_probs=26.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      +.+++|.|+||+|||...-.-+.+.+ .  .+.+++|+=|..+
T Consensus       430 n~n~~I~G~tGsGKS~~~~~l~~~~~-~--~g~~v~iiD~~~s  469 (797)
T TIGR02746       430 NYNIAVVGGSGAGKSFFMQELIVDNL-S--RGGKVWVIDVGRS  469 (797)
T ss_pred             ccceEEEcCCCCCHHHHHHHHHHHHH-h--CCCEEEEEeCCCC
Confidence            35899999999999987654333332 2  3456777666543

The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=89.81  E-value=1.5  Score=40.54  Aligned_cols=58  Identities=16%  Similarity=0.027  Sum_probs=45.7

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ++.+++|++|+++-+..+++.++++..  +.++..++|+++..++...+.    ...+|+|+|-
T Consensus       659 ~g~qv~if~n~i~~~e~l~~~L~~~~p--~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~  720 (926)
T TIGR00580       659 RGGQVFYVHNRIESIEKLATQLRELVP--EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT  720 (926)
T ss_pred             cCCeEEEEECCcHHHHHHHHHHHHhCC--CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC
Confidence            456899999999999999888887643  578999999998776655443    3579999993

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.

>KOG0652|consensus

Probab=89.80  E-value=0.85  Score=36.04  Aligned_cols=63  Identities=17%  Similarity=0.174  Sum_probs=36.1

Q ss_pred             cccccccccccCC-CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHH
Q psy9277          26 EDVEVVSTFDNMG-LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSIS   89 (178)
Q Consensus        26 ~~~~~~~~f~~~~-l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~   89 (178)
                      -+..|..+|++.| |...|.+..... ...++.-.+--=--+.--+.++..+|+|+|||+.+-.-
T Consensus       162 vDekPtE~YsDiGGldkQIqELvEAi-VLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAc  225 (424)
T KOG0652|consen  162 VDEKPTEQYSDIGGLDKQIQELVEAI-VLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARAC  225 (424)
T ss_pred             eccCCcccccccccHHHHHHHHHHHh-ccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHH
Confidence            3556777888885 666555544332 11222211110011223579999999999999876443

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=89.78  E-value=1.1  Score=40.30  Aligned_cols=56  Identities=16%  Similarity=0.141  Sum_probs=44.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc--------CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD--------YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--------~~~~IlV~TP  158 (178)
                      .+.++++|+.|..-|..+|+.++....    .+.++++-....++.+...        +++.|+|+|.
T Consensus       439 ~~~kvlvI~NTV~~Aie~Y~~Lk~~~~----~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQ  502 (733)
T COG1203         439 EGKKVLVIVNTVDRAIELYEKLKEKGP----KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ  502 (733)
T ss_pred             cCCcEEEEEecHHHHHHHHHHHHhcCC----CEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEee
Confidence            457899999999999999999987744    7788888877665555444        4678999995

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

Probab=89.76  E-value=0.41  Score=37.83  Aligned_cols=18  Identities=33%  Similarity=0.506  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll   88 (178)
                      =+++.++|||||+.....
T Consensus       129 LviiVGaTGSGKSTtmAa  146 (375)
T COG5008         129 LVIIVGATGSGKSTTMAA  146 (375)
T ss_pred             eEEEECCCCCCchhhHHH
Confidence            478899999999977543

>TIGR03689 pup_AAA proteasome ATPase

Probab=89.75  E-value=0.24  Score=42.50  Aligned_cols=54  Identities=20%  Similarity=0.266  Sum_probs=29.7

Q ss_pred             cccccccCC-CCHHHHHHHHh--CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          30 VVSTFDNMG-LREDLLRGIYA--YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        30 ~~~~f~~~~-l~~~i~~~l~~--~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+|++++ +++.+.+....  ..+..+..+...-   +...+++++.||+|+|||+..
T Consensus       177 p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~g---l~~p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       177 PDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYD---LKPPKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhcc---CCCCcceEEECCCCCcHHHHH
Confidence            456788886 55433332221  1122222221111   223578999999999999764

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]

Probab=89.74  E-value=0.6  Score=42.36  Aligned_cols=24  Identities=29%  Similarity=0.461  Sum_probs=18.2

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      +.+|+||||+|||...-+-+.+..
T Consensus       438 hT~I~G~tGaGKTvLl~~llaq~~  461 (796)
T COG3451         438 HTLIIGPTGAGKTVLLSFLLAQAL  461 (796)
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHH
Confidence            899999999999976554444433

>PRK06893 DNA replication initiation factor; Validated

Probab=89.70  E-value=0.74  Score=35.17  Aligned_cols=37  Identities=5%  Similarity=0.045  Sum_probs=23.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..+++.||+|+|||.... .+.+.+..  ++..++|+.-
T Consensus        39 ~~~l~l~G~~G~GKThL~~-ai~~~~~~--~~~~~~y~~~   75 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLK-AVSNHYLL--NQRTAIYIPL   75 (229)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHH--cCCCeEEeeH
Confidence            3457999999999996543 34444333  2345666554

>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=89.70  E-value=0.26  Score=40.51  Aligned_cols=37  Identities=30%  Similarity=0.382  Sum_probs=23.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      +|+.+++.+|+|+|||..+ +.+.+.|..  +-|++.+..
T Consensus        49 aGr~iLiaGppGtGKTAlA-~~ia~eLG~--~~PF~~isg   85 (398)
T PF06068_consen   49 AGRAILIAGPPGTGKTALA-MAIAKELGE--DVPFVSISG   85 (398)
T ss_dssp             TT-EEEEEE-TTSSHHHHH-HHHHHHCTT--TS-EEEEEG
T ss_pred             cCcEEEEeCCCCCCchHHH-HHHHHHhCC--CCCeeEccc
Confidence            3789999999999999665 455555543  345555544

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=89.69  E-value=1.1  Score=36.45  Aligned_cols=24  Identities=33%  Similarity=0.540  Sum_probs=17.9

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .++++.||+|+|||.+.- .++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~~-~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVTK-YVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHHH-HHHHHH
Confidence            689999999999997643 344433

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.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=89.69  E-value=0.6  Score=32.54  Aligned_cols=22  Identities=23%  Similarity=0.280  Sum_probs=17.0

Q ss_pred             HHHcCCcEEEEcCCCChHHHHH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ....+..+++.|++|+||+.++
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            3344789999999999999764

>KOG2340|consensus

Probab=89.64  E-value=1.7  Score=37.57  Aligned_cols=73  Identities=23%  Similarity=0.348  Sum_probs=54.5

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCC-CChH--HHHHHHHHHHHhhhcC----------------------------CCc
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQS-GTGK--TATFSISILQSLDTQL----------------------------RET  101 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~apt-GsGK--Tl~~ll~il~~l~~~~----------------------------~~~  101 (178)
                      ..+|+.|.+.+....+-+|++..-.| +.|+  +-.|.+=+++++.+.+                            ..+
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            46899999999999988888765443 3455  4566777777663210                            137


Q ss_pred             eEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277         102 QVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus       102 ~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      ++|||||+|+-|-.+.+.+..++.
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~  318 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLS  318 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhc
Confidence            899999999999999999988743

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=89.58  E-value=0.83  Score=34.60  Aligned_cols=19  Identities=16%  Similarity=0.319  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..++++|++|+|||....
T Consensus        42 ~~~~~l~G~~G~GKT~La~   60 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQ   60 (227)
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            5689999999999996543

>PRK08118 topology modulation protein; Reviewed

Probab=89.53  E-value=0.28  Score=35.60  Aligned_cols=17  Identities=24%  Similarity=0.485  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +.++|+||+|||||...
T Consensus         2 ~rI~I~G~~GsGKSTla   18 (167)
T PRK08118          2 KKIILIGSGGSGKSTLA   18 (167)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            35899999999999654

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=89.50  E-value=0.43  Score=38.37  Aligned_cols=46  Identities=17%  Similarity=0.242  Sum_probs=26.9

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+|.|||||||+-..---+-..+. +...-.+++|+|++..+--...
T Consensus        90 ~~VYGPTG~GKSqLlRNLis~~lI-~P~PETVfFItP~~~mIpp~E~  135 (369)
T PF02456_consen   90 GVVYGPTGSGKSQLLRNLISCQLI-QPPPETVFFITPQKDMIPPQEI  135 (369)
T ss_pred             EEEECCCCCCHHHHHHHhhhcCcc-cCCCCceEEECCCCCCCCHHHH
Confidence            578999999998443211111111 1223478999998766544433

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=89.43  E-value=0.28  Score=41.90  Aligned_cols=56  Identities=18%  Similarity=0.193  Sum_probs=33.4

Q ss_pred             cccccccccCCCCHHHHHHHHhCC--CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYG--FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g--~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..+..+|+++.-.+.+.+.+.+.-  +..+..++..   .....+++++.||+|+|||...
T Consensus        48 ~~~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~---g~~~~~giLL~GppGtGKT~la  105 (495)
T TIGR01241        48 EKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKL---GAKIPKGVLLVGPPGTGKTLLA  105 (495)
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhc---CCCCCCcEEEECCCCCCHHHHH
Confidence            356778999876666665554321  1122222111   1122468999999999999765

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=89.40  E-value=0.28  Score=35.15  Aligned_cols=20  Identities=25%  Similarity=0.398  Sum_probs=17.1

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..++++|++|||||...-
T Consensus         3 ~~~~i~l~G~~GsGKstla~   22 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGR   22 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHH
Confidence            46789999999999997754

>PF05729 NACHT: NACHT domain

Probab=89.40  E-value=0.92  Score=31.91  Aligned_cols=25  Identities=20%  Similarity=0.372  Sum_probs=17.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      -++|.|++|+|||.... -++..+..
T Consensus         2 ~l~I~G~~G~GKStll~-~~~~~~~~   26 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLR-KLAQQLAE   26 (166)
T ss_pred             EEEEECCCCCChHHHHH-HHHHHHHh
Confidence            37899999999997643 44444443

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=89.33  E-value=1.8  Score=33.15  Aligned_cols=37  Identities=24%  Similarity=0.193  Sum_probs=24.7

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhh---------hcCCCceEEEEc
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLD---------TQLRETQVLCLS  107 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~---------~~~~~~~~lil~  107 (178)
                      -.++.||.|+|||...+--++....         ....+.+++|+.
T Consensus         3 ~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~   48 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLS   48 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEE
Confidence            4689999999999887655544221         112345788887

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>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=89.32  E-value=5.3  Score=28.72  Aligned_cols=100  Identities=16%  Similarity=0.182  Sum_probs=53.8

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhc-----------------CCCceEEEEcCcHH----HHHHHHHHHHHhccC--
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQ-----------------LRETQVLCLSPTRE----LAVQIQKVVLALGDF--  126 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~-----------------~~~~~~lil~Pt~~----L~~q~~~~~~~~~~~--  126 (178)
                      ...++.||.|+||+..+..-+-..+-..                 ...+...++.|...    .+.|+.+....+...  
T Consensus        20 ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~~~   99 (162)
T PF13177_consen   20 HALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLSPS   99 (162)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS-T
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHHHh
Confidence            3689999999999877554333222111                 22456788888754    455655444444322  


Q ss_pred             -CCceEEEEEcCccHHHHHH--H---hcC---CCcE-EEeC-hHHHHHHHHcCC
Q psy9277         127 -MNVQCHACIGGTNLSEDLR--K---LDY---GQHV-VSGT-PGRVFDMIRSSQ  169 (178)
Q Consensus       127 -~~~~~~~~~g~~~~~~~~~--~---~~~---~~~I-lV~T-P~~l~~~l~~~~  169 (178)
                       .+.++.++...........  .   +++   .+.+ ++++ |.+|+.-++++-
T Consensus       100 ~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~~il~TI~SRc  153 (162)
T PF13177_consen  100 EGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPSKILPTIRSRC  153 (162)
T ss_dssp             TSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GGGS-HHHHTTS
T ss_pred             cCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChHHChHHHHhhc
Confidence             2578888876655433222  1   222   2233 3333 666777666653

...

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=89.32  E-value=0.26  Score=37.75  Aligned_cols=20  Identities=35%  Similarity=0.429  Sum_probs=17.0

Q ss_pred             HHcCCcEEEEcCCCChHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTAT   85 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~   85 (178)
                      +..|.-+.+.+|+|||||..
T Consensus        28 i~~Ge~vaI~GpSGSGKSTL   47 (226)
T COG1136          28 IEAGEFVAIVGPSGSGKSTL   47 (226)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            44589999999999999954

>KOG0924|consensus

Probab=89.27  E-value=2.7  Score=37.50  Aligned_cols=70  Identities=20%  Similarity=0.228  Sum_probs=44.7

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHH-HHhccCCC
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVV-LALGDFMN  128 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~-~~~~~~~~  128 (178)
                      ....+.+.+..|-.+.-+++.+.||||||.-..-    .++........+|-|  |.|.-|..+++.+ .++.-.+|
T Consensus       357 vf~~R~~ll~~ir~n~vvvivgETGSGKTTQl~Q----yL~edGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG  429 (1042)
T KOG0924|consen  357 VFACRDQLLSVIRENQVVVIVGETGSGKTTQLAQ----YLYEDGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLG  429 (1042)
T ss_pred             hHHHHHHHHHHHhhCcEEEEEecCCCCchhhhHH----HHHhcccccCCeeeecCchHHHHHHHHHHHHHHhCCccc
Confidence            3556666777777788999999999999965432    233322222234433  8888888888766 45533333

>PLN02165 adenylate isopentenyltransferase

Probab=89.26  E-value=0.34  Score=39.32  Aligned_cols=20  Identities=20%  Similarity=0.273  Sum_probs=17.1

Q ss_pred             CCcEEEEcCCCChHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll   88 (178)
                      |.-+++.||||||||..+..
T Consensus        43 g~iivIiGPTGSGKStLA~~   62 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVD   62 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            66799999999999987654

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=89.24  E-value=3.7  Score=33.20  Aligned_cols=58  Identities=7%  Similarity=0.047  Sum_probs=42.7

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH-------Hhc-CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR-------KLD-YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~-------~~~-~~~~IlV~TP  158 (178)
                      .+.+++|+++|++-+..+++.+++...  +..+..++|+.+..++..       ... ....|+|+|.
T Consensus       221 ~~~~~lVf~~t~~~~~~~~~~L~~~~~--~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~  286 (358)
T TIGR01587       221 KGGKIAIIVNTVDRAQEFYQQLKENAP--EEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ  286 (358)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhhcC--CCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc
Confidence            456899999999999999999876532  346888899887655432       223 3468999995

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=89.22  E-value=0.61  Score=37.34  Aligned_cols=18  Identities=33%  Similarity=0.575  Sum_probs=15.5

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll   88 (178)
                      ++++.||+|+|||.....
T Consensus        38 ~lll~Gp~GtGKT~la~~   55 (337)
T PRK12402         38 HLLVQGPPGSGKTAAVRA   55 (337)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            799999999999977543

>KOG0060|consensus

Probab=89.20  E-value=0.27  Score=42.62  Aligned_cols=22  Identities=27%  Similarity=0.572  Sum_probs=18.3

Q ss_pred             HHHcCCcEEEEcCCCChHHHHH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      .+.+|++++|++|+|+|||-.+
T Consensus       457 ~V~~g~~LLItG~sG~GKtSLl  478 (659)
T KOG0060|consen  457 EVPSGQNLLITGPSGCGKTSLL  478 (659)
T ss_pred             EecCCCeEEEECCCCCchhHHH
Confidence            3556999999999999999543

>PRK10689 transcription-repair coupling factor; Provisional

Probab=89.18  E-value=1.9  Score=40.89  Aligned_cols=57  Identities=19%  Similarity=0.058  Sum_probs=44.8

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ++.+++|++|+++-+..+++.+.+...  +.++..++|+++..++...+.    ...+|+|+|
T Consensus       808 r~gqv~vf~n~i~~ie~la~~L~~~~p--~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaT  868 (1147)
T PRK10689        808 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCT  868 (1147)
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCC--CCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEC
Confidence            356899999999999999888877643  467888999998876655443    357999999

>PRK12678 transcription termination factor Rho; Provisional

Probab=89.18  E-value=1.5  Score=38.48  Aligned_cols=67  Identities=19%  Similarity=0.323  Sum_probs=39.7

Q ss_pred             cccccccccccccCC-CCHHHHHHHHhCCCCCCcHHHHHHHHHHH---cCCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          24 TSEDVEVVSTFDNMG-LREDLLRGIYAYGFEKPSAIQQRSIKPIV---KGRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        24 ~~~~~~~~~~f~~~~-l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~---~g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      ..+.......|+++- +++.-.-.|..    .+...-..+|..++   .|.-.+|.+|.|+|||... ..|...+.
T Consensus       371 ~~e~~~~r~~F~~Ltp~~P~~R~~le~----e~~~~giRvIDll~PIGkGQR~LIvgpp~aGKTtLL-~~IAn~i~  441 (672)
T PRK12678        371 SPEEAKKRPEFGKLTPLYPNERLRLET----EPKKLTTRVIDLIMPIGKGQRGLIVSPPKAGKTTIL-QNIANAIT  441 (672)
T ss_pred             ChHHhccCCCcccCCCCChHHhccccc----CcccccceeeeeecccccCCEeEEeCCCCCCHHHHH-HHHHHHHh
Confidence            334444556676653 44432222220    35555556665544   5899999999999999775 34555443

>KOG0332|consensus

Probab=89.18  E-value=2.2  Score=35.29  Aligned_cols=54  Identities=17%  Similarity=0.121  Sum_probs=44.1

Q ss_pred             ceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc---C-CCcEEEeCh
Q psy9277         101 TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTP  158 (178)
Q Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~IlV~TP  158 (178)
                      .+++|.|.|++-|..++..+...    |..+.+++|+....++...+.   . ...|+|+|-
T Consensus       331 gqsiIFc~tk~ta~~l~~~m~~~----Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTn  388 (477)
T KOG0332|consen  331 GQSIIFCHTKATAMWLYEEMRAE----GHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTN  388 (477)
T ss_pred             hheEEEEeehhhHHHHHHHHHhc----CceeEEeeccchhHHHHHHHHHHhcCcceEEEEec
Confidence            57899999999999999999766    788999999988777655443   2 358999984

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=89.14  E-value=1  Score=38.69  Aligned_cols=54  Identities=22%  Similarity=0.310  Sum_probs=35.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      .|.-+++.|++|+|||...+--+.+.+..  .+..++|++ +.+-..++.+.+..++
T Consensus        30 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~--~ge~~lyis-~ee~~~~i~~~~~~~g   83 (509)
T PRK09302         30 KGRPTLVSGTAGTGKTLFALQFLVNGIKR--FDEPGVFVT-FEESPEDIIRNVASFG   83 (509)
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHh--cCCCEEEEE-ccCCHHHHHHHHHHcC
Confidence            47889999999999998766544444432  144666664 4455556666665554

>PTZ00035 Rad51 protein; Provisional

Probab=89.06  E-value=2.2  Score=34.76  Aligned_cols=38  Identities=18%  Similarity=0.007  Sum_probs=23.3

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhh---hcCCCceEEEEc
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLD---TQLRETQVLCLS  107 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~---~~~~~~~~lil~  107 (178)
                      .-+.+.|++|+|||......+.....   ....+..++|+.
T Consensus       119 ~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyId  159 (337)
T PTZ00035        119 SITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYID  159 (337)
T ss_pred             eEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEE
Confidence            45789999999999877544433211   111234676765

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=89.02  E-value=0.54  Score=38.07  Aligned_cols=24  Identities=29%  Similarity=0.428  Sum_probs=19.6

Q ss_pred             HHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          64 KPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        64 ~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      -.+..++++++.+++|+|||....
T Consensus        59 ~~l~~~~~ilL~G~pGtGKTtla~   82 (327)
T TIGR01650        59 AGFAYDRRVMVQGYHGTGKSTHIE   82 (327)
T ss_pred             HHHhcCCcEEEEeCCCChHHHHHH
Confidence            345568999999999999997754

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=89.00  E-value=0.29  Score=37.39  Aligned_cols=20  Identities=35%  Similarity=0.559  Sum_probs=16.7

Q ss_pred             HHcCCcEEEEcCCCChHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTAT   85 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~   85 (178)
                      +..|.-+.+++|+|||||..
T Consensus        25 v~~Gevv~iiGpSGSGKSTl   44 (240)
T COG1126          25 VEKGEVVVIIGPSGSGKSTL   44 (240)
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34588899999999999954

>KOG0989|consensus

Probab=88.95  E-value=0.72  Score=37.04  Aligned_cols=25  Identities=24%  Similarity=0.072  Sum_probs=20.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQS   93 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~   93 (178)
                      .-+.+..||+|+|||-+.+...-+.
T Consensus        57 lp~~LFyGPpGTGKTStalafar~L   81 (346)
T KOG0989|consen   57 LPHYLFYGPPGTGKTSTALAFARAL   81 (346)
T ss_pred             CceEEeeCCCCCcHhHHHHHHHHHh
Confidence            4589999999999998887655443

>KOG1807|consensus

Probab=88.89  E-value=2.1  Score=38.55  Aligned_cols=80  Identities=16%  Similarity=0.074  Sum_probs=56.8

Q ss_pred             HHHHHHhC--CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCcHHHHHHHH
Q psy9277          43 LLRGIYAY--GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        43 i~~~l~~~--g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt~~L~~q~~  117 (178)
                      +++++...  |...+..-|..|+...+..+--++++|+|+|||++-+..+-..+..+   ....-.+++|-|..-+.|..
T Consensus       365 ~~n~lePp~~g~~ildsSq~~A~qs~ltyelsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhavdq~l  444 (1025)
T KOG1807|consen  365 IVNALEPPGPGLVILDSSQQFAKQSKLTYELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAVDQYL  444 (1025)
T ss_pred             hhhhcCCCCCCceeecHHHHHHHHHHhhhhhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHHHHHH
Confidence            44444322  33456678999999999999999999999999999876554444332   12235788898988888877


Q ss_pred             HHHHH
Q psy9277         118 KVVLA  122 (178)
Q Consensus       118 ~~~~~  122 (178)
                      ..+..
T Consensus       445 igiy~  449 (1025)
T KOG1807|consen  445 IGIYY  449 (1025)
T ss_pred             HHHHh
Confidence            76643

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=88.84  E-value=0.98  Score=37.11  Aligned_cols=37  Identities=22%  Similarity=0.351  Sum_probs=23.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      ..++++.||+|+|||.+.- .++..+.....+...+++
T Consensus        55 ~~~~lI~G~~GtGKT~l~~-~v~~~l~~~~~~~~~v~i   91 (394)
T PRK00411         55 PLNVLIYGPPGTGKTTTVK-KVFEELEEIAVKVVYVYI   91 (394)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHhcCCcEEEEE
Confidence            3689999999999997743 334444332223444554

>PTZ00301 uridine kinase; Provisional

Probab=88.73  E-value=1.1  Score=33.97  Aligned_cols=15  Identities=27%  Similarity=0.377  Sum_probs=13.0

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      +.|.|++|||||...
T Consensus         6 IgIaG~SgSGKTTla   20 (210)
T PTZ00301          6 IGISGASGSGKSSLS   20 (210)
T ss_pred             EEEECCCcCCHHHHH
Confidence            578899999999776

>PRK07261 topology modulation protein; Provisional

Probab=88.71  E-value=0.36  Score=35.18  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .++++|++|||||..+-
T Consensus         2 ri~i~G~~GsGKSTla~   18 (171)
T PRK07261          2 KIAIIGYSGSGKSTLAR   18 (171)
T ss_pred             EEEEEcCCCCCHHHHHH
Confidence            47899999999997764

>PRK14530 adenylate kinase; Provisional

Probab=88.68  E-value=0.35  Score=36.44  Aligned_cols=20  Identities=20%  Similarity=0.295  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+++.||+|||||...-
T Consensus         2 ~~~~I~i~G~pGsGKsT~~~   21 (215)
T PRK14530          2 SQPRILLLGAPGAGKGTQSS   21 (215)
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            46689999999999997653

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=88.66  E-value=1.5  Score=31.85  Aligned_cols=41  Identities=12%  Similarity=0.135  Sum_probs=25.4

Q ss_pred             HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          67 VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      .....|++.|++|+||++++-  .++.......++.+.+=|..
T Consensus        20 ~~~~pVlI~GE~GtGK~~lA~--~IH~~s~r~~~pfi~vnc~~   60 (168)
T PF00158_consen   20 SSDLPVLITGETGTGKELLAR--AIHNNSPRKNGPFISVNCAA   60 (168)
T ss_dssp             TSTS-EEEECSTTSSHHHHHH--HHHHCSTTTTS-EEEEETTT
T ss_pred             CCCCCEEEEcCCCCcHHHHHH--HHHHhhhcccCCeEEEehhh
Confidence            346899999999999997653  33433333345666665554

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=88.65  E-value=0.83  Score=38.37  Aligned_cols=18  Identities=22%  Similarity=0.479  Sum_probs=15.9

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +++++.+|||+|||..+-
T Consensus        48 ~~ILLiGppG~GKT~lAr   65 (441)
T TIGR00390        48 KNILMIGPTGVGKTEIAR   65 (441)
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            699999999999997653

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>KOG0391|consensus

Probab=88.59  E-value=4.1  Score=38.70  Aligned_cols=106  Identities=18%  Similarity=0.146  Sum_probs=69.8

Q ss_pred             CcHHHHHHHHHHH---c-CCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          55 PSAIQQRSIKPIV---K-GRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        55 ~~~~Q~~~i~~i~---~-g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      ++.+|..-+..+.   + +-|-++.-.-|-|||.- .+.++.++..+ .+.+=-|||+||-.+.+. ...+++++-  ++
T Consensus       616 LReYQkiGLdWLatLYeknlNGILADEmGLGKTIQ-tISllAhLACeegnWGPHLIVVpTsviLnW-EMElKRwcP--gl  691 (1958)
T KOG0391|consen  616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQ-TISLLAHLACEEGNWGPHLIVVPTSVILNW-EMELKRWCP--GL  691 (1958)
T ss_pred             HHHHHHhhHHHHHHHHHhcccceehhhhcccchhH-HHHHHHHHHhcccCCCCceEEeechhhhhh-hHHHhhhCC--cc
Confidence            5667777665433   2 56888888999999965 34556666543 333456899999776553 334677754  78


Q ss_pred             eEEEEEcCccHHHHHHH-hc--CCCcEEEeChHHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRK-LD--YGQHVVSGTPGRVFDM  164 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~-~~--~~~~IlV~TP~~l~~~  164 (178)
                      ++..++|........+. +.  +..||+|+....+..-
T Consensus       692 KILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd  729 (1958)
T KOG0391|consen  692 KILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQD  729 (1958)
T ss_pred             eEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhH
Confidence            88999988755433222 22  3469999988766443

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=88.59  E-value=0.6  Score=37.66  Aligned_cols=27  Identities=22%  Similarity=0.412  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          60 QRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        60 ~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..++-.++.|..+++.+|+|+|||...
T Consensus        34 ~~~l~a~~~~~~vll~G~PG~gKT~la   60 (329)
T COG0714          34 ELALLALLAGGHVLLEGPPGVGKTLLA   60 (329)
T ss_pred             HHHHHHHHcCCCEEEECCCCccHHHHH
Confidence            334456677999999999999999765

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=88.58  E-value=0.4  Score=34.87  Aligned_cols=19  Identities=32%  Similarity=0.459  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |+-++++|++|||||...-
T Consensus         2 ~~~i~l~G~~gsGKst~a~   20 (175)
T cd00227           2 GRIIILNGGSSAGKSSIAR   20 (175)
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            5679999999999997764

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=88.43  E-value=4.1  Score=34.03  Aligned_cols=63  Identities=14%  Similarity=0.048  Sum_probs=37.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHH---HHHHHHHhccCCCceEEEEEcCcc
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ---IQKVVLALGDFMNVQCHACIGGTN  139 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q---~~~~~~~~~~~~~~~~~~~~g~~~  139 (178)
                      .+.++-||+|+|||..+-+-.-.      -+....-+..+.+=+.+   +.+..++.... |-+++++.+...
T Consensus        49 ~SmIl~GPPG~GKTTlA~liA~~------~~~~f~~~sAv~~gvkdlr~i~e~a~~~~~~-gr~tiLflDEIH  114 (436)
T COG2256          49 HSMILWGPPGTGKTTLARLIAGT------TNAAFEALSAVTSGVKDLREIIEEARKNRLL-GRRTILFLDEIH  114 (436)
T ss_pred             ceeEEECCCCCCHHHHHHHHHHh------hCCceEEeccccccHHHHHHHHHHHHHHHhc-CCceEEEEehhh
Confidence            48999999999999776442211      22234445555444444   44444444332 677777776653

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.38  E-value=9.3  Score=32.96  Aligned_cols=18  Identities=28%  Similarity=0.403  Sum_probs=15.1

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll   88 (178)
                      -++++||+|+|||.+...
T Consensus        38 a~Lf~GppGtGKTTlA~~   55 (504)
T PRK14963         38 AYLFSGPRGVGKTTTARL   55 (504)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            359999999999988653

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=88.37  E-value=3.2  Score=32.50  Aligned_cols=30  Identities=30%  Similarity=0.483  Sum_probs=21.6

Q ss_pred             HHHcCC-cEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          65 PIVKGR-DVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        65 ~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      .+..|+ -+.++++.|||||..-- .++..+.
T Consensus        46 ~i~d~qg~~~vtGevGsGKTv~~R-al~~s~~   76 (269)
T COG3267          46 AIADGQGILAVTGEVGSGKTVLRR-ALLASLN   76 (269)
T ss_pred             HHhcCCceEEEEecCCCchhHHHH-HHHHhcC
Confidence            344455 78999999999998876 4554443

>TIGR00767 rho transcription termination factor Rho

Probab=88.31  E-value=4.8  Score=33.69  Aligned_cols=29  Identities=31%  Similarity=0.390  Sum_probs=20.7

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      +-.|+.+++.||+|+|||.... .+...+.
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~~-~i~~~I~  193 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLLQ-KIAQAIT  193 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHHH-HHHHhhc
Confidence            3358899999999999997543 3444443

Members of this family differ in the specificity of RNA binding.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=88.23  E-value=8.8  Score=30.92  Aligned_cols=39  Identities=18%  Similarity=0.281  Sum_probs=25.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhc-------------CCCceEEEEcCc
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQ-------------LRETQVLCLSPT  109 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~-------------~~~~~~lil~Pt  109 (178)
                      ...+++||.|+||+..+.. +...+...             ...|-..++.|+
T Consensus        27 ha~Lf~G~~G~Gk~~~A~~-~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~   78 (314)
T PRK07399         27 PAYLFAGPEGVGRKLAALC-FIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPT   78 (314)
T ss_pred             ceEEEECCCCCCHHHHHHH-HHHHHcCCCCCCCcHhcccccCCCCCEEEEecc
Confidence            4789999999999966532 33333221             233566888885

>PRK00300 gmk guanylate kinase; Provisional

Probab=88.19  E-value=0.41  Score=35.55  Aligned_cols=19  Identities=26%  Similarity=0.504  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|+-+++.||+|||||...
T Consensus         4 ~g~~i~i~G~sGsGKstl~   22 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLV   22 (205)
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999643

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=88.18  E-value=0.41  Score=34.80  Aligned_cols=18  Identities=28%  Similarity=0.427  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +-+++.||+|||||...-
T Consensus         2 ~~~~i~G~sGsGKttl~~   19 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLD   19 (179)
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            457899999999998764

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=88.14  E-value=1.8  Score=35.73  Aligned_cols=25  Identities=36%  Similarity=0.672  Sum_probs=18.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      .|+++.|+||+|||...-. ++..+.
T Consensus        43 ~n~~iyG~~GTGKT~~~~~-v~~~l~   67 (366)
T COG1474          43 SNIIIYGPTGTGKTATVKF-VMEELE   67 (366)
T ss_pred             ccEEEECCCCCCHhHHHHH-HHHHHH
Confidence            4799999999999977543 334343

>KOG2373|consensus

Probab=88.12  E-value=0.64  Score=38.11  Aligned_cols=89  Identities=16%  Similarity=0.133  Sum_probs=46.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH------------HHhc---cCCCceEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV------------LALG---DFMNVQCHA  133 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~------------~~~~---~~~~~~~~~  133 (178)
                      |.=.++.+|||||||....=..+......-+...+=+=.|.+-|+.-+...+            +.+.   +.+..-...
T Consensus       273 GElTvlTGpTGsGKTTFlsEYsLDL~~QGVnTLwgSFEi~n~rla~~mL~Qyagyrl~drl~~y~HWadrFErlplyfmt  352 (514)
T KOG2373|consen  273 GELTVLTGPTGSGKTTFLSEYSLDLFTQGVNTLWGSFEIPNKRLAHWMLVQYAGYRLLDRLNSYKHWADRFERLPLYFMT  352 (514)
T ss_pred             CceEEEecCCCCCceeEehHhhHHHHhhhhhheeeeeecchHHHHHHHHHHHccCchHhhhhhhhHHHHHHhccchHhhh
Confidence            5678999999999997644444443332222223334446666665443322            1111   222333445


Q ss_pred             EEcCccHHHHHHHhc------CCCcEEEeC
Q psy9277         134 CIGGTNLSEDLRKLD------YGQHVVSGT  157 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~------~~~~IlV~T  157 (178)
                      +.|....+..+..+.      +-+||||-.
T Consensus       353 fhgqq~~~~vi~~i~ha~yV~di~HViIDN  382 (514)
T KOG2373|consen  353 FHGQQFMEKVINEIAHAIYVEDIQHVIIDN  382 (514)
T ss_pred             hcccchHHHHHHHHHHHHHHHhhhhhhhhh
Confidence            566666654444332      345777644

>KOG0392|consensus

Probab=88.08  E-value=3.4  Score=39.16  Aligned_cols=105  Identities=15%  Similarity=0.118  Sum_probs=68.4

Q ss_pred             CcHHHHHHHHHH--Hc--CCcEEEEcCCCChHHHHHHHHHHHHhhhcCC-----Cce-EEEEcCcHHHHHHHHHHHHHhc
Q psy9277          55 PSAIQQRSIKPI--VK--GRDVIAQAQSGTGKTATFSISILQSLDTQLR-----ETQ-VLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        55 ~~~~Q~~~i~~i--~~--g~~v~v~aptGsGKTl~~ll~il~~l~~~~~-----~~~-~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      ++.+|.+-+.-+  ++  +-+-++|-.-|-|||+-.+--+.......+.     ... .+||||. .|+-.....+.+|+
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            567888866543  33  5688999999999997654333322222100     123 7999996 57777777777776


Q ss_pred             cCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHH
Q psy9277         125 DFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       125 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~  162 (178)
                      ..  +++..++|........+.--+..+|+|+....+-
T Consensus      1055 pf--L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~R 1090 (1549)
T KOG0392|consen 1055 PF--LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVR 1090 (1549)
T ss_pred             ch--hhhhhhcCChHHHHHHHhhccccceEEeeHHHHH
Confidence            55  5667777776655444443446799999987663

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=88.08  E-value=0.4  Score=38.51  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +=++++||||||||....
T Consensus         5 ~~i~i~GptgsGKt~la~   22 (307)
T PRK00091          5 KVIVIVGPTASGKTALAI   22 (307)
T ss_pred             eEEEEECCCCcCHHHHHH
Confidence            347999999999997765

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=87.97  E-value=0.45  Score=42.72  Aligned_cols=54  Identities=19%  Similarity=0.270  Sum_probs=31.2

Q ss_pred             ccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          31 VSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+|++++-.+.+.+.|++.   .+..+..++..   .+...+.+++.||+|+|||+..-
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~---g~~~~~giLL~GppGtGKT~lak  505 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKM---GIRPPKGVLLFGPPGTGKTLLAK  505 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhc---CCCCCceEEEECCCCCCHHHHHH
Confidence            45677777666666666442   11111111110   11224679999999999997653

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=87.95  E-value=0.33  Score=34.68  Aligned_cols=15  Identities=20%  Similarity=0.406  Sum_probs=12.5

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      ++++||+|||||..+
T Consensus         1 i~l~G~~GsGKSTla   15 (163)
T TIGR01313         1 FVLMGVAGSGKSTIA   15 (163)
T ss_pred             CEEECCCCCCHHHHH
Confidence            468999999999654

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=87.92  E-value=0.41  Score=40.03  Aligned_cols=19  Identities=21%  Similarity=0.375  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||||+|||..+-
T Consensus       108 ~~~iLl~Gp~GtGKT~lAr  126 (412)
T PRK05342        108 KSNILLIGPTGSGKTLLAQ  126 (412)
T ss_pred             CceEEEEcCCCCCHHHHHH
Confidence            3679999999999998764

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=87.88  E-value=0.59  Score=32.73  Aligned_cols=15  Identities=27%  Similarity=0.598  Sum_probs=12.6

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      +++.||+|||||...
T Consensus         2 i~i~GpsGsGKstl~   16 (137)
T cd00071           2 IVLSGPSGVGKSTLL   16 (137)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999643

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>KOG1533|consensus

Probab=87.84  E-value=0.64  Score=36.01  Aligned_cols=24  Identities=25%  Similarity=0.419  Sum_probs=17.0

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      ..+|+||+||||| .|...+.+.+.
T Consensus         4 gqvVIGPPgSGKs-TYc~g~~~fls   27 (290)
T KOG1533|consen    4 GQVVIGPPGSGKS-TYCNGMSQFLS   27 (290)
T ss_pred             ceEEEcCCCCCcc-chhhhHHHHHH
Confidence            3589999999998 45555555443

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

Probab=87.82  E-value=8.5  Score=36.29  Aligned_cols=97  Identities=18%  Similarity=0.124  Sum_probs=68.0

Q ss_pred             HHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHh------------------------------hhcCCCceEEEEcC
Q psy9277          59 QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSL------------------------------DTQLRETQVLCLSP  108 (178)
Q Consensus        59 Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l------------------------------~~~~~~~~~lil~P  108 (178)
                      |++-+..+....||+--+.|--=+|+--.+.=+..+                              ..-.+++++.||.|
T Consensus       732 ~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~N  811 (1139)
T COG1197         732 HKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLRGGQVFYVHN  811 (1139)
T ss_pred             HHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHHhcCCEEEEEec
Confidence            566666666666666666666666644332222211                              11235789999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277         109 TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus       109 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ..+-..++...++.+..  +.++++.+|.+...+....+.    ...||+|||
T Consensus       812 rV~~Ie~~~~~L~~LVP--EarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~T  862 (1139)
T COG1197         812 RVESIEKKAERLRELVP--EARIAVAHGQMRERELEEVMLDFYNGEYDVLVCT  862 (1139)
T ss_pred             chhhHHHHHHHHHHhCC--ceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEe
Confidence            99999999999998865  578999999998876655443    468999999

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=87.72  E-value=0.86  Score=36.49  Aligned_cols=47  Identities=17%  Similarity=0.196  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC---CcEEEEcCCCChHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKG---RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g---~~v~v~aptGsGKTl~~   86 (178)
                      +...+.+.|.+.++..+.+- ...|..+...   .-+++.|++|+|||..+
T Consensus        60 l~~~V~~~L~~~~~~~~~~~-y~~~~~i~~~~~p~iIlI~G~sgsGKStlA  109 (301)
T PRK04220         60 LRRRVYYKLIEKDYEEVAEK-YLLWRRIRKSKEPIIILIGGASGVGTSTIA  109 (301)
T ss_pred             HHHHHHHHHHHhCcHhHHHH-HHHHHHHhcCCCCEEEEEECCCCCCHHHHH
Confidence            44566677777776654432 4444444442   36899999999999754

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=87.69  E-value=0.37  Score=33.20  Aligned_cols=20  Identities=25%  Similarity=0.386  Sum_probs=16.9

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.|++|+|||...
T Consensus         9 ~~g~~~~i~G~nGsGKStLl   28 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKSTLL   28 (137)
T ss_dssp             ETTSEEEEEESTTSSHHHHH
T ss_pred             cCCCEEEEEccCCCccccce
Confidence            45788999999999999654

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=87.68  E-value=0.45  Score=32.10  Aligned_cols=21  Identities=29%  Similarity=0.237  Sum_probs=17.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll   88 (178)
                      .|+-+.+.+|+|+|||....+
T Consensus        14 ~ge~v~I~GpSGsGKSTLl~~   34 (107)
T cd00820          14 GKVGVLITGDSGIGKTELALE   34 (107)
T ss_pred             CCEEEEEEcCCCCCHHHHHHH
Confidence            467899999999999976644

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=87.67  E-value=9.4  Score=35.02  Aligned_cols=19  Identities=26%  Similarity=0.349  Sum_probs=16.0

Q ss_pred             cEEEEcCCCChHHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSIS   89 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~   89 (178)
                      -+++++|.|+|||.+..+-
T Consensus        39 a~Lf~Gp~G~GKTt~A~~l   57 (824)
T PRK07764         39 AYLFSGPRGCGKTSSARIL   57 (824)
T ss_pred             eEEEECCCCCCHHHHHHHH
Confidence            4799999999999887653

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=87.64  E-value=4.5  Score=36.20  Aligned_cols=59  Identities=12%  Similarity=0.114  Sum_probs=45.3

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      ..++.+-.++.+|-|.|||++..+.+...+..  .+.+++|.+|...-++++++.+..+..
T Consensus       183 ~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--~Gi~IlvTAH~~~ts~evF~rv~~~le  241 (752)
T PHA03333        183 DEYGKCYTAATVPRRCGKTTIMAIILAAMISF--LEIDIVVQAQRKTMCLTLYNRVETVVH  241 (752)
T ss_pred             HHHhhcceEEEeccCCCcHHHHHHHHHHHHHh--cCCeEEEECCChhhHHHHHHHHHHHHH
Confidence            34456778889999999999877665544432  357899999999999999988766654

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=87.60  E-value=4.2  Score=33.04  Aligned_cols=86  Identities=23%  Similarity=0.226  Sum_probs=50.1

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC-c-HHHHHHHHHHHHHhccCCCceEEEE-EcCccHHHH----
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP-T-RELAVQIQKVVLALGDFMNVQCHAC-IGGTNLSED----  143 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~~~~~~-~g~~~~~~~----  143 (178)
                      -+++++-.|+|||...--  +.+.+.+ .+.++++.+- | |+=|.++...+-   +..|+.++.- .|..+..--    
T Consensus       141 Vil~vGVNG~GKTTTIaK--LA~~l~~-~g~~VllaA~DTFRAaAiEQL~~w~---er~gv~vI~~~~G~DpAaVafDAi  214 (340)
T COG0552         141 VILFVGVNGVGKTTTIAK--LAKYLKQ-QGKSVLLAAGDTFRAAAIEQLEVWG---ERLGVPVISGKEGADPAAVAFDAI  214 (340)
T ss_pred             EEEEEecCCCchHhHHHH--HHHHHHH-CCCeEEEEecchHHHHHHHHHHHHH---HHhCCeEEccCCCCCcHHHHHHHH
Confidence            478899999999977532  2222222 4445555552 2 787777766663   3347766652 455444221    


Q ss_pred             HHHhcCCCc-EEEeChHHHH
Q psy9277         144 LRKLDYGQH-VVSGTPGRVF  162 (178)
Q Consensus       144 ~~~~~~~~~-IlV~TP~~l~  162 (178)
                      .....++.| ++|=|.|||+
T Consensus       215 ~~Akar~~DvvliDTAGRLh  234 (340)
T COG0552         215 QAAKARGIDVVLIDTAGRLH  234 (340)
T ss_pred             HHHHHcCCCEEEEeCccccc
Confidence            122235665 5577999984

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=87.56  E-value=0.44  Score=39.85  Aligned_cols=18  Identities=22%  Similarity=0.416  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      .++++.+|||+|||..+-
T Consensus       117 ~~iLL~GP~GsGKT~lAr  134 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQ  134 (413)
T ss_pred             ceEEEECCCCcCHHHHHH
Confidence            579999999999998763

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PRK14737 gmk guanylate kinase; Provisional

Probab=87.45  E-value=0.57  Score=34.70  Aligned_cols=18  Identities=22%  Similarity=0.355  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      ++-++++||+|+|||...
T Consensus         4 ~~~ivl~GpsG~GK~tl~   21 (186)
T PRK14737          4 PKLFIISSVAGGGKSTII   21 (186)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            556899999999999654

>KOG1205|consensus

Probab=87.36  E-value=6.1  Score=31.40  Aligned_cols=86  Identities=13%  Similarity=0.209  Sum_probs=54.7

Q ss_pred             HcCCcEEEEcC-CCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH
Q psy9277          67 VKGRDVIAQAQ-SGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR  145 (178)
Q Consensus        67 ~~g~~v~v~ap-tGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  145 (178)
                      ..|+-++|.|- .|-|+.++|.+.-        .+.+.+.++-+..-.+.+.+.+++.....  ++..+..+.+..++..
T Consensus        10 ~~~kvVvITGASsGIG~~lA~~la~--------~G~~l~lvar~~rrl~~v~~~l~~~~~~~--~v~~~~~Dvs~~~~~~   79 (282)
T KOG1205|consen   10 LAGKVVLITGASSGIGEALAYELAK--------RGAKLVLVARRARRLERVAEELRKLGSLE--KVLVLQLDVSDEESVK   79 (282)
T ss_pred             hCCCEEEEeCCCcHHHHHHHHHHHh--------CCCceEEeehhhhhHHHHHHHHHHhCCcC--ccEEEeCccCCHHHHH
Confidence            45677777765 7899999997643        44455555555555555667777766544  5666666665544433


Q ss_pred             -------HhcCCCcEEEeChHHHH
Q psy9277         146 -------KLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       146 -------~~~~~~~IlV~TP~~l~  162 (178)
                             ....+.||+|.+.|...
T Consensus        80 ~~~~~~~~~fg~vDvLVNNAG~~~  103 (282)
T KOG1205|consen   80 KFVEWAIRHFGRVDVLVNNAGISL  103 (282)
T ss_pred             HHHHHHHHhcCCCCEEEecCcccc
Confidence                   22357899998887653

>TIGR00665 DnaB replicative DNA helicase

Probab=87.32  E-value=2.7  Score=35.19  Aligned_cols=40  Identities=20%  Similarity=0.073  Sum_probs=25.8

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      +..|.-+++.|++|+|||...+--+.+....  .+..+++++
T Consensus       192 ~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~--~g~~vl~~S  231 (434)
T TIGR00665       192 LQPSDLIILAARPSMGKTAFALNIAENAAIK--EGKPVAFFS  231 (434)
T ss_pred             CCCCeEEEEEeCCCCChHHHHHHHHHHHHHh--CCCeEEEEe
Confidence            3446788999999999997665444443332  234566665

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

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

Probab=87.28  E-value=6.6  Score=35.52  Aligned_cols=109  Identities=17%  Similarity=0.077  Sum_probs=67.8

Q ss_pred             CCCcHHHHHHHHHHH-----cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC-CceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          53 EKPSAIQQRSIKPIV-----KGRDVIAQAQSGTGKTATFSISILQSLDTQLR-ETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~-----~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~-~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      ..+.++|.+.+..+.     .+.+.++...-|-|||+-.+..+.+....... .+.+++++|+..+ .+..+.+.++...
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~~-~nw~~e~~k~~~~  415 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLL-SNWKREFEKFAPD  415 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHHHH-HHHHHHHhhhCcc
Confidence            456788888776544     16788888999999997766555442222222 3578999997554 4455555666544


Q ss_pred             CCceEEEEEcCccH----HHHHHHhcC-C----CcEEEeChHHHHH
Q psy9277         127 MNVQCHACIGGTNL----SEDLRKLDY-G----QHVVSGTPGRVFD  163 (178)
Q Consensus       127 ~~~~~~~~~g~~~~----~~~~~~~~~-~----~~IlV~TP~~l~~  163 (178)
                      ... +....|....    .+....+.+ .    .+++++|-+.+..
T Consensus       416 ~~~-~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~  460 (866)
T COG0553         416 LRL-VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRR  460 (866)
T ss_pred             ccc-eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHH
Confidence            332 5566665541    222222222 2    6899999988876

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=87.19  E-value=0.48  Score=38.02  Aligned_cols=17  Identities=24%  Similarity=0.282  Sum_probs=14.1

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      =++++|||+||||-..+
T Consensus         5 ~i~I~GPTAsGKT~lai   21 (308)
T COG0324           5 LIVIAGPTASGKTALAI   21 (308)
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            37899999999996653

>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=87.16  E-value=1.3  Score=33.62  Aligned_cols=15  Identities=20%  Similarity=0.222  Sum_probs=12.6

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      +-+.|++|||||...
T Consensus         2 igI~G~sGSGKTTla   16 (220)
T cd02025           2 IGIAGSVAVGKSTTA   16 (220)
T ss_pred             EEeeCCCCCCHHHHH
Confidence            457899999999775

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>TIGR03263 guanyl_kin guanylate kinase

Probab=87.16  E-value=0.53  Score=34.16  Aligned_cols=18  Identities=28%  Similarity=0.479  Sum_probs=14.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      |+-+++.||+|||||...
T Consensus         1 g~ii~l~G~~GsGKsTl~   18 (180)
T TIGR03263         1 GLLIVISGPSGVGKSTLV   18 (180)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456899999999999753

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=87.05  E-value=1.7  Score=35.15  Aligned_cols=46  Identities=20%  Similarity=0.165  Sum_probs=28.3

Q ss_pred             HHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        61 ~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      ++-.....+..|++.|++|+||+.++-  .++.......++.+.+=|.
T Consensus        14 ~~~~~a~~~~pVLI~GE~GtGK~~lAr--~iH~~s~r~~~pfv~vnc~   59 (329)
T TIGR02974        14 QVSRLAPLDRPVLIIGERGTGKELIAA--RLHYLSKRWQGPLVKLNCA   59 (329)
T ss_pred             HHHHHhCCCCCEEEECCCCChHHHHHH--HHHHhcCccCCCeEEEeCC
Confidence            333344457899999999999997653  3443333334455555443

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=86.91  E-value=1.1  Score=40.74  Aligned_cols=38  Identities=18%  Similarity=0.310  Sum_probs=23.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      +.+|.|+||+|||...-.-+.+ +... .+.+++++=+.+
T Consensus       443 n~~I~G~tGsGKS~l~~~l~~~-~~~~-~g~~v~i~D~~~  480 (811)
T PRK13873        443 HTLVVGPTGAGKSVLLALMALQ-FRRY-PGAQVFAFDFGG  480 (811)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH-hhhc-CCCeEEEEeCCC
Confidence            8999999999999776543332 2211 234555555544

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=86.75  E-value=1.2  Score=33.47  Aligned_cols=42  Identities=19%  Similarity=0.126  Sum_probs=26.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPT  109 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt  109 (178)
                      .|.-+.+.|++|+|||...+.-+...+...   .....++|+...
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e   62 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecC
Confidence            367899999999999987765444432211   011466776654

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.

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=86.72  E-value=1.8  Score=36.78  Aligned_cols=41  Identities=17%  Similarity=0.351  Sum_probs=32.3

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +-...+.++++|++.+.+.|.+                  +.+.+++.+|+|+|||..+
T Consensus       240 Pvvk~~ledY~L~dkl~eRL~e------------------raeGILIAG~PGaGKsTFa  280 (604)
T COG1855         240 PVVKLSLEDYGLSDKLKERLEE------------------RAEGILIAGAPGAGKSTFA  280 (604)
T ss_pred             eeEEechhhcCCCHHHHHHHHh------------------hhcceEEecCCCCChhHHH
Confidence            4456778899999999888754                  2467999999999999554

>cd01918 HprK_C HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria

Probab=86.69  E-value=0.54  Score=33.65  Aligned_cols=19  Identities=32%  Similarity=0.419  Sum_probs=16.7

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |+.+++++++|+|||...+
T Consensus        14 g~gvLi~G~sG~GKStlal   32 (149)
T cd01918          14 GIGVLITGPSGIGKSELAL   32 (149)
T ss_pred             CEEEEEEcCCCCCHHHHHH
Confidence            7889999999999997663

It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=86.68  E-value=4.6  Score=37.59  Aligned_cols=56  Identities=18%  Similarity=0.245  Sum_probs=44.8

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc------CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD------YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~------~~~~IlV~T  157 (178)
                      .+.++||+|.+++-+..+.+.++.   ..|+++..++|+++..++...+.      .++.|+|+|
T Consensus       492 ~~~KvLVF~~~~~t~~~L~~~L~~---~~Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsT  553 (956)
T PRK04914        492 RSEKVLVICAKAATALQLEQALRE---REGIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCS  553 (956)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHhh---ccCeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEec
Confidence            356999999999999999988843   23789999999998877655543      257899999

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=86.65  E-value=3.3  Score=34.59  Aligned_cols=45  Identities=24%  Similarity=0.187  Sum_probs=29.1

Q ss_pred             HHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          61 RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        61 ~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      ..+.-+..|.-+++.|++|+|||...+--+.+....  .+..++|++
T Consensus       186 ~~~~G~~~g~liviag~pg~GKT~~al~ia~~~a~~--~g~~v~~fS  230 (421)
T TIGR03600       186 RLTNGLVKGDLIVIGARPSMGKTTLALNIAENVALR--EGKPVLFFS  230 (421)
T ss_pred             HHhcCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHh--CCCcEEEEE
Confidence            334445557789999999999997766554443322  244566666

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=86.63  E-value=1.8  Score=34.93  Aligned_cols=44  Identities=18%  Similarity=0.181  Sum_probs=27.4

Q ss_pred             HHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          64 KPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        64 ~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      .....+..|++.|.+|+||+.++-  .++.......++.+.+=|..
T Consensus        24 ~~a~~~~pVlI~GE~GtGK~~lA~--~iH~~s~r~~~pfv~v~c~~   67 (326)
T PRK11608         24 RLAPLDKPVLIIGERGTGKELIAS--RLHYLSSRWQGPFISLNCAA   67 (326)
T ss_pred             HHhCCCCCEEEECCCCCcHHHHHH--HHHHhCCccCCCeEEEeCCC
Confidence            334458899999999999997653  33433332334555554443

>PRK09694 helicase Cas3; Provisional

Probab=86.55  E-value=5.8  Score=36.58  Aligned_cols=58  Identities=14%  Similarity=0.156  Sum_probs=41.2

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHH-------HHh-cCC----CcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL-------RKL-DYG----QHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-------~~~-~~~----~~IlV~T  157 (178)
                      .+.+++|+++|++-|+++++.+++... .+..+.++++.....++.       ... +++    ..|+|+|
T Consensus       559 ~g~~vLVf~NTV~~Aq~ly~~L~~~~~-~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaT  628 (878)
T PRK09694        559 AGAQVCLICNLVDDAQKLYQRLKELNN-TQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVAT  628 (878)
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhhCC-CCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEEC
Confidence            466899999999999999999986532 146788888887654441       112 222    3699999

>KOG4150|consensus

Probab=86.54  E-value=1.6  Score=38.20  Aligned_cols=92  Identities=17%  Similarity=0.231  Sum_probs=65.9

Q ss_pred             CCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          38 GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        38 ~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      ++++..-.++...|...++..|.+++..++.             |+++|-.|+.+.+...- ...++|+.|+.++|+.+.
T Consensus       371 ~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~-------------~~~~~~~~~~~~~~~~~-~~~~~Y~~~~~~~~~~~~  436 (1034)
T KOG4150|consen  371 KLSETTKSALKRIGLNTLYSHQAEAISAALA-------------KSLCYNVPVFEELCKDT-NSCALYLFPTKALAQDQL  436 (1034)
T ss_pred             CCCchhHHHHHhcCcceeecCHHHHHHHHhh-------------hccccccHHHHHHHhcc-cceeeeecchhhHHHHHH
Confidence            4667777888888888888889888877664             44566667766554433 358999999999999999


Q ss_pred             HHHHHhccCC--CceEEEEEcCccHHHH
Q psy9277         118 KVVLALGDFM--NVQCHACIGGTNLSED  143 (178)
Q Consensus       118 ~~~~~~~~~~--~~~~~~~~g~~~~~~~  143 (178)
                      +.+.++++.+  .+....+.|+...++.
T Consensus       437 R~L~~L~~~F~~~~~~~~~~~~~~~K~~  464 (1034)
T KOG4150|consen  437 RALSDLIKGFEASINMGVYDGDTPYKDR  464 (1034)
T ss_pred             HHHHHHHHHHHhhcCcceEeCCCCcCCH
Confidence            9988877654  3344455566555443

>PRK13767 ATP-dependent helicase; Provisional

Probab=86.52  E-value=6.4  Score=36.33  Aligned_cols=59  Identities=14%  Similarity=-0.065  Sum_probs=43.6

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccC--CCceEEEEEcCccHHHHHHHh---cC-CCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDF--MNVQCHACIGGTNLSEDLRKL---DY-GQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~--~~~~~~~~~g~~~~~~~~~~~---~~-~~~IlV~TP  158 (178)
                      +.++||.|+|+..|..++..+++....  .+..+...+|+.+.+++....   ++ ...|+|||.
T Consensus       284 ~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs  348 (876)
T PRK13767        284 HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSST  348 (876)
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECC
Confidence            457999999999999999988765332  346678889998877654433   23 368999986

>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=86.47  E-value=0.71  Score=34.97  Aligned_cols=21  Identities=38%  Similarity=0.547  Sum_probs=18.0

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|..+++.+|+|||||...
T Consensus        28 ia~ge~vv~lGpSGcGKTTLL   48 (259)
T COG4525          28 IASGELVVVLGPSGCGKTTLL   48 (259)
T ss_pred             ecCCCEEEEEcCCCccHHHHH
Confidence            456899999999999999654

>KOG0340|consensus

Probab=86.39  E-value=4.4  Score=33.33  Aligned_cols=69  Identities=12%  Similarity=0.209  Sum_probs=48.5

Q ss_pred             HHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          85 TFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        85 ~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      +|+.-++...... ....++|.+.+.--++-++..++.+    +++++.+++.++.+++...+.    +...|+|+|-
T Consensus       240 aYLv~~Lr~~~~~-~~~simIFvnttr~cQ~l~~~l~~l----e~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTD  312 (442)
T KOG0340|consen  240 AYLVHLLRDFENK-ENGSIMIFVNTTRECQLLSMTLKNL----EVRVVSLHSQMPQKERLAALSRFRSNAARILIATD  312 (442)
T ss_pred             HHHHHHHhhhhhc-cCceEEEEeehhHHHHHHHHHHhhh----ceeeeehhhcchHHHHHHHHHHHhhcCccEEEEec
Confidence            4555555443332 3456777787776676666666544    999999999999998887774    4578999994

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=86.39  E-value=0.55  Score=37.05  Aligned_cols=18  Identities=33%  Similarity=0.445  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      -+|++..+|+|+|||+.+
T Consensus       151 PknVLFyGppGTGKTm~A  168 (368)
T COG1223         151 PKNVLFYGPPGTGKTMMA  168 (368)
T ss_pred             cceeEEECCCCccHHHHH
Confidence            479999999999999654

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=86.33  E-value=4.6  Score=31.23  Aligned_cols=40  Identities=28%  Similarity=0.194  Sum_probs=27.5

Q ss_pred             HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          67 VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      ..|.=+++.|+||.|||...+-.+.+....  .+..++|++.
T Consensus        17 ~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~--~~~~vly~Sl   56 (259)
T PF03796_consen   17 RPGELTVIAARPGVGKTAFALQIALNAALN--GGYPVLYFSL   56 (259)
T ss_dssp             -TT-EEEEEESTTSSHHHHHHHHHHHHHHT--TSSEEEEEES
T ss_pred             CcCcEEEEEecccCCchHHHHHHHHHHHHh--cCCeEEEEcC
Confidence            345678999999999998776666555443  2357888774

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=86.30  E-value=1.7  Score=33.42  Aligned_cols=59  Identities=19%  Similarity=0.147  Sum_probs=31.7

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCc
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGT  138 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~  138 (178)
                      ++++.||+|.|||..+.+-+ +    .........-.|..+-+.++...+..+.    -..+++.+..
T Consensus        52 h~lf~GPPG~GKTTLA~IIA-~----e~~~~~~~~sg~~i~k~~dl~~il~~l~----~~~ILFIDEI  110 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLARIIA-N----ELGVNFKITSGPAIEKAGDLAAILTNLK----EGDILFIDEI  110 (233)
T ss_dssp             EEEEESSTTSSHHHHHHHHH-H----HCT--EEEEECCC--SCHHHHHHHHT------TT-EEEECTC
T ss_pred             eEEEECCCccchhHHHHHHH-h----ccCCCeEeccchhhhhHHHHHHHHHhcC----CCcEEEEech
Confidence            79999999999997654322 1    1122344445566555566665555442    2345566554

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>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=86.28  E-value=2.3  Score=33.94  Aligned_cols=42  Identities=24%  Similarity=0.198  Sum_probs=25.1

Q ss_pred             EEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHH
Q psy9277          73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQ  115 (178)
Q Consensus        73 ~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q  115 (178)
                      ++.++.|+|||.+....++...........+++. ++..-+.+
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~~~~vi~~-~~~~~~~~   42 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPPGRRVIIA-STYRQARD   42 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--EEEEE-ESSHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCCCcEEEEe-cCHHHHHH
Confidence            4678999999999887777766554333345555 66555555

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=86.20  E-value=0.46  Score=42.65  Aligned_cols=54  Identities=20%  Similarity=0.274  Sum_probs=31.4

Q ss_pred             cccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+|++++-.+...+.++++   .+..+...+..   .+..++.+++.||+|+|||...
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---gi~~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHL---GIEPPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhc---CCCCCceEEEECCCCCChHHHH
Confidence            456788876555555555432   11111111111   1234689999999999999664

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=86.18  E-value=0.58  Score=34.65  Aligned_cols=15  Identities=33%  Similarity=0.390  Sum_probs=12.9

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      |.|+||+|||||...
T Consensus         2 IgI~G~sgSGKTTla   16 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLA   16 (194)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999765

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>PRK13342 recombination factor protein RarA; Reviewed

Probab=86.11  E-value=6.3  Score=32.92  Aligned_cols=19  Identities=37%  Similarity=0.438  Sum_probs=15.9

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll   88 (178)
                      .++++.||+|+|||...-.
T Consensus        37 ~~ilL~GppGtGKTtLA~~   55 (413)
T PRK13342         37 SSMILWGPPGTGKTTLARI   55 (413)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            3899999999999977643

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=86.10  E-value=0.2  Score=43.25  Aligned_cols=19  Identities=37%  Similarity=0.445  Sum_probs=16.7

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||.++-
T Consensus        86 ~~~vLi~Ge~GtGKt~lAr  104 (531)
T TIGR02902        86 PQHVIIYGPPGVGKTAAAR  104 (531)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4789999999999998764

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=86.00  E-value=0.65  Score=32.58  Aligned_cols=17  Identities=24%  Similarity=0.356  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      +++++|++|||||...-
T Consensus         1 ~i~l~G~~GsGKstla~   17 (154)
T cd00464           1 NIVLIGMMGAGKTTVGR   17 (154)
T ss_pred             CEEEEcCCCCCHHHHHH
Confidence            58899999999997763

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>KOG0731|consensus

Probab=85.99  E-value=0.55  Score=42.08  Aligned_cols=56  Identities=20%  Similarity=0.272  Sum_probs=32.9

Q ss_pred             ccccccccccCC-CCH---HHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          27 DVEVVSTFDNMG-LRE---DLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        27 ~~~~~~~f~~~~-l~~---~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.+...+|+|.. +++   ++.+-+.=  .+.|-.+|..   -+.--+.+++++|+|+|||+.+-
T Consensus       303 ~~~t~V~FkDVAG~deAK~El~E~V~f--LKNP~~Y~~l---GAKiPkGvLL~GPPGTGKTLLAK  362 (774)
T KOG0731|consen  303 EGNTGVKFKDVAGVDEAKEELMEFVKF--LKNPEQYQEL---GAKIPKGVLLVGPPGTGKTLLAK  362 (774)
T ss_pred             CCCCCCccccccCcHHHHHHHHHHHHH--hcCHHHHHHc---CCcCcCceEEECCCCCcHHHHHH
Confidence            555567888864 443   33333321  1233333332   22335799999999999998764

>PHA00729 NTP-binding motif containing protein

Probab=85.92  E-value=0.64  Score=35.64  Aligned_cols=50  Identities=14%  Similarity=0.090  Sum_probs=30.1

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhc----------CCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQ----------LRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~----------~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      ++++.|++|+|||..+.. +...+...          -...+-.+++...+|...+...+.
T Consensus        19 nIlItG~pGvGKT~LA~a-La~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~   78 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALK-VARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAID   78 (226)
T ss_pred             EEEEECCCCCCHHHHHHH-HHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHh
Confidence            899999999999966543 22222100          011233455566777777766553

>KOG0733|consensus

Probab=85.92  E-value=1.1  Score=39.37  Aligned_cols=56  Identities=21%  Similarity=0.277  Sum_probs=31.3

Q ss_pred             cccccccccCC-CCHHHHHHHHhCC-CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          28 VEVVSTFDNMG-LREDLLRGIYAYG-FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        28 ~~~~~~f~~~~-l~~~i~~~l~~~g-~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ++.-.+|+++| ++..+.+...-.. ++.|-.+++-   -+.=-+.+++++|+|+|||..+
T Consensus       183 ~~snv~f~diGG~d~~~~el~~li~~i~~Pe~~~~l---Gv~PprGvLlHGPPGCGKT~lA  240 (802)
T KOG0733|consen  183 PESNVSFSDIGGLDKTLAELCELIIHIKHPEVFSSL---GVRPPRGVLLHGPPGCGKTSLA  240 (802)
T ss_pred             CCCCcchhhccChHHHHHHHHHHHHHhcCchhHhhc---CCCCCCceeeeCCCCccHHHHH
Confidence            33345788886 4443333322111 3333333322   1122579999999999999765

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=85.82  E-value=1.1  Score=33.96  Aligned_cols=41  Identities=15%  Similarity=0.041  Sum_probs=26.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcC
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSP  108 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~P  108 (178)
                      .|.-+.+.+++|+|||...+.-++......   ..+..++|+.-
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            467889999999999988765544422211   01246777763

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 .

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=85.82  E-value=0.53  Score=38.28  Aligned_cols=21  Identities=33%  Similarity=0.477  Sum_probs=17.4

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|.-+++.||+|||||...
T Consensus        26 i~~Gef~vllGPSGcGKSTlL   46 (338)
T COG3839          26 IEDGEFVVLLGPSGCGKSTLL   46 (338)
T ss_pred             EcCCCEEEEECCCCCCHHHHH
Confidence            345889999999999999653

>PRK13891 conjugal transfer protein TrbE; Provisional

Probab=85.80  E-value=1.4  Score=40.29  Aligned_cols=39  Identities=13%  Similarity=0.161  Sum_probs=25.8

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      +.+|.||||+|||...-.-+.+....  .+.+++++=|-++
T Consensus       490 h~~I~G~tGsGKS~l~~~L~~~~~k~--~~~~v~i~D~~~s  528 (852)
T PRK13891        490 HTFMFGPTGAGKSTHLGIIAAQLRRY--AGMSIYAFDKGMS  528 (852)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc--CCCEEEEEcCCcc
Confidence            58999999999997765434332221  3457777777654

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=85.79  E-value=6.1  Score=31.39  Aligned_cols=40  Identities=28%  Similarity=0.316  Sum_probs=26.5

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEE-EcCCCChHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIA-QAQSGTGKTATF   86 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v-~aptGsGKTl~~   86 (178)
                      ++|+++-.++.+.+.+...               +.+|  .++++ .||+|+|||...
T Consensus        18 ~~~~~~~~~~~~~~~l~~~---------------~~~~~~~~~lll~G~~G~GKT~la   60 (316)
T PHA02544         18 STIDECILPAADKETFKSI---------------VKKGRIPNMLLHSPSPGTGKTTVA   60 (316)
T ss_pred             CcHHHhcCcHHHHHHHHHH---------------HhcCCCCeEEEeeCcCCCCHHHHH
Confidence            6777777777777666421               1123  24555 899999999764

>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=85.77  E-value=8.2  Score=25.67  Aligned_cols=56  Identities=16%  Similarity=0.219  Sum_probs=40.7

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---cC-CCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---DY-GQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~-~~~IlV~TP  158 (178)
                      .+.++|+.+++...+.++.+.+.+    .+..+..++|+.+..+.....   .+ ...|+++|.
T Consensus        27 ~~~~~lvf~~~~~~~~~~~~~l~~----~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~   86 (131)
T cd00079          27 KGGKVLIFCPSKKMLDELAELLRK----PGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATD   86 (131)
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHh----cCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcC
Confidence            356899999999999999988876    367788888887654443332   22 357888885

>KOG0330|consensus

Probab=85.74  E-value=2.8  Score=34.87  Aligned_cols=56  Identities=16%  Similarity=0.145  Sum_probs=44.2

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+..+||.|.|..-++.+.-.++.+    |+...-++|+++.+.+...+.    ..++|+|||-
T Consensus       299 ~g~s~iVF~~t~~tt~~la~~L~~l----g~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TD  358 (476)
T KOG0330|consen  299 AGNSVIVFCNTCNTTRFLALLLRNL----GFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTD  358 (476)
T ss_pred             cCCcEEEEEeccchHHHHHHHHHhc----CcceecccchhhHHHHHHHHHHHhccCCcEEEecc
Confidence            3457899999988888777777655    899999999999887766654    3589999993

>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]

Probab=85.74  E-value=1.6  Score=35.50  Aligned_cols=45  Identities=20%  Similarity=0.127  Sum_probs=38.5

Q ss_pred             CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh
Q psy9277          52 FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        52 ~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      +.--++.|..=+..+.+..=++..+|-|+|||+.......+.+..
T Consensus       126 I~~kt~~Q~~y~eai~~~di~fGiGpAGTGKTyLava~av~al~~  170 (348)
T COG1702         126 IIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKTYLAVAKAVDALGA  170 (348)
T ss_pred             eEecChhHHHHHHHHHhcCeeeeecccccCChhhhHHhHhhhhhh
Confidence            445689999999999999999999999999999888877777654

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=85.72  E-value=1.3  Score=35.34  Aligned_cols=41  Identities=10%  Similarity=-0.035  Sum_probs=26.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhh---cCCCceEEEEcCc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDT---QLRETQVLCLSPT  109 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~---~~~~~~~lil~Pt  109 (178)
                      |.-+.+++++|+|||...+-.+.+....   ...+..++||.-.
T Consensus        95 g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te  138 (310)
T TIGR02236        95 QAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTE  138 (310)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECC
Confidence            4567899999999998766555443221   1112378888743

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=85.68  E-value=0.78  Score=28.00  Aligned_cols=15  Identities=27%  Similarity=0.465  Sum_probs=12.7

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      +.++++.|||||...
T Consensus         2 i~i~G~~gsGKst~~   16 (69)
T cd02019           2 IAITGGSGSGKSTVA   16 (69)
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999654

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=85.68  E-value=8.6  Score=35.25  Aligned_cols=58  Identities=19%  Similarity=0.187  Sum_probs=46.4

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcC----CCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY----GQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~IlV~TP  158 (178)
                      ...+||.+|++.-+..+++.+++... .++.+..++|+.+.+++...+..    ...|||+|.
T Consensus       209 ~g~iLVFlpg~~eI~~l~~~L~~~~~-~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATn  270 (819)
T TIGR01970       209 TGSILVFLPGQAEIRRVQEQLAERLD-SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATN  270 (819)
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhhcC-CCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecc
Confidence            45899999999999999998876432 37889999999998887776652    258999994

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.

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=85.66  E-value=0.66  Score=36.89  Aligned_cols=17  Identities=12%  Similarity=0.167  Sum_probs=14.2

Q ss_pred             EEEEcCCCChHHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFSI   88 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll   88 (178)
                      +++.||||+|||....-
T Consensus         2 i~i~G~t~~GKs~la~~   18 (287)
T TIGR00174         2 IFIMGPTAVGKSQLAIQ   18 (287)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999976643

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=85.59  E-value=3.7  Score=33.07  Aligned_cols=22  Identities=18%  Similarity=-0.014  Sum_probs=17.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISIL   91 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il   91 (178)
                      .-+.+.+++|+|||...+..+.
T Consensus        97 ~i~~i~G~~g~GKT~l~~~~~~  118 (316)
T TIGR02239        97 SITEIFGEFRTGKTQLCHTLAV  118 (316)
T ss_pred             eEEEEECCCCCCcCHHHHHHHH
Confidence            4578999999999987754443

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=85.56  E-value=16  Score=29.41  Aligned_cols=18  Identities=28%  Similarity=0.361  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      ...++.||+|+|||....
T Consensus        37 ~~~Ll~G~~G~GKt~~a~   54 (355)
T TIGR02397        37 HAYLFSGPRGTGKTSIAR   54 (355)
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            357999999999996653

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.

>PLN02796 D-glycerate 3-kinase

Probab=85.51  E-value=1.7  Score=35.47  Aligned_cols=16  Identities=31%  Similarity=0.322  Sum_probs=13.8

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      +.|.|++|||||...-
T Consensus       103 IGI~G~sGSGKSTLa~  118 (347)
T PLN02796        103 IGISAPQGCGKTTLVF  118 (347)
T ss_pred             EEEECCCCCcHHHHHH
Confidence            8899999999997643

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=85.41  E-value=10  Score=29.97  Aligned_cols=20  Identities=20%  Similarity=0.190  Sum_probs=16.5

Q ss_pred             CCc-EEEEcCCCChHHHHHHH
Q psy9277          69 GRD-VIAQAQSGTGKTATFSI   88 (178)
Q Consensus        69 g~~-v~v~aptGsGKTl~~ll   88 (178)
                      ... +++.||+|+|||.++..
T Consensus        23 ~~halL~~Gp~G~Gktt~a~~   43 (325)
T COG0470          23 LPHALLFYGPPGVGKTTAALA   43 (325)
T ss_pred             CCceeeeeCCCCCCHHHHHHH
Confidence            455 99999999999987643

>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B

Probab=85.38  E-value=3.7  Score=39.00  Aligned_cols=48  Identities=19%  Similarity=0.319  Sum_probs=34.2

Q ss_pred             EEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          73 IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        73 ~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      +|.|+.|||||...+--+.+.+.....++..++++|... .-+..+.+.
T Consensus         5 fi~G~aGSGKT~~l~~ri~~~l~~~~~~~~~illVPeq~-TF~~e~rl~   52 (1158)
T TIGR02773         5 FIYGRAGTGKSTFCIDEIKQKIKENPLGKPIILIVPDQM-TFQMEQALL   52 (1158)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHhhCCCCCcEEEEcCCcc-cHHHHHHHH
Confidence            788999999998876666666655445778999999874 333444443

DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=85.38  E-value=4  Score=36.36  Aligned_cols=55  Identities=16%  Similarity=0.216  Sum_probs=41.7

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ++.+++|.++|+..+..+.+.+.+.    ++.+..++|+.+..++...+.    ...+|+|||
T Consensus       441 ~g~~vLIf~~tk~~ae~L~~~L~~~----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t  499 (655)
T TIGR00631       441 RNERVLVTTLTKKMAEDLTDYLKEL----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGI  499 (655)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHhhh----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEc
Confidence            5678999999999999999888765    678888888877654433332    346888888

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

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=85.34  E-value=1.1  Score=34.67  Aligned_cols=22  Identities=32%  Similarity=0.534  Sum_probs=14.5

Q ss_pred             EEcCCCChHHHHHHHHHHHHhhh
Q psy9277          74 AQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        74 v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      |.||.||||| .|.-.+-+.+..
T Consensus         1 ViGpaGSGKT-T~~~~~~~~~~~   22 (238)
T PF03029_consen    1 VIGPAGSGKT-TFCKGLSEWLES   22 (238)
T ss_dssp             -EESTTSSHH-HHHHHHHHHHTT
T ss_pred             CCCCCCCCHH-HHHHHHHHHHHh
Confidence            5799999999 445555554443

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	178
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		7e-75
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		8e-75
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		8e-75
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		4e-72
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-66
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		6e-65
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		6e-54
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		1e-52
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		1e-52
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-48
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		8e-46
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		3e-45
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		7e-45
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-43
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		8e-31
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-27
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		2e-24
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		7e-24
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		5e-23
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		5e-23
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-21
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		1e-20
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-20
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-20
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-20
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-20
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		8e-20
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		9e-20
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-19
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-19
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-19
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-18
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		5e-18
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-17
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		1e-16
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		2e-16
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-16
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-16
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-14
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-14
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		5e-14
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		7e-14
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-13
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		8e-12
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		1e-11
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-11
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-11
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		2e-10
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		2e-10

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  275 bits (704), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)
Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 6   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 65
Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 66  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 125
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 126 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 171

>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 =  275 bits (704), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)
Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66
Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

>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 =  275 bits (704), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 130/166 (78%), Positives = 147/166 (88%)
Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 7   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 66
Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 67  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 126
Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR
Sbjct: 127 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR 172

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  266 bits (681), Expect = 4e-72,   Method: Compositional matrix adjust.
 Identities = 125/155 (80%), Positives = 140/155 (90%)
Query: 17  LSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQA 76
           ++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ+
Sbjct: 1   MTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQS 60
Query: 77  QSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG 136
           QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +LALGD+MNVQCHACIG
Sbjct: 61  QSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIG 120
Query: 137 GTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
           GTN+ ED+RKLDYGQHVV+GTPGRVFDMIR    R
Sbjct: 121 GTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLR 155

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  246 bits (629), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 114/139 (82%), Positives = 127/139 (91%)
Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
           TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ+QSGTGKTATFS+S+LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 93  SLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH 152
            LD Q+RETQ L L+PTRELAVQ+QK +LALGD+MNVQCHACIGGTN+ ED+RKLDYGQH
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQH 121
Query: 153 VVSGTPGRVFDMIRSSQGR 171
           VV+GTPGRVFDMIR    R
Sbjct: 122 VVAGTPGRVFDMIRRRSLR 140

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  242 bits (618), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 112/134 (83%), Positives = 125/134 (93%)
Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
           TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ+QSGTGKTATFS+S+LQ
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 93  SLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH 152
            LD Q+RETQ L L+PTRELAVQ+QK +LALGD+MNVQ HACIGGTN+ ED+RKLDYGQH
Sbjct: 62  CLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSHACIGGTNVGEDIRKLDYGQH 121
Query: 153 VVSGTPGRVFDMIR 166
           VV+GTPGRVFDMIR
Sbjct: 122 VVAGTPGRVFDMIR 135

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  206 bits (524), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 96/138 (69%), Positives = 114/138 (82%), Gaps = 1/138 (0%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E+V  FD+M L+E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 27  EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAI 86
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           SILQ L+ + +ETQ L L+PTRELA QIQKV+LALGD+M   CHACIGGTN+  +++KL 
Sbjct: 87  SILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQ 146
Query: 149 Y-GQHVVSGTPGRVFDMI 165
               H+V GTPGRVFDM+
Sbjct: 147 AEAPHIVVGTPGRVFDML 164

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  202 bits (513), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 94/138 (68%), Positives = 113/138 (81%), Gaps = 1/138 (0%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E+V +FD+M L E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 11  EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 70
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           SILQ ++  L+ TQ L L+PTRELA QIQKVV+ALGD+M   CHACIGGTN+  +++KL 
Sbjct: 71  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 130
Query: 149 Y-GQHVVSGTPGRVFDMI 165
               H++ GTPGRVFDM+
Sbjct: 131 MEAPHIIVGTPGRVFDML 148

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  201 bits (512), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 94/138 (68%), Positives = 113/138 (81%), Gaps = 1/138 (0%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E+V +FD+M L E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 37  EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 96
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           SILQ ++  L+ TQ L L+PTRELA QIQKVV+ALGD+M   CHACIGGTN+  +++KL 
Sbjct: 97  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 156
Query: 149 Y-GQHVVSGTPGRVFDMI 165
               H++ GTPGRVFDM+
Sbjct: 157 MEAPHIIVGTPGRVFDML 174

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  188 bits (478), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 89/138 (64%), Positives = 107/138 (77%), Gaps = 1/138 (0%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E+V +FD+M L E LLRGIYAYGFE PSAIQQR+I P + G DVIAQAQSGTG TATF+I
Sbjct: 12  EIVDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAI 71
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           SILQ ++  L  TQ L L+PTRELA QIQ VV+ALGD+M   CHACIGGTN+  +++ L 
Sbjct: 72  SILQQIELDLXATQALVLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQ 131
Query: 149 Y-GQHVVSGTPGRVFDMI 165
               H++ GTPGRVFDM+
Sbjct: 132 MEAPHIIVGTPGRVFDML 149

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  179 bits (454), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 89/156 (57%), Positives = 117/156 (75%), Gaps = 2/156 (1%)
Query: 16  DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQ 75
           D+   + +T+ D +VV  FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQ
Sbjct: 7   DIEESQIQTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQ 65
Query: 76  AQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI 135
           AQSGTGKT TFSI+ LQ +DT ++  Q L L+PTRELA+QIQKVV+AL   M+++ HACI
Sbjct: 66  AQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACI 125
Query: 136 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
           GGT+  ED   L   Q +V GTPGRVFD I+  + R
Sbjct: 126 GGTSFVEDAEGLRDAQ-IVVGTPGRVFDNIQRRRFR 160

>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 =  177 bits (448), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 86/143 (60%), Positives = 110/143 (76%), Gaps = 1/143 (0%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           +VV  FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGTGKT TFSI
Sbjct: 11  KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 70
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           + LQ +DT ++  Q L L+PTRELA+QIQKVV+AL   M+++ HACIGGT+  ED   L 
Sbjct: 71  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 130
Query: 149 YGQHVVSGTPGRVFDMIRSSQGR 171
             Q +V GTPGRVFD I+  + R
Sbjct: 131 DAQ-IVVGTPGRVFDNIQRRRFR 152

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  176 bits (446), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 86/143 (60%), Positives = 109/143 (76%), Gaps = 1/143 (0%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           +VV  FD+M L E LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGTGKT TFSI
Sbjct: 18  KVVYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSI 77
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           + LQ +DT ++  Q L L+PTRELA+QIQKVV+AL   M+++ HACIGGT+  ED   L 
Sbjct: 78  AALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 137
Query: 149 YGQHVVSGTPGRVFDMIRSSQGR 171
             Q +V GTPGRVFD I+  + R
Sbjct: 138 DAQ-IVVGTPGRVFDNIQRRRFR 159

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  172 bits (435), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 87/156 (55%), Positives = 114/156 (73%), Gaps = 2/156 (1%)
Query: 16  DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQ 75
           D+   + +T+ D +VV  FD+  L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQ
Sbjct: 6   DIEESQIQTNYD-KVVYKFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQ 64
Query: 76  AQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI 135
           AQSGTGKT TFSI+ LQ +DT ++  Q L L+PTRELA+QIQKVV AL    +++ HACI
Sbjct: 65  AQSGTGKTGTFSIAALQRIDTSVKAPQALXLAPTRELALQIQKVVXALAFHXDIKVHACI 124
Query: 136 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR 171
           GGT+  ED   L   Q +V GTPGRVFD I+  + R
Sbjct: 125 GGTSFVEDAEGLRDAQ-IVVGTPGRVFDNIQRRRFR 159

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  129 bits (324), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 89/133 (66%)
Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           +TF++  L+ +LL GI+  GFEKPS IQ+ +I   + GRD++A+A++GTGKTA F I  L
Sbjct: 21  NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 80
Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
           + +  +L + Q L + PTRELA+Q  +VV  LG    + C    GGTNL +D+ +L+   
Sbjct: 81  EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETV 140
Query: 152 HVVSGTPGRVFDM 164
           H++ GTPGRV D+
Sbjct: 141 HILVGTPGRVLDL 153

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  117 bits (293), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 55/134 (41%), Positives = 88/134 (65%), Gaps = 1/134 (0%)
Query: 34  FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
           F++  L+ +LL GI+  G+EKPS IQ+ SI   + GRD++A+A++GTGK+  + I +L+ 
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64
Query: 94  LDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQH 152
           LD +    Q + + PTRELA+Q+ ++ + +   M   +  A  GGTNL +D+ +LD   H
Sbjct: 65  LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVH 124
Query: 153 VVSGTPGRVFDMIR 166
           VV  TPGR+ D+I+
Sbjct: 125 VVIATPGRILDLIK 138

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  108 bits (270), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 85/133 (63%), Gaps = 2/133 (1%)
Query: 34  FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
           F+++ L   +L G+ A GFE+PS +Q ++I     G D+I QA+SGTGKT  FS   L S
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 94  LDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN-VQCHACIGGTNLSEDLRKLDYGQH 152
           L  +   TQ+L L+PTRE+AVQI  V+ A+G  M  ++CH  IGGT LS+D  +L    H
Sbjct: 86  LVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKKC-H 144
Query: 153 VVSGTPGRVFDMI 165
           +  G+PGR+  +I
Sbjct: 145 IAVGSPGRIKQLI 157

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score =  106 bits (265), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 55/152 (36%), Positives = 96/152 (63%), Gaps = 6/152 (3%)
Query: 17  LSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIA 74
           L++++ + +  +    +FD +GL  +LL+GIYA  F+KPS IQ+R++  ++    R++IA
Sbjct: 7   LADIQADPNSPLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIA 66
Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           Q+QSGTGKTA FS+++L  ++ +    Q +CL+P+RELA Q  +VV  +G F  +     
Sbjct: 67  QSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLI 126
Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
           +  +   E  ++++    V+ GTPG V D++R
Sbjct: 127 VPDS--FEKNKQIN--AQVIVGTPGTVLDLMR 154

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  103 bits (257), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 89/139 (64%), Gaps = 6/139 (4%)
Query: 30  VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS 87
           +  +FD +GL  +LL+GIYA  F+KPS IQ+R++  ++    R++IAQ+QSGTGKTA FS
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
           +++L  ++ +    Q +CL+P+RELA Q  +VV  +G F  +     +  +   E  +++
Sbjct: 63  LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--FEKNKQI 120
Query: 148 DYGQHVVSGTPGRVFDMIR 166
           +    V+ GTPG V D++R
Sbjct: 121 N--AQVIVGTPGTVLDLMR 137

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  103 bits (257), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 89/139 (64%), Gaps = 6/139 (4%)
Query: 30  VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS 87
           +  +FD +GL  +LL+GIYA  F+KPS IQ+R++  ++    R++IAQ+QSGTGKTA FS
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62
Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
           +++L  ++ +    Q +CL+P+RELA Q  +VV  +G F  +     +  +   E  +++
Sbjct: 63  LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDS--FEKNKQI 120
Query: 148 DYGQHVVSGTPGRVFDMIR 166
           +    V+ GTPG V D++R
Sbjct: 121 N--AQVIVGTPGTVLDLMR 137

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 96.7 bits (239), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 83/138 (60%), Gaps = 8/138 (5%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV---KGRDVIAQAQSGTGKTATFS 87
           V +F+ + L+  LL+G+YA GF +PS IQ+ ++ P++     +++IAQ+QSGTGKTA F 
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFV 149
Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRK 146
           +++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++    + G  L    R 
Sbjct: 150 LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RG 206
Query: 147 LDYGQHVVSGTPGRVFDM 164
               + +V GTPG V D 
Sbjct: 207 QKISEQIVIGTPGTVLDW 224

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 95.9 bits (237), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 83/138 (60%), Gaps = 8/138 (5%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV---KGRDVIAQAQSGTGKTATFS 87
           V +F+ + L+  LL+G+YA GF +PS IQ+ ++ P++     +++IAQ+QSGTGKTA F 
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFV 82
Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRK 146
           +++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++    + G  L    R 
Sbjct: 83  LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RG 139
Query: 147 LDYGQHVVSGTPGRVFDM 164
               + +V GTPG V D 
Sbjct: 140 QKISEQIVIGTPGTVLDW 157

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 95.5 bits (236), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 83/138 (60%), Gaps = 8/138 (5%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG---RDVIAQAQSGTGKTATFS 87
           V +F+ + L+  LL+G+YA GF +PS IQ+ ++ P++     +++IAQ+QSGTGKTA F 
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENAL-PLMLAEPPQNLIAQSQSGTGKTAAFV 149
Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRK 146
           +++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++    + G  L    R 
Sbjct: 150 LAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RG 206
Query: 147 LDYGQHVVSGTPGRVFDM 164
               + +V GTPG V D 
Sbjct: 207 QKISEQIVIGTPGTVLDW 224

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 82/137 (59%), Gaps = 6/137 (4%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSI 88
           V +F+ + L+  LL+G+YA GF +PS IQ+ ++  ++    +++IAQ+QSGTGKTA F +
Sbjct: 40  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 99
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
           ++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++    + G  L    R  
Sbjct: 100 AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RGQ 156
Query: 148 DYGQHVVSGTPGRVFDM 164
              + +V GTPG V D 
Sbjct: 157 KISEQIVIGTPGTVLDW 173

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 82/137 (59%), Gaps = 6/137 (4%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSI 88
           V +F+ + L+  LL+G+YA GF +PS IQ+ ++  ++    +++IAQ+QSGTGKTA F +
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
           ++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++    + G  L    R  
Sbjct: 84  AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RGQ 140
Query: 148 DYGQHVVSGTPGRVFDM 164
              + +V GTPG V D 
Sbjct: 141 KISEQIVIGTPGTVLDW 157

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 95.1 bits (235), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 52/137 (37%), Positives = 82/137 (59%), Gaps = 6/137 (4%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSI 88
           V +F+ + L+  LL+G+YA GF +PS IQ+ ++  ++    +++IAQ+QSGTGKTA F +
Sbjct: 61  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 120
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
           ++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++    + G  L    R  
Sbjct: 121 AMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLE---RGQ 177
Query: 148 DYGQHVVSGTPGRVFDM 164
              + +V GTPG V D 
Sbjct: 178 KISEQIVIGTPGTVLDW 194

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 92.8 bits (229), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 54/140 (38%), Positives = 76/140 (54%), Gaps = 2/140 (1%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
           +S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ 
Sbjct: 6   MSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT 65
Query: 91  LQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDY 149
           LQ L+    +  VL +  TRELA QI K       +M NV+     GG ++ +D   L  
Sbjct: 66  LQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 125
Query: 150 G-QHVVSGTPGRVFDMIRSS 168
              H+V GTPGR+  + R+ 
Sbjct: 126 NCPHIVVGTPGRILALARNK 145

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 92.8 bits (229), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 54/138 (39%), Positives = 75/138 (54%), Gaps = 2/138 (1%)
Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ L
Sbjct: 14  SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 73
Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
           Q L+    +  VL +  TRELA QI K       +M NV+     GG ++ +D   L   
Sbjct: 74  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 133
Query: 151 -QHVVSGTPGRVFDMIRS 167
             H+V GTPGR+  + R+
Sbjct: 134 CPHIVVGTPGRILALARN 151

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 75/139 (53%), Gaps = 2/139 (1%)
Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ L
Sbjct: 8   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
           Q L+    +  VL +  TRELA QI K       +M NV+     GG ++ +D   L   
Sbjct: 68  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 151 -QHVVSGTPGRVFDMIRSS 168
             H+V GTPGR+  + R+ 
Sbjct: 128 CPHIVVGTPGRILALARNK 146

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 54/139 (38%), Positives = 75/139 (53%), Gaps = 2/139 (1%)
Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ L
Sbjct: 8   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 67
Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
           Q L+    +  VL +  TRELA QI K       +M NV+     GG ++ +D   L   
Sbjct: 68  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 127
Query: 151 -QHVVSGTPGRVFDMIRSS 168
             H+V GTPGR+  + R+ 
Sbjct: 128 CPHIVVGTPGRILALARNK 146

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 91.3 bits (225), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 78/142 (54%)
Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E   TF ++G+ + L       G+ KP+ IQ  +I   ++GRD+I  A++G+GKT  F++
Sbjct: 40  EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFAL 99
Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
            IL +L    +    L L+PTRELA QI +   ALG  + VQ    +GG +       L 
Sbjct: 100 PILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALA 159
Query: 149 YGQHVVSGTPGRVFDMIRSSQG 170
              H++  TPGR+ D + +++G
Sbjct: 160 KKPHIIIATPGRLIDHLENTKG 181

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 89.0 bits (219), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 54/145 (37%), Positives = 85/145 (58%), Gaps = 12/145 (8%)
Query: 39  LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
           + E+ L+ I   GF   + IQ +SI+P+++GRD++A A++G+GKT  F I  ++ L  +L
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVE-LIVKL 119
Query: 99  R-----ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA---CIGGTNLSEDLRKLDYG 150
           R      T VL LSPTRELA+Q   V   L + M    H     +GG+N S + +KL  G
Sbjct: 120 RFMPRNGTGVLILSPTRELAMQTFGV---LKELMTHHVHTYGLIMGGSNRSAEAQKLGNG 176
Query: 151 QHVVSGTPGRVFDMIRSSQGRRTTN 175
            +++  TPGR+ D ++++ G    N
Sbjct: 177 INIIVATPGRLLDHMQNTPGFMYKN 201

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 87.0 bits (214), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 47/140 (33%), Positives = 72/140 (51%), Gaps = 4/140 (2%)
Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           + F     +  ++  I    F KP+ IQ+R I   ++G   + Q+Q+GTGKT  + + I 
Sbjct: 4   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIX 63
Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDLRKL 147
           + +  +  E Q +  +PTRELA QI    L +  F      +     IGGT+  + L KL
Sbjct: 64  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKL 123
Query: 148 DYGQHVVSGTPGRVFDMIRS 167
           +   H+V GTPGR+ D IR 
Sbjct: 124 NVQPHIVIGTPGRINDFIRE 143

>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 = 84.7 bits (208), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 81/155 (52%), Gaps = 21/155 (13%)
Query: 30  VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSIS 89
           V+  FD + L   +   I    +++P+ IQ+ +I  I++ RD++A AQ+G+GKTA F I 
Sbjct: 21  VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIP 80
Query: 90  ILQSLDTQLRETQ---------VLCLSPTRELAVQI----QKVVLALGDFMNVQCHACI- 135
           I+  L  Q    Q          L L+PTRELA+QI    QK  L      N    +C+ 
Sbjct: 81  IINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL------NTPLRSCVV 134
Query: 136 -GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ 169
            GG +    +R++  G H++  TPGR+ D I  ++
Sbjct: 135 YGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNK 169

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 52/148 (35%), Positives = 79/148 (53%), Gaps = 6/148 (4%)
Query: 24  TSEDV-EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGK 82
           T  DV + +  F +  LR+ ++  +   G++ P+ IQ+ SI  I  GRD++A AQ+G+GK
Sbjct: 47  TGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGK 106
Query: 83  TATFSISILQSL-----DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGG 137
           TA F + IL  L     + +L   QV+ +SPTRELA+QI            ++     GG
Sbjct: 107 TAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGG 166
Query: 138 TNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
           T+       +  G HVV  TPGR+ D +
Sbjct: 167 TSFRHQNECITRGCHVVIATPGRLLDFV 194

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 45/136 (33%), Positives = 73/136 (53%), Gaps = 5/136 (3%)
Query: 34  FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
           F +  L+ ++L  ++  G   P+ IQ  ++   ++G+D+I QA++GTGKT  F++ I + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 94  LDTQL---RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYG 150
           L       R+ + L L+PTRELA+Q+   + A+   + V   A  GGT   +    L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLRG 120
Query: 151 QHVVSGTPGRVFDMIR 166
              V  TPGR  D +R
Sbjct: 121 ADAVVATPGRALDYLR 136

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 81.6 bits (200), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 44/134 (32%), Positives = 79/134 (58%), Gaps = 3/134 (2%)
Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISIL 91
            F+ + L +++L  I   GFEKP+ IQ + I   +    +++AQA++G+GKTA+F+I ++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
           + L  +    + + L+PTRELA+Q+   + +L    N++     GG  +   ++ L    
Sbjct: 67  E-LVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124
Query: 152 HVVSGTPGRVFDMI 165
           ++V GTPGR+ D I
Sbjct: 125 NIVVGTPGRILDHI 138

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 80.9 bits (198), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 44/136 (32%), Positives = 73/136 (53%), Gaps = 5/136 (3%)
Query: 34  FDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS 93
           F +  L+ ++L  ++  G   P+ I+  ++   ++G+D+I QA++GTGKT  F++ I + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 94  LDTQL---RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYG 150
           L       R+ + L L+PTRELA+Q+   + A+   + V   A  GGT   +    L  G
Sbjct: 63  LAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLRG 120
Query: 151 QHVVSGTPGRVFDMIR 166
              V  TPGR  D +R
Sbjct: 121 ADAVVATPGRALDYLR 136

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 92/161 (57%), Gaps = 13/161 (8%)
Query: 23  ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGT 80
           + S++V + S  +   L +++ + I    F   + +QQ++IKPI+  +  DVIA+A++GT
Sbjct: 12  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71
Query: 81  GKTATFSISILQSLDTQLRETQVLC----LSPTRELAVQIQKVVLALGDFMN--VQCHAC 134
           GKT  F I I Q L     ++Q +     ++PTR+LA+QI+  V  + D MN  ++ +AC
Sbjct: 72  GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHD-MNYGLKKYAC 130
Query: 135 ---IGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGR 171
              +GGT+    + K++    ++V  TPGR+ D++     +
Sbjct: 131 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNK 171

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 92/161 (57%), Gaps = 13/161 (8%)
Query: 23  ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGT 80
           + S++V + S  +   L +++ + I    F   + +QQ++IKPI+  +  DVIA+A++GT
Sbjct: 63  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 122
Query: 81  GKTATFSISILQSLDTQLRETQVLC----LSPTRELAVQIQKVVLALGDFMN--VQCHAC 134
           GKT  F I I Q L     ++Q +     ++PTR+LA+QI+  V  + D MN  ++ +AC
Sbjct: 123 GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHD-MNYGLKKYAC 181
Query: 135 ---IGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGR 171
              +GGT+    + K++    ++V  TPGR+ D++     +
Sbjct: 182 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNK 222

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 73.9 bits (180), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 80/153 (52%), Gaps = 18/153 (11%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
           + +F ++ + E ++  I    + +P+ +Q+ +I  I + RD++A AQ+G+GKTA F + I
Sbjct: 14  IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPI 73
Query: 91  LQSLDTQ-----LRETQ-------------VLCLSPTRELAVQIQKVVLALGDFMNVQCH 132
           L  + +      LR  +              L L+PTRELAVQI +          V+  
Sbjct: 74  LSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPC 133
Query: 133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
              GG ++ + +R L+ G H++  TPGR+ DM+
Sbjct: 134 VVYGGADIGQQIRDLERGCHLLVATPGRLVDMM 166

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/155 (32%), Positives = 87/155 (56%), Gaps = 13/155 (8%)
Query: 23  ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR--DVIAQAQSGT 80
           + S++V + S  +   L +++ + I    F   + +QQ++IKPI+     DVIA+A++GT
Sbjct: 12  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71
Query: 81  GKTATFSISILQSL-----DTQLRETQVLCLSPTRELAVQIQKVVLALGD----FMNVQC 131
           GKT  F I I Q L     D+Q     V+ ++PTR+LA+QI+  V  + D         C
Sbjct: 72  GKTFAFLIPIFQHLINTKFDSQYMVKAVI-VAPTRDLALQIEAEVKKIHDMNYGLKKYAC 130
Query: 132 HACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMI 165
            + +GGT+    + K++  + ++V  TPGR+ D++
Sbjct: 131 VSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVL 165

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score = 66.2 bits (160), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 80/141 (56%), Gaps = 7/141 (4%)
Query: 27  DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF 86
           +V  ++ F +  L +  L+G+    +   + IQ+++I   ++G+DV+  A++G+GKT  F
Sbjct: 20  NVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAF 79
Query: 87  SISILQSLDTQLRETQ-----VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS 141
            + +L++L  +L+ T      VL +SPTRELA Q  +V+  +G   +      IGG +L 
Sbjct: 80  LVPVLEAL-YRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLK 138
Query: 142 EDLRKLDYGQHVVSGTPGRVF 162
            +  +++   +++  TPGR+ 
Sbjct: 139 HEAERIN-NINILVCTPGRLL 158

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 71/126 (56%), Gaps = 7/126 (5%)
Query: 39  LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
           + E + + I   GF+  + +Q ++I  +++G++V+ +A++G+GKTA ++I IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55
Query: 99  RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP 158
              + L ++PTREL  Q+   +  +G +M+ +     GG      + ++     VV+ TP
Sbjct: 56  -GMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVA-TP 113
Query: 159 GRVFDM 164
           GR+ D+
Sbjct: 114 GRLLDL 119

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 42/129 (32%), Positives = 71/129 (55%), Gaps = 7/129 (5%)
Query: 42  DLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL--R 99
           DLL+ I   G  KP+ IQ ++   I++G D+I  AQ+GTGKT ++ +     LD+Q   R
Sbjct: 30  DLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR 89
Query: 100 ETQ----VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVS 155
           E +    +L L+PTRELA+ ++    +   +  ++     GG N +  +  +  G  ++ 
Sbjct: 90  EQRNGPGMLVLTPTRELALHVEAEC-SKYSYKGLKSICIYGGRNRNGQIEDISKGVDIII 148
Query: 156 GTPGRVFDM 164
            TPGR+ D+
Sbjct: 149 ATPGRLNDL 157

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 64.7 bits (156), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 70/130 (53%), Gaps = 10/130 (7%)
Query: 43  LLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE-T 101
           LL+ I   GF+ P+ IQ ++I  ++ GR+++A A +G+GKT  FSI IL  L     +  
Sbjct: 40  LLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGF 99
Query: 102 QVLCLSPTRELAVQIQKVVLALGDFMNVQCH----ACIGGTNL-SEDLRKLDYGQHVVSG 156
           + L +SPTRELA QI + ++ + +    + H    A +       +  +K D    ++  
Sbjct: 100 RALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFD----ILVT 155
Query: 157 TPGRVFDMIR 166
           TP R+  +++
Sbjct: 156 TPNRLIYLLK 165

>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 72/151 (47%), Gaps = 7/151 (4%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
           V  F       +++  I    F +P+AIQ +     + G D++  AQ+G+GKT ++ +  
Sbjct: 42  VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPA 101
Query: 91  LQSLDTQL---RETQVLCL--SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
           +  ++ Q    R    +CL  +PTRELA Q+Q+V         ++     GG      +R
Sbjct: 102 IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 161
Query: 146 KLDYGQHVVSGTPGRVFDMIRSSQG--RRTT 174
            L+ G  +   TPGR+ D +   +   RRTT
Sbjct: 162 DLERGVEICIATPGRLIDFLECGKTNLRRTT 192

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 43/151 (28%), Positives = 72/151 (47%), Gaps = 7/151 (4%)
Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
           V  F       +++  I    F +P+AIQ +     + G D++  AQ+G+GKT ++ +  
Sbjct: 28  VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPA 87
Query: 91  LQSLDTQL---RETQVLCL--SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
           +  ++ Q    R    +CL  +PTRELA Q+Q+V         ++     GG      +R
Sbjct: 88  IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147
Query: 146 KLDYGQHVVSGTPGRVFDMIRSSQG--RRTT 174
            L+ G  +   TPGR+ D +   +   RRTT
Sbjct: 148 DLERGVEICIATPGRLIDFLECGKTNLRRTT 178

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	178
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	3e-94
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-89
3bor_A	237	Human initiation factor 4A-II; translation initiat	4e-89
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	6e-89
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	2e-87
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	4e-82
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	1e-81
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	2e-79
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	5e-79
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-77
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	2e-74
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	5e-73
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	5e-73
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-69
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-62
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	1e-49
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-48
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	5e-45
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	9e-44
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	2e-43
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-43
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	7e-43
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	7e-41
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-38
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	7e-38
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-37
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-36
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	4e-36
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	5e-35
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	7e-35
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-29
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-04
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	4e-04
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	4e-04
3b6e_A	216	Interferon-induced helicase C domain-containing P;	4e-04

>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 =  278 bits (714), Expect = 3e-94
 Identities = 132/173 (76%), Positives = 150/173 (86%), Gaps = 4/173 (2%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           MA  GS   + +  ED++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQ
Sbjct: 6   MATSGSARKRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQ 65

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+IK I+KGRDVIAQ+QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +
Sbjct: 66  RAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGL 125

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
           LALGD+MNVQCHACIGGTN+ ED+RKLDYGQHVV+GTPGRVFDMIR    RR+
Sbjct: 126 LALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIR----RRS 174

>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 =  266 bits (682), Expect = 2e-89
 Identities = 100/174 (57%), Positives = 124/174 (71%), Gaps = 5/174 (2%)

Query: 1   MAAGGSRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ 60
           M+A     ++   P+ +       S   E+V +FD+M L E LLRGIYAYGFEKPSAIQQ
Sbjct: 9   MSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQ 68

Query: 61  RSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV 120
           R+I P +KG DVIAQAQSGTGKTATF+ISILQ ++  L+ TQ L L+PTRELA QIQKVV
Sbjct: 69  RAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVV 128

Query: 121 LALGDFMNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRSSQGRRT 173
           +ALGD+M   CHACIGGTN+  +++KL     H++ GTPGRVFDM+     RR 
Sbjct: 129 MALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLN----RRY 178

>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 =  259 bits (664), Expect = 4e-89
 Identities = 99/150 (66%), Positives = 117/150 (78%), Gaps = 5/150 (3%)

Query: 25  SEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTA 84
           S   E+V  FD+M L+E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTA
Sbjct: 23  SNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTA 82

Query: 85  TFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL 144
           TF+ISILQ L+ + +ETQ L L+PTRELA QIQKV+LALGD+M   CHACIGGTN+  ++
Sbjct: 83  TFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEM 142

Query: 145 RKLDY-GQHVVSGTPGRVFDMIRSSQGRRT 173
           +KL     H+V GTPGRVFDM+     RR 
Sbjct: 143 QKLQAEAPHIVVGTPGRVFDMLN----RRY 168

>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 =  258 bits (662), Expect = 6e-89
 Identities = 88/153 (57%), Positives = 114/153 (74%), Gaps = 6/153 (3%)

Query: 21  EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
           + +T+ D +VV  FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGT
Sbjct: 4   QIQTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGT 62

Query: 81  GKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNL 140
           GKT TFSI+ LQ +DT ++  Q L L+PTRELA+QIQKVV+AL   M+++ HACIGGT+ 
Sbjct: 63  GKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSF 122

Query: 141 SEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
            ED   L     +V GTPGRVFD I+    RR 
Sbjct: 123 VEDAEGLR-DAQIVVGTPGRVFDNIQ----RRR 150

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score =  260 bits (667), Expect = 2e-87
 Identities = 89/159 (55%), Positives = 116/159 (72%), Gaps = 6/159 (3%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
            D+   + +T+ D +VV  FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+A
Sbjct: 5   TDIEESQIQTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLA 63

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
           QAQSGTGKT TFSI+ LQ +DT ++  Q L L+PTRELA+QIQKVV+AL   M+++ HAC
Sbjct: 64  QAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHAC 123

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
           IGGT+  ED   L     +V GTPGRVFD I+    RR 
Sbjct: 124 IGGTSFVEDAEGLRDA-QIVVGTPGRVFDNIQ----RRR 157

>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 =  247 bits (633), Expect = 4e-82
 Identities = 63/151 (41%), Positives = 95/151 (62%), Gaps = 6/151 (3%)

Query: 25  SEDV--EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGK 82
           ++DV     +TF++  L+ +LL GI+  GFEKPS IQ+ +I   + GRD++A+A++GTGK
Sbjct: 12  TDDVLNTKGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGK 71

Query: 83  TATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE 142
           TA F I  L+ +  +L + Q L + PTRELA+Q  +VV  LG    + C    GGTNL +
Sbjct: 72  TAAFVIPTLEKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRD 131

Query: 143 DLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT 173
           D+ +L+   H++ GTPGRV D+      R+ 
Sbjct: 132 DILRLNETVHILVGTPGRVLDLAS----RKV 158

>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 =  240 bits (615), Expect = 1e-81
 Identities = 64/154 (41%), Positives = 94/154 (61%), Gaps = 3/154 (1%)

Query: 15  EDLSNVEFETSEDVEV-VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVI 73
           +DLS+    T + +    + F+++ L   +L G+ A GFE+PS +Q ++I     G D+I
Sbjct: 6   QDLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLI 65

Query: 74  AQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCH 132
            QA+SGTGKT  FS   L SL  +   TQ+L L+PTRE+AVQI  V+ A+G  M  ++CH
Sbjct: 66  VQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECH 125

Query: 133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
             IGGT LS+D  +L    H+  G+PGR+  +I 
Sbjct: 126 VFIGGTPLSQDKTRLKKC-HIAVGSPGRIKQLIE 158

>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 =  240 bits (616), Expect = 2e-79
 Identities = 51/155 (32%), Positives = 88/155 (56%), Gaps = 6/155 (3%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDV 72
             +  ++ + +  +  V +F+ + L+  LL+G+YA GF +PS IQ+ ++  ++    +++
Sbjct: 8   NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 67

Query: 73  IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQC 131
           IAQ+QSGTGKTA F +++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++ 
Sbjct: 68  IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 127

Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
              + G  L    +     + +V GTPG V D   
Sbjct: 128 AYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCS 159

>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 =  236 bits (603), Expect = 5e-79
 Identities = 51/155 (32%), Positives = 88/155 (56%), Gaps = 6/155 (3%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDV 72
             +  ++ + +  +  V +F+ + L+  LL+G+YA GF +PS IQ+ ++  ++    +++
Sbjct: 75  NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 134

Query: 73  IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQC 131
           IAQ+QSGTGKTA F +++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++ 
Sbjct: 135 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 194

Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
              + G  L    +     + +V GTPG V D   
Sbjct: 195 AYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCS 226

>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 =  238 bits (609), Expect = 1e-77
 Identities = 51/155 (32%), Positives = 88/155 (56%), Gaps = 6/155 (3%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDV 72
             +  ++ + +  +  V +F+ + L+  LL+G+YA GF +PS IQ+ ++  ++    +++
Sbjct: 75  NQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 134

Query: 73  IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQC 131
           IAQ+QSGTGKTA F +++L  ++   +  Q LCLSPT ELA+Q  KV+  +G F   ++ 
Sbjct: 135 IAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKL 194

Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR 166
              + G  L    +     + +V GTPG V D   
Sbjct: 195 AYAVRGNKLERGQKI---SEQIVIGTPGTVLDWCS 226

>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 =  227 bits (581), Expect = 2e-74
 Identities = 54/146 (36%), Positives = 87/146 (59%), Gaps = 10/146 (6%)

Query: 30  VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFS 87
           +  +FD +GL  +LL+GIYA  F+KPS IQ+R++  ++    R++IAQ+QSGTGKTA FS
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62

Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
           +++L  ++ +    Q +CL+P+RELA Q  +VV  +G F  +     +  +      +  
Sbjct: 63  LTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSF----EKNK 118

Query: 148 DYGQHVVSGTPGRVFDMIRSSQGRRT 173
                V+ GTPG V D++R    R+ 
Sbjct: 119 QINAQVIVGTPGTVLDLMR----RKL 140

>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 =  224 bits (572), Expect = 5e-73
 Identities = 54/140 (38%), Positives = 75/140 (53%), Gaps = 2/140 (1%)

Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
            + S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F +
Sbjct: 5   HMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL 64

Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKL 147
           + LQ L+    +  VL +  TRELA QI K       +M NV+     GG ++ +D   L
Sbjct: 65  ATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVL 124

Query: 148 DYG-QHVVSGTPGRVFDMIR 166
                H+V GTPGR+  + R
Sbjct: 125 KKNCPHIVVGTPGRILALAR 144

>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 =  217 bits (556), Expect = 5e-73
 Identities = 55/143 (38%), Positives = 90/143 (62%), Gaps = 5/143 (3%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           + F++  L+ +LL GI+  G+EKPS IQ+ SI   + GRD++A+A++GTGK+  + I +L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYG 150
           + LD +    Q + + PTRELA+Q+ ++ + +   M   +  A  GGTNL +D+ +LD  
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 151 QHVVSGTPGRVFDMIRSSQGRRT 173
            HVV  TPGR+ D+I+    +  
Sbjct: 123 VHVVIATPGRILDLIK----KGV 141

>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 =  209 bits (533), Expect = 2e-69
 Identities = 55/148 (37%), Positives = 77/148 (52%), Gaps = 2/148 (1%)

Query: 21  EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
           + + S      S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG 
Sbjct: 3   DVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGM 62

Query: 81  GKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTN 139
           GKTA F ++ LQ L+    +  VL +  TRELA QI K       +M NV+     GG +
Sbjct: 63  GKTAVFVLATLQQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS 122

Query: 140 LSEDLRKLDYG-QHVVSGTPGRVFDMIR 166
           + +D   L     H+V GTPGR+  + R
Sbjct: 123 IKKDEEVLKKNCPHIVVGTPGRILALAR 150

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  158 bits (402), Expect = 1e-49
 Identities = 47/139 (33%), Positives = 74/139 (53%), Gaps = 4/139 (2%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           + F     +  ++  I    F KP+ IQ+R I   ++G  ++ Q+Q+GTGKT  + + I+
Sbjct: 4   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 63

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDLRKL 147
           + +  +  E Q +  +PTRELA QI    L +  F      +     IGGT+  + L KL
Sbjct: 64  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 123

Query: 148 DYGQHVVSGTPGRVFDMIR 166
           +   H+V GTPGR+ D IR
Sbjct: 124 NVQPHIVIGTPGRINDFIR 142

>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 =  157 bits (398), Expect = 1e-48
 Identities = 50/156 (32%), Positives = 81/156 (51%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIA 74
            D      +   + E   TF ++G+ + L       G+ KP+ IQ  +I   ++GRD+I 
Sbjct: 26  HDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIG 85

Query: 75  QAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC 134
            A++G+GKT  F++ IL +L    +    L L+PTRELA QI +   ALG  + VQ    
Sbjct: 86  LAETGSGKTGAFALPILNALLETPQRLFALVLTPTRELAFQISEQFEALGSSIGVQSAVI 145

Query: 135 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG 170
           +GG +       L    H++  TPGR+ D + +++G
Sbjct: 146 VGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKG 181

>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 =  146 bits (371), Expect = 5e-45
 Identities = 45/137 (32%), Positives = 74/137 (54%), Gaps = 5/137 (3%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQ 92
            F +  L+ ++L  ++  G   P+ IQ  ++   ++G+D+I QA++GTGKT  F++ I +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 93  SLDT---QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY 149
            L     + R+ + L L+PTRELA+Q+   + A+   + V   A  GGT   +    L  
Sbjct: 62  RLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVV--AVYGGTGYGKQKEALLR 119

Query: 150 GQHVVSGTPGRVFDMIR 166
           G   V  TPGR  D +R
Sbjct: 120 GADAVVATPGRALDYLR 136

>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 =  151 bits (384), Expect = 9e-44
 Identities = 47/164 (28%), Positives = 85/164 (51%), Gaps = 11/164 (6%)

Query: 23  ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPI--VKGRDVIAQAQSGT 80
           + S++V + S  +   L +++ + I    F   + +QQ++IKPI   +  DVIA+A++GT
Sbjct: 12  DNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGT 71

Query: 81  GKTATFSISILQSLDTQLRE----TQVLCLSPTRELAVQIQKVVLALGDFM----NVQCH 132
           GKT  F I I Q L     +     + + ++PTR+LA+QI+  V  + D         C 
Sbjct: 72  GKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACV 131

Query: 133 ACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRRTTN 175
           + +GGT+    + K++    ++V  TPGR+ D++     +    
Sbjct: 132 SLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRF 175

>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 =  150 bits (381), Expect = 2e-43
 Identities = 48/181 (26%), Positives = 89/181 (49%), Gaps = 11/181 (6%)

Query: 6   SRITKKVIPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP 65
               K    + +   + + S++V + S  +   L +++ + I    F   + +QQ++IKP
Sbjct: 46  VHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKP 105

Query: 66  I--VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE----TQVLCLSPTRELAVQIQKV 119
           I   +  DVIA+A++GTGKT  F I I Q L     +     + + ++PTR+LA+QI+  
Sbjct: 106 ILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAE 165

Query: 120 VLALGDF----MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRRTT 174
           V  + D         C + +GGT+    + K++    ++V  TPGR+ D++     +   
Sbjct: 166 VKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFR 225

Query: 175 N 175
            
Sbjct: 226 F 226

>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 =  143 bits (362), Expect = 3e-43
 Identities = 40/154 (25%), Positives = 80/154 (51%), Gaps = 5/154 (3%)

Query: 21  EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
           +     +V  ++ F +  L +  L+G+    +   + IQ+++I   ++G+DV+  A++G+
Sbjct: 14  QNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGS 73

Query: 81  GKTATFSISILQSLD----TQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG 136
           GKT  F + +L++L     T      VL +SPTRELA Q  +V+  +G   +      IG
Sbjct: 74  GKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIG 133

Query: 137 GTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG 170
           G +L  +  +++   +++  TPGR+   +  +  
Sbjct: 134 GKDLKHEAERIN-NINILVCTPGRLLQHMDETVS 166

>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 =  145 bits (368), Expect = 7e-43
 Identities = 45/142 (31%), Positives = 81/142 (57%), Gaps = 7/142 (4%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISIL 91
            F+ + L +++L  I   GFEKP+ IQ + I   +    +++AQA++G+GKTA+F+I ++
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
           + ++      + + L+PTRELA+Q+   + +L    N++     GG  +   ++ L    
Sbjct: 67  ELVNEN-NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 124

Query: 152 HVVSGTPGRVFDMIRSSQGRRT 173
           ++V GTPGR+ D I     R T
Sbjct: 125 NIVVGTPGRILDHIN----RGT 142

>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 =  137 bits (347), Expect = 7e-41
 Identities = 50/162 (30%), Positives = 85/162 (52%), Gaps = 6/162 (3%)

Query: 15  EDLSNVEFETSEDVEVVSTFDNMG--LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDV 72
           E                ++F ++   + E+ L+ I   GF   + IQ +SI+P+++GRD+
Sbjct: 35  ESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDL 94

Query: 73  IAQAQSGTGKTATFSISILQSL----DTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN 128
           +A A++G+GKT  F I  ++ +          T VL LSPTRELA+Q   V+  L     
Sbjct: 95  LAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHV 154

Query: 129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG 170
                 +GG+N S + +KL  G +++  TPGR+ D ++++ G
Sbjct: 155 HTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPG 196

>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 =  130 bits (330), Expect = 2e-38
 Identities = 47/164 (28%), Positives = 77/164 (46%), Gaps = 16/164 (9%)

Query: 24  TSEDVEV---VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGT 80
           T  D      +  FD + L   +   I    +++P+ IQ+ +I  I++ RD++A AQ+G+
Sbjct: 12  TGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGS 71

Query: 81  GKTATFSISILQSLDTQ---------LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC 131
           GKTA F I I+  L  Q             + L L+PTRELA+QI            ++ 
Sbjct: 72  GKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRS 131

Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
               GG +    +R++  G H++  TPGR+ D I     +   +
Sbjct: 132 CVVYGGADTHSQIREVQMGCHLLVATPGRLVDFI----EKNKIS 171

>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 =  131 bits (333), Expect = 7e-38
 Identities = 34/128 (26%), Positives = 70/128 (54%), Gaps = 7/128 (5%)

Query: 39  LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
           + E + + I   GF+  + +Q ++I  +++G++V+ +A++G+GKTA ++I IL+      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE------ 54

Query: 99  RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP 158
              + L ++PTREL  Q+   +  +G +M+ +     GG      + ++     +V  TP
Sbjct: 55  LGMKSLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATP 113

Query: 159 GRVFDMIR 166
           GR+ D+  
Sbjct: 114 GRLLDLWS 121

>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 =  132 bits (334), Expect = 2e-37
 Identities = 52/174 (29%), Positives = 81/174 (46%), Gaps = 21/174 (12%)

Query: 18  SNVEFETSEDVEV----------VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV 67
           S + F    ++ V          +  F +  LR+ ++  +   G++ P+ IQ+ SI P++
Sbjct: 32  SGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSI-PVI 90

Query: 68  -KGRDVIAQAQSGTGKTATFSISILQSLDTQ--LRETQ---VLCLSPTRELAVQIQKVVL 121
             GRD++A AQ+G+GKTA F + IL  L       E     V+ +SPTRELA+QI     
Sbjct: 91  SSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEAR 150

Query: 122 ALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
                  ++     GGT+       +  G HVV  TPGR+ D +     R    
Sbjct: 151 KFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFV----DRTFIT 200

>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 =  126 bits (318), Expect = 1e-36
 Identities = 40/147 (27%), Positives = 73/147 (49%), Gaps = 6/147 (4%)

Query: 31  VSTFDNM----GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF 86
           ++TF  +     +   LL+ I   GF+ P+ IQ ++I  ++ GR+++A A +G+GKT  F
Sbjct: 24  IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAF 83

Query: 87  SISILQSLDTQLRET-QVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL- 144
           SI IL  L     +  + L +SPTRELA QI + ++ + +    + H        ++   
Sbjct: 84  SIPILMQLKQPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFG 143

Query: 145 RKLDYGQHVVSGTPGRVFDMIRSSQGR 171
            K      ++  TP R+  +++     
Sbjct: 144 PKSSKKFDILVTTPNRLIYLLKQDPPG 170

>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 =  124 bits (314), Expect = 4e-36
 Identities = 39/140 (27%), Positives = 66/140 (47%), Gaps = 5/140 (3%)

Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISI 90
           V  F       +++  I    F +P+AIQ +     + G D++  AQ+G+GKT ++ +  
Sbjct: 28  VLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPA 87

Query: 91  LQSLDTQ--LRETQ---VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR 145
           +  ++ Q  L        L L+PTRELA Q+Q+V         ++     GG      +R
Sbjct: 88  IVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR 147

Query: 146 KLDYGQHVVSGTPGRVFDMI 165
            L+ G  +   TPGR+ D +
Sbjct: 148 DLERGVEICIATPGRLIDFL 167

>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 =  121 bits (306), Expect = 5e-35
 Identities = 43/152 (28%), Positives = 72/152 (47%), Gaps = 12/152 (7%)

Query: 31  VSTF-DNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSIS 89
              F D      DLL+ I   G  KP+ IQ ++   I++G D+I  AQ+GTGKT ++ + 
Sbjct: 18  TCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMP 77

Query: 90  ILQSLDTQLRETQ------VLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSED 143
               LD+Q    +      +L L+PTRELA+ ++        +  ++     GG N +  
Sbjct: 78  GFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQ 136

Query: 144 LRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
           +  +  G  ++  TPGR+ D+        + N
Sbjct: 137 IEDISKGVDIIIATPGRLNDLQ----MNNSVN 164

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  125 bits (316), Expect = 7e-35
 Identities = 48/164 (29%), Positives = 82/164 (50%), Gaps = 24/164 (14%)

Query: 31  VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV-KGRDVIAQAQSGTGKTATFSIS 89
           + +F ++ + E ++  I    + +P+ +Q+ +I PI+ + RD++A AQ+G+GKTA F + 
Sbjct: 14  IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAI-PIIKEKRDLMACAQTGSGKTAAFLLP 72

Query: 90  ILQSLDTQ---------------LRETQ---VLCLSPTRELAVQIQKVVLALGDFMNVQC 131
           IL  + +                 R  Q    L L+PTRELAVQI +          V+ 
Sbjct: 73  ILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRP 132

Query: 132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRTTN 175
               GG ++ + +R L+ G H++  TPGR+ DM+     R    
Sbjct: 133 CVVYGGADIGQQIRDLERGCHLLVATPGRLVDMM----ERGKIG 172

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  111 bits (279), Expect = 1e-29
 Identities = 23/129 (17%), Positives = 41/129 (31%), Gaps = 8/129 (6%)

Query: 39  LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL 98
             ED          +  +  Q+   K IV+G+     A +G GKT    ++ L       
Sbjct: 6   EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR--- 62

Query: 99  RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVV 154
           +  +   + PT  L  Q  + +  L D   V+           E  +          H++
Sbjct: 63  KGKKSALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHIL 121

Query: 155 SGTPGRVFD 163
             +   V  
Sbjct: 122 VFSTQFVSK 130

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 41.1 bits (95), Expect = 1e-04
 Identities = 19/121 (15%), Positives = 43/121 (35%), Gaps = 2/121 (1%)

Query: 50  YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLS 107
           Y  +K  + Q    +P + G++ +  A +G+GKT  +              R+ +V+ L+
Sbjct: 244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLA 303

Query: 108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS 167
               +  Q + V     +          G    +  + K+     ++  TP  + +    
Sbjct: 304 TKVPVYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFED 363

Query: 168 S 168
            
Sbjct: 364 G 364

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 40.3 bits (93), Expect = 2e-04
 Identities = 20/117 (17%), Positives = 44/117 (37%), Gaps = 2/117 (1%)

Query: 54  KPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLSPTRE 111
           KP   Q     P +KG++ I  A +G GKT  +            Q ++ +V+  +    
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIP 72

Query: 112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
           +  Q + V     +    +     G T  +  + ++     ++  TP  + + ++  
Sbjct: 73  VYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKG 129

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 39.2 bits (90), Expect = 4e-04
 Identities = 18/117 (15%), Positives = 41/117 (35%), Gaps = 2/117 (1%)

Query: 54  KPSAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLSPTRE 111
           K  + Q    +P + G++ +  A +G+GKT  +              R+ +V+ L+    
Sbjct: 7   KARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVP 66

Query: 112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
           +  Q + V     +          G    +  + K+     ++  TP  + +     
Sbjct: 67  VYEQQKNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDG 123

>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 = 39.0 bits (90), Expect = 4e-04
 Identities = 22/109 (20%), Positives = 42/109 (38%), Gaps = 3/109 (2%)

Query: 60  QRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV 119
           Q  I    K  + +    +G GKT    +     L       +VL L+PT+ L +Q  + 
Sbjct: 14  QEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGG--KVLMLAPTKPLVLQHAES 71

Query: 120 VLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS 168
              L +    +  A  G  +  E  +     + +V+ TP  + + + + 
Sbjct: 72  FRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVA-TPQTIENDLLAG 119

>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 = 38.3 bits (89), Expect = 4e-04
 Identities = 18/117 (15%), Positives = 43/117 (36%), Gaps = 3/117 (2%)

Query: 59  QQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQ---VLCLSPTRELAVQ 115
           Q    +P ++G+++I    +G+GKT          LD + + ++   V+ L     L  Q
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQ 97

Query: 116 IQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR 172
           + +           +     G T L     ++     ++  T   + + + + +   
Sbjct: 98  LFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGE 154

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	178
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.98
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.97
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.97
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.97
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.97
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.97
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.97
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.97
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.97
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.97
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.97
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.97
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.97
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.97
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.97
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.96
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.96
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.95
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.95
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.94
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.94
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.94
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.94
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.94
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.93
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.93
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.92
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.92
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.9
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.88
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.88
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.88
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.88
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.87
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.86
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.86
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.86
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.86
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.86
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.86
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.85
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.84
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.84
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.83
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.82
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.82
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.8
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.8
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.8
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.76
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.74
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.73
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.72
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.7
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.7
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.68
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.68
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.63
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.59
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.58
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.53
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.52
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.47
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.46
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.41
3h1t_A	590	Type I site-specific restriction-modification syst	99.41
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.39
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.35
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.32
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.22
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.19
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.16
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.15
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.07
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.04
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.02
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.95
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.83
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.45
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.96
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.87
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.85
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.83
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.74
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.68
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.62
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.56
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	97.51
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	97.31
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.24
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	97.2
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.88
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.85
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	96.3
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	96.24
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	96.05
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	96.02
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	95.89
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.78
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	95.58
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	95.28
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	95.17
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.07
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	94.91
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	94.85
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	94.83
3co5_A	143	Putative two-component system transcriptional RES	94.69
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	94.67
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	94.65
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	94.51
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	94.5
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	94.42
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	94.35
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.23
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	94.01
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	93.84
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	93.73
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	93.7
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.62
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	93.58
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	93.57
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	93.54
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.31
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	93.3
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.23
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	93.14
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	93.04
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	92.86
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	92.82
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	92.74
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	92.67
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	92.47
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	92.37
2qgz_A	308	Helicase loader, putative primosome component; str	92.33
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	92.26
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	91.48
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.24
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	92.2
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	92.1
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	92.07
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	92.07
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	92.05
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	91.96
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	91.95
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	91.88
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	91.74
2chg_A	226	Replication factor C small subunit; DNA-binding pr	91.73
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	91.71
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	91.61
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	91.49
2r44_A	331	Uncharacterized protein; putative ATPase, structur	91.45
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	91.43
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	91.41
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	91.41
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	91.4
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	91.37
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	91.25
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.25
3bos_A	242	Putative DNA replication factor; P-loop containing	91.24
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	91.19
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	91.02
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	90.99
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	90.93
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	90.86
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	90.83
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	90.78
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	90.75
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	90.66
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	90.65
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	90.63
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.63
1yks_A	440	Genome polyprotein [contains: flavivirin protease	90.62
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	90.5
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	90.47
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	90.45
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	90.43
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	90.4
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	90.37
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	90.37
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	90.37
2eyu_A	261	Twitching motility protein PILT; pilus retraction	90.35
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	90.27
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	90.2
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	90.19
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	90.17
2cvh_A	220	DNA repair and recombination protein RADB; filamen	90.16
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	89.99
1p9r_A	418	General secretion pathway protein E; bacterial typ	89.9
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	89.86
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	89.84
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	89.8
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	89.74
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	89.74
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	89.72
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	89.71
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.68
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	89.68
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	89.6
3ice_A	422	Transcription termination factor RHO; transcriptio	89.52
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	89.48
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	89.41
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	89.38
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	89.28
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.19
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	89.17
2z43_A	324	DNA repair and recombination protein RADA; archaea	89.01
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	88.96
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	88.86
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	88.62
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	88.53
1tue_A	212	Replication protein E1; helicase, replication, E1E	88.46
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	88.42
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	88.42
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	88.38
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	88.34
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	88.32
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	88.31
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	88.25
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	88.23
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	88.21
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	88.17
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	88.14
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.05
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	88.03
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	87.99
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	87.98
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	87.93
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	87.74
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	87.72
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	87.67
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	87.61
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	87.58
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	87.49
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	87.44
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	87.34
2ewv_A	372	Twitching motility protein PILT; pilus retraction	87.31
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	87.24
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	87.22
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	87.07
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	87.02
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	87.0
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	86.96
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	86.96
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	86.94
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	86.91
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	86.9
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	86.88
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	86.85
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	86.81
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	86.68
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	86.55
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	86.39
1u94_A	356	RECA protein, recombinase A; homologous recombinat	86.35
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	86.31
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	86.19
4gl2_A	699	Interferon-induced helicase C domain-containing P;	86.14
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	86.09
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	86.03
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	85.89
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	85.89
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	85.83
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	85.8
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	85.78
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	85.77
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	85.73
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	85.71
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	85.69
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	85.66
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	85.63
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	85.55
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	85.48
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	85.47
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	85.42
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	85.23
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	85.22
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	85.15
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	85.13
2r6a_A	454	DNAB helicase, replicative helicase; replication,	85.07
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	85.03
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	85.01
1via_A	175	Shikimate kinase; structural genomics, transferase	84.98
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	84.87
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	84.75
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	84.69
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	84.67
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	84.67
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	84.63
2chq_A	319	Replication factor C small subunit; DNA-binding pr	84.63
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	84.55
4a74_A	231	DNA repair and recombination protein RADA; hydrola	84.5
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	84.49
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	84.49
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	84.49
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	84.47
1xp8_A	366	RECA protein, recombinase A; recombination, radior	84.45
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	84.24
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	84.17
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	84.13
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	84.12
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	84.02
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	84.01
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	83.96
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	83.96
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	83.84
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	83.81
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	83.75
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	83.72
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	83.7
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	83.58
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	83.51
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	83.5
3io5_A	333	Recombination and repair protein; storage dimer, i	83.45
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	83.44
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	83.42
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	83.34
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	83.33
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	83.32
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	83.27
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	83.14
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	83.11
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	83.11
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	83.11
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	83.1
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	82.99
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	82.99
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	82.92
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	82.84
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	82.84
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	82.82
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	82.8
3kta_A	182	Chromosome segregation protein SMC; structural mai	82.77
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	82.75
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	82.66
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	82.64
1sgw_A	214	Putative ABC transporter; structural genomics, P p	82.63
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	82.53
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	82.53
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	82.48
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	82.42
3pvs_A	447	Replication-associated recombination protein A; ma	82.32
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	82.27
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	82.26
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	82.24
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	82.24
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	82.23
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	82.14
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	82.11
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	82.11
2ghi_A	260	Transport protein; multidrug resistance protein, M	82.04
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	82.03
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	81.89
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	81.77
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	81.76
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	81.7
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	81.62
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	81.61
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	81.54
1g6h_A	257	High-affinity branched-chain amino acid transport	81.5
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	81.49
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	81.47
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	81.44
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	81.39
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	81.36
1ji0_A	240	ABC transporter; ATP binding protein, structural g	81.26
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	81.23
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	81.16
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	81.14
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	81.13
1b0u_A	262	Histidine permease; ABC transporter, transport pro	81.12
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	81.12
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	81.05
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	80.98
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	80.95
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	80.94
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	80.93
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	80.87
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	80.86
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	80.82
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	80.76
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	80.73
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	80.68
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	80.65
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	80.65
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	80.62
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	80.62
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	80.53
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	80.46
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	80.38
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	80.37
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	80.37
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	80.34
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	80.25
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	80.23
2vli_A	183	Antibiotic resistance protein; transferase, tunica	80.21
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	80.18
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	80.18
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	80.11
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	80.09
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	80.08

>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=6.3e-32  Score=206.90  Aligned_cols=153  Identities=25%  Similarity=0.406  Sum_probs=139.1

Q ss_pred             cccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc--
Q psy9277          20 VEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ--   97 (178)
Q Consensus        20 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~--   97 (178)
                      +.+.....+.+..+|+++++++.+++++.+.||.+|+++|.++|+.+++|+|+++++|||||||++|++|++..+...  
T Consensus        17 i~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~   96 (242)
T 3fe2_A           17 ITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF   96 (242)
T ss_dssp             EEEESSCCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCC
T ss_pred             eEEeCCCCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccc
Confidence            444556678889999999999999999999999999999999999999999999999999999999999999988643  


Q ss_pred             ---CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277          98 ---LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus        98 ---~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                         ..++++||++||++|+.|+++.++.+....++++..++|+.+...+...+.++++|+|+||++|.+++.++....
T Consensus        97 ~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~  174 (242)
T 3fe2_A           97 LERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNL  174 (242)
T ss_dssp             CCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHHTSCCC
T ss_pred             cccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCCc
Confidence               346789999999999999999999999888999999999999998888888889999999999999998776543

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.98  E-value=3.3e-31  Score=218.68  Aligned_cols=150  Identities=33%  Similarity=0.465  Sum_probs=137.0

Q ss_pred             cccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC---
Q psy9277          22 FETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL---   98 (178)
Q Consensus        22 ~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~---   98 (178)
                      +...+.+.+..+|++++|++.++++|+++||.+|+++|.++||.+++|+|+++++|||||||++|++|+++.+....   
T Consensus        46 ~~~~~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~  125 (434)
T 2db3_A           46 VTGSDVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHEL  125 (434)
T ss_dssp             EESSSCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCC
T ss_pred             ecCCCCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhccccc
Confidence            34455567889999999999999999999999999999999999999999999999999999999999999887543   


Q ss_pred             --CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277          99 --RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus        99 --~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                        .++++||++||++||.|+++.+++++...++++..++|+.+...+...+..+++|+|+||++|.+++.++...
T Consensus       126 ~~~~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~  200 (434)
T 2db3_A          126 ELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFIT  200 (434)
T ss_dssp             CTTCCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCC
T ss_pred             ccCCccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcc
Confidence              3579999999999999999999999988899999999999998888888889999999999999999877654

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.97  E-value=1.5e-30  Score=200.44  Aligned_cols=142  Identities=34%  Similarity=0.550  Sum_probs=132.0

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      ...+..+|+++++++.++++|+++||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....+.+++|+
T Consensus        38 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil  117 (249)
T 3ber_A           38 EEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVL  117 (249)
T ss_dssp             HHHHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEE
T ss_pred             cccccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999998877667899999


Q ss_pred             cCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         107 SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       107 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      +||++|+.|+++.++.+....++++..++|+.....+...+..+++|+|+||++|.+++.+.
T Consensus       118 ~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~  179 (249)
T 3ber_A          118 TPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENT  179 (249)
T ss_dssp             CSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHS
T ss_pred             eCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcC
Confidence            99999999999999999988899999999999888877777788999999999999998863

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.97  E-value=8.8e-31  Score=200.03  Aligned_cols=151  Identities=64%  Similarity=0.985  Sum_probs=121.5

Q ss_pred             ccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCC
Q psy9277          21 EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRE  100 (178)
Q Consensus        21 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~  100 (178)
                      ....++.+++..+|++++++++++++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....+
T Consensus        19 ~~~~~~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~~~   98 (237)
T 3bor_A           19 GVIESNWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKE   98 (237)
T ss_dssp             --------CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTSCS
T ss_pred             CcccCCCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCC
Confidence            33445567788999999999999999999999999999999999999999999999999999999999999988765567


Q ss_pred             ceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCC-CcEEEeChHHHHHHHHcCCCC
Q psy9277         101 TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYG-QHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~-~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      .+++|++||++|+.|+++.++.++...++.+..++|+.....+...+..+ ++|+|+||++|.+++.++...
T Consensus        99 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~  170 (237)
T 3bor_A           99 TQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLS  170 (237)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSC
T ss_pred             ceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcC
Confidence            79999999999999999999999988889999999998877776666655 899999999999999876544

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.97  E-value=3.5e-30  Score=192.05  Aligned_cols=140  Identities=39%  Similarity=0.726  Sum_probs=129.4

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      .+|++++++++++++|.++||.+|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....+.+++|++|+++
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            57999999999999999999999999999999999999999999999999999999999998876666789999999999


Q ss_pred             HHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         112 LAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      |+.|+++.++.+.... ++++..+.|+....++...+..+++|+|+||++|.+++.++...
T Consensus        83 L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~  143 (206)
T 1vec_A           83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAK  143 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcC
Confidence            9999999999998877 78899999999988887788888999999999999999876544

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.97  E-value=7.6e-31  Score=207.24  Aligned_cols=139  Identities=37%  Similarity=0.654  Sum_probs=123.8

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEE
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVL  104 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~l  104 (178)
                      +.....+|++++|++.++++|.++||..|+++|.++||.++.|  +|+++++|||||||++|++|+++.+.....++++|
T Consensus        87 p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~l  166 (300)
T 3fmo_B           87 PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCL  166 (300)
T ss_dssp             CCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEE
T ss_pred             CcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEE
Confidence            3445789999999999999999999999999999999999997  99999999999999999999999998777778999


Q ss_pred             EEcCcHHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         105 CLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       105 il~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      |++||++||.|+++.++.+.... ++.+..++|+......   ...+++|+||||++|++++.+.
T Consensus       167 il~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~TP~~l~~~l~~~  228 (300)
T 3fmo_B          167 CLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKL  228 (300)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTT
T ss_pred             EEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhh---hcCCCCEEEECHHHHHHHHHhc
Confidence            99999999999999999998764 6888888888765432   2457899999999999999763

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.97  E-value=1.4e-30  Score=196.48  Aligned_cols=142  Identities=33%  Similarity=0.551  Sum_probs=127.6

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      +..+|++++++++++++++++||.+|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....+.+++|++||
T Consensus         2 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt   81 (219)
T 1q0u_A            2 AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPT   81 (219)
T ss_dssp             --CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             CCCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCc
Confidence            34689999999999999999999999999999999999999999999999999999999999998766667899999999


Q ss_pred             HHHHHHHHHHHHHhccCC----CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         110 RELAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      ++|+.|+++.++++....    ++.+..++|+.+.......+..+++|+|+||++|.+++.++...
T Consensus        82 ~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~  147 (219)
T 1q0u_A           82 RELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALD  147 (219)
T ss_dssp             HHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCC
Confidence            999999999999998776    78888899998877666666668999999999999999876554

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.97  E-value=3.1e-30  Score=195.51  Aligned_cols=149  Identities=28%  Similarity=0.436  Sum_probs=126.4

Q ss_pred             cccccccccccccc-CCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----
Q psy9277          23 ETSEDVEVVSTFDN-MGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----   97 (178)
Q Consensus        23 ~~~~~~~~~~~f~~-~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----   97 (178)
                      +....+++..+|++ ++++++++++|.+.||.+|+++|.++++.+++|+|+++++|||+|||++|++|++..+...    
T Consensus        10 ~~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~   89 (228)
T 3iuy_A           10 EKRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR   89 (228)
T ss_dssp             SCCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC------
T ss_pred             ccCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchh
Confidence            34456788899999 8999999999999999999999999999999999999999999999999999999887532    


Q ss_pred             --CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277          98 --LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus        98 --~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                        ..+++++|++||++|+.|+++.++.+. ..++++..++|+.....+...+.++++|+|+||++|.+++.+.....
T Consensus        90 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~  165 (228)
T 3iuy_A           90 EQRNGPGMLVLTPTRELALHVEAECSKYS-YKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNL  165 (228)
T ss_dssp             ---CCCSEEEECSSHHHHHHHHHHHHHHC-CTTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCC
T ss_pred             hccCCCcEEEEeCCHHHHHHHHHHHHHhc-ccCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCc
Confidence              256789999999999999999999986 45888999999998888777788889999999999999988776543

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.97  E-value=2.4e-30  Score=199.09  Aligned_cols=145  Identities=32%  Similarity=0.521  Sum_probs=131.6

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC---------
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL---------   98 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~---------   98 (178)
                      .++..+|+++++++.++++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....         
T Consensus        19 ~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~   98 (253)
T 1wrb_A           19 TNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKT   98 (253)
T ss_dssp             CSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CC
T ss_pred             CCccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhcccccccccc
Confidence            34788999999999999999999999999999999999999999999999999999999999999886432         


Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      .++++||++||++|+.|+++.++.+....++++..++|+.....+...+..+++|+|+||++|.+++.++...+
T Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~  172 (253)
T 1wrb_A           99 AYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISL  172 (253)
T ss_dssp             BCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCC
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCCh
Confidence            24689999999999999999999998888899999999998888878888889999999999999998776543

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.97  E-value=1.1e-29  Score=192.95  Aligned_cols=144  Identities=42%  Similarity=0.606  Sum_probs=126.9

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      .+.+..+|++++++++++++|++.||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....+.++||+
T Consensus        19 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil   98 (230)
T 2oxc_A           19 LLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILIL   98 (230)
T ss_dssp             -----CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEE
T ss_pred             CCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999988766667899999


Q ss_pred             cCcHHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         107 SPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       107 ~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +|+++|+.|+++.++.+.... ++++..+.|+....++...+. +++|+|+||++|.+++.++...
T Consensus        99 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~Iiv~Tp~~l~~~~~~~~~~  163 (230)
T 2oxc_A           99 APTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK-KCHIAVGSPGRIKQLIELDYLN  163 (230)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT-SCSEEEECHHHHHHHHHTTSSC
T ss_pred             eCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc-CCCEEEECHHHHHHHHhcCCcc
Confidence            999999999999999998765 889999999998877766554 7999999999999999876544

>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=1.3e-29  Score=206.60  Aligned_cols=158  Identities=80%  Similarity=1.207  Sum_probs=142.8

Q ss_pred             CCCCCCcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHH
Q psy9277          14 PEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQS   93 (178)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~   93 (178)
                      ..+......+.++++++..+|+++++++.++++|.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.
T Consensus        19 ~~~~~~~~~~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~   98 (410)
T 2j0s_A           19 EEDMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC   98 (410)
T ss_dssp             -CCSSSCCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             cccCcccccCCCCCccCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHH
Confidence            34556666777777788899999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277          94 LDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus        94 l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +.....+.++||++|+++|+.|+++.++.+....++++..+.|+.....+...+..+++|+|+||++|.+++.++...
T Consensus        99 l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~  176 (410)
T 2j0s_A           99 LDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLR  176 (410)
T ss_dssp             CCTTSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSC
T ss_pred             HhhccCCceEEEEcCcHHHHHHHHHHHHHHhccCCeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCcc
Confidence            765556789999999999999999999999988899999999999998888888788999999999999999876544

>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=1.5e-29  Score=191.03  Aligned_cols=144  Identities=59%  Similarity=0.908  Sum_probs=123.2

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      ..++..+|+++++++.+++.+.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....+.+++|+
T Consensus         9 ~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil   88 (224)
T 1qde_A            9 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALML   88 (224)
T ss_dssp             CCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEE
T ss_pred             cCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEE
Confidence            44567889999999999999999999999999999999999999999999999999999999999998776677899999


Q ss_pred             cCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         107 SPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       107 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +|+++|+.|+++.++.+....++++..+.|+....++...+.+ ++|+|+||++|.+++.++...
T Consensus        89 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~  152 (224)
T 1qde_A           89 APTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFR  152 (224)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSC
T ss_pred             ECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcc
Confidence            9999999999999999998889999999999887776655554 899999999999999876544

>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=2e-29  Score=205.48  Aligned_cols=151  Identities=30%  Similarity=0.461  Sum_probs=135.6

Q ss_pred             ccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC-
Q psy9277          21 EFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR-   99 (178)
Q Consensus        21 ~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~-   99 (178)
                      .......+.+..+|++++|++.++++|..+||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+..... 
T Consensus         4 ~~~~~~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~   83 (417)
T 2i4i_A            4 EATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPG   83 (417)
T ss_dssp             EEESTTCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCC
T ss_pred             ccCCCcCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhcccc
Confidence            3344455677889999999999999999999999999999999999999999999999999999999999998765322 


Q ss_pred             -----------------CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHH
Q psy9277         100 -----------------ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       100 -----------------~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~  162 (178)
                                       ++++||++||++|+.|+++.++.+....++++..++|+.....+...+..+++|+|+||++|.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~  163 (417)
T 2i4i_A           84 EALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLV  163 (417)
T ss_dssp             HHHHHHHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHH
T ss_pred             chhhccccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCCceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHH
Confidence                             268999999999999999999999988899999999999998888888888999999999999


Q ss_pred             HHHHcCCCC
Q psy9277         163 DMIRSSQGR  171 (178)
Q Consensus       163 ~~l~~~~~~  171 (178)
                      +++.++...
T Consensus       164 ~~l~~~~~~  172 (417)
T 2i4i_A          164 DMMERGKIG  172 (417)
T ss_dssp             HHHHTTSBC
T ss_pred             HHHHcCCcC
Confidence            999876543

>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=9.2e-29  Score=188.31  Aligned_cols=140  Identities=28%  Similarity=0.502  Sum_probs=124.6

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----CCCceE
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----LRETQV  103 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----~~~~~~  103 (178)
                      ..+..+|+++++++.++++|.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+...    ..+.++
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            4567889999999999999999999999999999999999999999999999999999999999987642    245789


Q ss_pred             EEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         104 LCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       104 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      +|++||++|+.|+++.++.+....++++..++|+.....+...+ .+++|+|+||++|.+++.+.
T Consensus       101 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~  164 (236)
T 2pl3_A          101 LIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDET  164 (236)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHC
T ss_pred             EEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhc
Confidence            99999999999999999999988889999999998877665555 47899999999999998765

>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=3.6e-29  Score=193.97  Aligned_cols=140  Identities=34%  Similarity=0.550  Sum_probs=124.3

Q ss_pred             cccccccCC--CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc----CCCceE
Q psy9277          30 VVSTFDNMG--LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ----LRETQV  103 (178)
Q Consensus        30 ~~~~f~~~~--l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~----~~~~~~  103 (178)
                      ...+|++++  +++.++++|+++||..|+++|.++++.++.|+|+++++|||||||++|++|+++.+...    ..+.++
T Consensus        50 ~~~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~  129 (262)
T 3ly5_A           50 EDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGV  129 (262)
T ss_dssp             GGGCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCE
T ss_pred             ccCChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceE
Confidence            355677777  99999999999999999999999999999999999999999999999999999988652    245689


Q ss_pred             EEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         104 LCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       104 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +|++||++||.|+++.+++++...++.+..++|+.....+...+..+++|+|+||+++.+++.+..
T Consensus       130 lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~  195 (262)
T 3ly5_A          130 LILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTP  195 (262)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCT
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccC
Confidence            999999999999999999999988999999999999888888777789999999999999987754

>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=99.97  E-value=6.3e-29  Score=187.24  Aligned_cols=144  Identities=38%  Similarity=0.571  Sum_probs=126.4

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      .....+|++++|++.++++|.+.||..|+++|.++++.+++|+++++++|||+|||++|++|++..+.....+.+++|++
T Consensus        10 ~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   89 (220)
T 1t6n_A           10 SIHSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMC   89 (220)
T ss_dssp             ----CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEEC
T ss_pred             cccCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEe
Confidence            34456799999999999999999999999999999999999999999999999999999999999876655566999999


Q ss_pred             CcHHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcC-CCcEEEeChHHHHHHHHcCCCC
Q psy9277         108 PTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       108 Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      |+++|+.|+++.++++.... ++++..+.|+.....+...+.. .++|+|+||++|.+++++....
T Consensus        90 Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~  155 (220)
T 1t6n_A           90 HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLN  155 (220)
T ss_dssp             SCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSC
T ss_pred             CCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCC
Confidence            99999999999999998776 7899999999888777666654 4799999999999999876544

>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=99.96  E-value=3.7e-29  Score=191.47  Aligned_cols=150  Identities=27%  Similarity=0.472  Sum_probs=127.8

Q ss_pred             cccccccccccccccccC----CCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          20 VEFETSEDVEVVSTFDNM----GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        20 ~~~~~~~~~~~~~~f~~~----~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      +.+...+.+.+..+|+++    ++++++++++.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+.
T Consensus        13 i~~~~~~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~   92 (245)
T 3dkp_A           13 IHVQGTDLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLK   92 (245)
T ss_dssp             EEEESSSCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC
T ss_pred             eEecCCCCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHh
Confidence            344555677888999987    8999999999999999999999999999999999999999999999999999999886


Q ss_pred             hc-CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH-HhcCCCcEEEeChHHHHHHHHcCC
Q psy9277          96 TQ-LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR-KLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus        96 ~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~-~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      .. ..+.+++|++||++|+.|+++.++++....++++..+.|+........ ....+++|+|+||++|.+++.+..
T Consensus        93 ~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~  168 (245)
T 3dkp_A           93 QPANKGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDP  168 (245)
T ss_dssp             SCCSSSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSS
T ss_pred             hcccCCceEEEEeCCHHHHHHHHHHHHHHhcccCceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCC
Confidence            42 345689999999999999999999999988888887776654433221 223578999999999999998763

>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=99.96  E-value=2.6e-28  Score=181.89  Aligned_cols=137  Identities=32%  Similarity=0.551  Sum_probs=123.0

Q ss_pred             ccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCc
Q psy9277          33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPT  109 (178)
Q Consensus        33 ~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt  109 (178)
                      +|+++++++++++++.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+...   ..+++++|++|+
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            69999999999999999999999999999999999999999999999999999999999987542   346789999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      ++|+.|+++.++.+...  +++..++|+.....+...+..+++|+|+||+++.+++.++...
T Consensus        82 ~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~  141 (207)
T 2gxq_A           82 RELALQVASELTAVAPH--LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLD  141 (207)
T ss_dssp             HHHHHHHHHHHHHHCTT--SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHHHHhhc--ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcc
Confidence            99999999999998764  6778888998877776777778999999999999999876544

>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=99.95  E-value=3.2e-27  Score=192.13  Aligned_cols=153  Identities=62%  Similarity=0.948  Sum_probs=136.6

Q ss_pred             cccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC
Q psy9277          20 VEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR   99 (178)
Q Consensus        20 ~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~   99 (178)
                      .....+.+.+...+|+++++++.+++.|.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....
T Consensus        28 ~~~~~~~~~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~  107 (414)
T 3eiq_A           28 EGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLK  107 (414)
T ss_dssp             --CCCCCCCCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTSC
T ss_pred             ccccCCCccchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcCC
Confidence            34445566778899999999999999999999999999999999999999999999999999999999999998876666


Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc-CCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      +.+++|++|+++|+.|+++.++.++...+..+..++|+.....+...+. .+++|+|+||++|.+++.++....
T Consensus       108 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~  181 (414)
T 3eiq_A          108 ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSP  181 (414)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHGGGSCCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCS
T ss_pred             ceeEEEEeChHHHHHHHHHHHHHHhcccCceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccc
Confidence            7899999999999999999999999888999999999998887777666 578999999999999998765543

>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=99.95  E-value=9.4e-27  Score=188.91  Aligned_cols=142  Identities=42%  Similarity=0.729  Sum_probs=129.4

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      ...+|++++|++.++++|.+.||..|+++|.++++.+++|+++++++|||+|||++|++|++..+.....+.+++|++|+
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~   98 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPT   98 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSS
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCC
Confidence            45689999999999999999999999999999999999999999999999999999999999988765566799999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      ++|+.|+++.++.+....++++..+.|+.....+...+..+++|+|+||++|.+++.+....
T Consensus        99 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~  160 (400)
T 1s2m_A           99 RELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVAD  160 (400)
T ss_dssp             HHHHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcc
Confidence            99999999999999988899999999999988877777778999999999999998876543

>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=99.94  E-value=2.9e-26  Score=185.20  Aligned_cols=141  Identities=38%  Similarity=0.597  Sum_probs=125.5

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ..+|+++++++.++++|.++||..|+++|.++++.+++|+++++.+|||+|||++|++|++..+.....+.++||++|++
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~   86 (391)
T 1xti_A            7 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTR   86 (391)
T ss_dssp             --CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCH
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCH
Confidence            35799999999999999999999999999999999999999999999999999999999999876655567999999999


Q ss_pred             HHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcC-CCcEEEeChHHHHHHHHcCCCC
Q psy9277         111 ELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDY-GQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +|+.|+++.++++.... ++++..+.|+.........+.. .++|+|+||++|.+++.+....
T Consensus        87 ~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~  149 (391)
T 1xti_A           87 ELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLN  149 (391)
T ss_dssp             HHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcc
Confidence            99999999999998776 7899999999888777666654 4799999999999998876543

>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=99.94  E-value=2.2e-26  Score=185.94  Aligned_cols=142  Identities=60%  Similarity=0.941  Sum_probs=128.8

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +...+|+++++++.++++|.+.||..|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....+++++|++|
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P   97 (394)
T 1fuu_A           18 KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAP   97 (394)
T ss_dssp             CCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECS
T ss_pred             cccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcC
Confidence            44578999999999999999999999999999999999999999999999999999999999998876666789999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         109 TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       109 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +++|+.|+++.+..+....++++..+.|+....+....+. +++|+|+||++|.+.+.++...
T Consensus        98 ~~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~  159 (394)
T 1fuu_A           98 TRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFR  159 (394)
T ss_dssp             SHHHHHHHHHHHHHHTTTSCCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHHHHHHHhccCCeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcc
Confidence            9999999999999999888999999999998877665554 6899999999999999876543

>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=99.94  E-value=9.2e-26  Score=183.25  Aligned_cols=143  Identities=36%  Similarity=0.645  Sum_probs=124.0

Q ss_pred             ccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCC
Q psy9277          23 ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRE  100 (178)
Q Consensus        23 ~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~  100 (178)
                      ....+.....+|+++++++.++++|.+.||..|+++|.++++.++++  +++++++|||+|||++|++|+++.+.....+
T Consensus        16 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~   95 (412)
T 3fht_A           16 DPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKY   95 (412)
T ss_dssp             CTTSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTSCS
T ss_pred             cCCCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcCCC
Confidence            34445566889999999999999999999999999999999999997  9999999999999999999999998776677


Q ss_pred             ceEEEEcCcHHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         101 TQVLCLSPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      ++++|++|+++|+.|+++.++++.... ++.+....++......   ...+++|+|+||++|.+++.+.
T Consensus        96 ~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~  161 (412)
T 3fht_A           96 PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKL  161 (412)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTS
T ss_pred             CCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhc
Confidence            799999999999999999999998764 6777777777655422   2346799999999999999653

>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=99.94  E-value=5.6e-26  Score=189.07  Aligned_cols=138  Identities=37%  Similarity=0.660  Sum_probs=119.8

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      .+..+|++++|++.++++|.++||..|+++|.++++.++++  ++++++||||||||++|++|+++.+.....++++||+
T Consensus        89 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil  168 (479)
T 3fmp_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCL  168 (479)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEE
T ss_pred             cCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEE
Confidence            34678999999999999999999999999999999999997  9999999999999999999999988776667799999


Q ss_pred             cCcHHHHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         107 SPTRELAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       107 ~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +|+++|+.|+++.++.+.... ++.+....++......   ...+++|+|+||++|.+++.+..
T Consensus       169 ~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~  229 (479)
T 3fmp_B          169 SPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLK  229 (479)
T ss_dssp             CSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSC
T ss_pred             eChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcC
Confidence            999999999999999987754 5777777777654322   13467999999999999997643

>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=99.94  E-value=1.3e-25  Score=181.09  Aligned_cols=138  Identities=38%  Similarity=0.693  Sum_probs=122.1

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      ...+|++++|+++++++|.+.||..|+++|.++++.++++  +++++++|||+|||++|++|++..+.....+.+++|++
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~   82 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLA   82 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEEC
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEEC
Confidence            4689999999999999999999999999999999999998  99999999999999999999999887666678999999


Q ss_pred             CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         108 PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       108 Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      |+++|+.|+++.++.+....++.+....++......    ..+++|+|+||++|.+++.+....
T Consensus        83 P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~~~~~  142 (395)
T 3pey_A           83 PSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRRKLMQ  142 (395)
T ss_dssp             SSHHHHHHHHHHHHHHTTTSCCCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHTTCBC
T ss_pred             CCHHHHHHHHHHHHHHhcccCeeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHcCCcc
Confidence            999999999999999998888888888777544321    236899999999999999876543

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.93  E-value=1.1e-24  Score=174.20  Aligned_cols=139  Identities=31%  Similarity=0.584  Sum_probs=124.5

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC-CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g-~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      ..+|++++|++.++++|++.||..|+++|.++++.++++ +++++.+|||+|||++|++|++..+... .+.+++|++|+
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            357999999999999999999999999999999999988 7999999999999999999999876543 45699999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      ++|+.|+++.+..+....++.+..+.|+.....+...+. +++|+|+||++|.+++.++...
T Consensus        84 ~~L~~q~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~  144 (367)
T 1hv8_A           84 RELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLN  144 (367)
T ss_dssp             HHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcc
Confidence            999999999999998888899999999998877766655 6899999999999999876544

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.93  E-value=4.2e-25  Score=188.02  Aligned_cols=138  Identities=33%  Similarity=0.570  Sum_probs=118.0

Q ss_pred             cccccccCC----CCHHHHHHHHhCCCCCCcHHHHHHHHHHH--cCCcEEEEcCCCChHHHHHHHHHHHHhhhcC----C
Q psy9277          30 VVSTFDNMG----LREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSISILQSLDTQL----R   99 (178)
Q Consensus        30 ~~~~f~~~~----l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~--~g~~v~v~aptGsGKTl~~ll~il~~l~~~~----~   99 (178)
                      ...+|+++.    |+++++++|.++||..|+++|.++++.++  .++++++++|||+|||++|++|+++.+....    .
T Consensus        15 ~~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~   94 (579)
T 3sqw_A           15 KEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQY   94 (579)
T ss_dssp             CCCCHHHHHHTTSSCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTT
T ss_pred             CCcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccC
Confidence            344555554    99999999999999999999999999999  7899999999999999999999999886642    2


Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhcc----CCCceEEEEEcCccHHHHHHHhc-CCCcEEEeChHHHHHHHHc
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGD----FMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~----~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP~~l~~~l~~  167 (178)
                      ++++|||+||++|+.|+++.++.+..    ...+.+..++|+.....+...+. .+++|+|+||++|.+++.+
T Consensus        95 ~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~  167 (579)
T 3sqw_A           95 MVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEK  167 (579)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHH
T ss_pred             CCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHh
Confidence            46899999999999999999988753    23567888899988887766664 3789999999999998865

>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=99.92  E-value=7e-25  Score=185.64  Aligned_cols=138  Identities=33%  Similarity=0.569  Sum_probs=117.1

Q ss_pred             ccccccCC----CCHHHHHHHHhCCCCCCcHHHHHHHHHHH--cCCcEEEEcCCCChHHHHHHHHHHHHhhhcC----CC
Q psy9277          31 VSTFDNMG----LREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFSISILQSLDTQL----RE  100 (178)
Q Consensus        31 ~~~f~~~~----l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~--~g~~v~v~aptGsGKTl~~ll~il~~l~~~~----~~  100 (178)
                      ..+|+++.    |++++++++.++||..|+++|.++++.++  .++|++++||||+|||++|++|+++.+....    .+
T Consensus        67 ~~~~~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~  146 (563)
T 3i5x_A           67 EVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYM  146 (563)
T ss_dssp             CCCHHHHHHTTSSCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTS
T ss_pred             CcCHHHHhhcCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCC
Confidence            44565554    99999999999999999999999999999  6789999999999999999999999987643    23


Q ss_pred             ceEEEEcCcHHHHHHHHHHHHHhccC----CCceEEEEEcCccHHHHHHHhc-CCCcEEEeChHHHHHHHHcC
Q psy9277         101 TQVLCLSPTRELAVQIQKVVLALGDF----MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~----~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP~~l~~~l~~~  168 (178)
                      +++|||+||++||.|+++.++.+...    ....+..++|+.....+...+. .+++|+|+||++|.+++.+.
T Consensus       147 ~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~  219 (563)
T 3i5x_A          147 VKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKY  219 (563)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHH
T ss_pred             eeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhc
Confidence            58999999999999999999887542    2466888899988877766653 47899999999999988653

>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=99.92  E-value=8.7e-24  Score=167.23  Aligned_cols=126  Identities=27%  Similarity=0.562  Sum_probs=114.7

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      |++++.++|+++||..|+++|.++++.+++++++++.+|||+|||++|++|+++.      +.+++|++|+++|+.|+++
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            6789999999999999999999999999999999999999999999999999873      5689999999999999999


Q ss_pred             HHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         119 VVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       119 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      .++++....++++..++|+.....+...+. .++|+|+||++|.+++.+....
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~  126 (337)
T 2z0m_A           75 HIRDIGRYMDTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVID  126 (337)
T ss_dssp             HHHHHTTTSCCCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHTTSCC
T ss_pred             HHHHHhhhcCCcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHcCCcc
Confidence            999999888999999999998887766655 4899999999999998876544

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.90  E-value=2.8e-23  Score=169.73  Aligned_cols=121  Identities=18%  Similarity=0.139  Sum_probs=103.8

Q ss_pred             HHHHHHHh-CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          42 DLLRGIYA-YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        42 ~i~~~l~~-~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      ++.+.+++ .|| +|+++|.++++.+++|+|+++++|||+|||++|+++++..+   ..+++++|++||++|+.|+++.+
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~---~~~~~~lil~Pt~~L~~q~~~~~   84 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERL   84 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh---cCCCEEEEEECCHHHHHHHHHHH
Confidence            34455544 466 79999999999999999999999999999999999988865   35679999999999999999999


Q ss_pred             HHhccCCCceEEEEEcCccH---HHHHHHhcCC-CcEEEeChHHHHHHHHc
Q psy9277         121 LALGDFMNVQCHACIGGTNL---SEDLRKLDYG-QHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       121 ~~~~~~~~~~~~~~~g~~~~---~~~~~~~~~~-~~IlV~TP~~l~~~l~~  167 (178)
                      +.++. .++++..++|+.+.   ..+...+..+ ++|+|+||++|.+++..
T Consensus        85 ~~~~~-~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~  134 (414)
T 3oiy_A           85 QKLAD-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK  134 (414)
T ss_dssp             HHHCC-SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH
T ss_pred             HHHcc-CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH
Confidence            99988 88999999999988   4455555555 89999999999887764

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.88  E-value=2.4e-22  Score=173.73  Aligned_cols=127  Identities=17%  Similarity=0.152  Sum_probs=106.9

Q ss_pred             HHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC--CceEEEEcCcHHHHHHHHHHHH
Q psy9277          44 LRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR--ETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        44 ~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      .+++..+||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....  +.++||++||++|+.|+++.++
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            45678899999999999999999999999999999999999999999998765432  2689999999999999999999


Q ss_pred             HhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         122 ALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       122 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      +++...++++..++|+.....+...+..+++|+|+||++|.+++.++.+
T Consensus        83 ~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~  131 (696)
T 2ykg_A           83 KYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI  131 (696)
T ss_dssp             HHTTTTTCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSS
T ss_pred             HHhccCCceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcc
Confidence            9998889999999998865544445555799999999999999987765

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.88  E-value=2.5e-22  Score=174.51  Aligned_cols=134  Identities=15%  Similarity=0.247  Sum_probs=116.2

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      ...+|++++|++++.+.+++.||..|+++|.++++. +.+++++++++|||||||++|.+++++.+..  .+.+++|++|
T Consensus         6 ~~~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~--~~~~il~i~P   83 (715)
T 2va8_A            6 EWMPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLK--NGGKAIYVTP   83 (715)
T ss_dssp             CCCBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHH--SCSEEEEECS
T ss_pred             ccCcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH--CCCeEEEEeC
Confidence            346799999999999999999999999999999999 7889999999999999999999999988764  3569999999


Q ss_pred             cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         109 TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       109 t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +++||.|+++.++.+ ...|+++...+|+....+.  .+ .+++|+|+||+++..++++..
T Consensus        84 ~r~La~q~~~~~~~~-~~~g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~  140 (715)
T 2va8_A           84 LRALTNEKYLTFKDW-ELIGFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRP  140 (715)
T ss_dssp             CHHHHHHHHHHHGGG-GGGTCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCC
T ss_pred             cHHHHHHHHHHHHHh-hcCCCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCCh
Confidence            999999999999655 3458899999988766543  12 368999999999999988754

>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=99.88  E-value=1.8e-22  Score=175.71  Aligned_cols=133  Identities=15%  Similarity=0.251  Sum_probs=115.5

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      .+|++++|++++.+.+++.||..|+++|.++++. +.+++++++++|||||||++|.+++++.+...  +.+++|++|++
T Consensus         1 ~~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--~~~~l~i~P~r   78 (720)
T 2zj8_A            1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--GGKAVYIVPLK   78 (720)
T ss_dssp             CBGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--CSEEEEECSSG
T ss_pred             CcHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--CCEEEEEcCcH
Confidence            3699999999999999999999999999999998 88899999999999999999999999887643  56999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      +|+.|+++.++.+.. .++++..++|+...+..   ....++|+|+||+++..++++...
T Consensus        79 aLa~q~~~~~~~l~~-~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~  134 (720)
T 2zj8_A           79 ALAEEKFQEFQDWEK-IGLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGSS  134 (720)
T ss_dssp             GGHHHHHHHTGGGGG-GTCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTCT
T ss_pred             HHHHHHHHHHHHHHh-cCCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcChh
Confidence            999999999975543 48899999998765432   123689999999999999887543

>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=99.87  E-value=5e-22  Score=166.97  Aligned_cols=120  Identities=14%  Similarity=0.144  Sum_probs=101.0

Q ss_pred             CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC--CceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          51 GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR--ETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      +..+|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....  +.++||++|+++|+.|+++.++.++...+
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~   83 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHHFERQG   83 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHGGGT
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHHHHHHHHHHHHHhcccC
Confidence            4457999999999999999999999999999999999999998876432  67899999999999999999999998889


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      +++..++|+.....+...+..+++|+|+||++|.+++.++..
T Consensus        84 ~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~  125 (556)
T 4a2p_A           84 YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTL  125 (556)
T ss_dssp             CCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSC
T ss_pred             ceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcc
Confidence            999999999977766666666799999999999999988765

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.87  E-value=9.2e-22  Score=165.07  Aligned_cols=117  Identities=18%  Similarity=0.150  Sum_probs=105.2

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC--CceEEEEcCcHHHHHHHHHHHHHhccCCCceE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR--ETQVLCLSPTRELAVQIQKVVLALGDFMNVQC  131 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  131 (178)
                      +|+++|.++++.++.|+++++++|||+|||++|++|+++.+.....  +.++||++|+++|+.|+++.++.++...++++
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~   83 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNI   83 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHHHHHHHHHHHHHHHTTTCCE
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHHHHHHHHHHHHHhccCCcEE
Confidence            6999999999999999999999999999999999999998876432  67899999999999999999999998889999


Q ss_pred             EEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         132 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       132 ~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      ..++|+.....+...+..+++|+|+||++|.+++.++..
T Consensus        84 ~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~  122 (555)
T 3tbk_A           84 ASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAI  122 (555)
T ss_dssp             EEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSS
T ss_pred             EEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcc
Confidence            999999977665555556799999999999999988765

>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=99.86  E-value=1.8e-21  Score=166.17  Aligned_cols=119  Identities=14%  Similarity=0.195  Sum_probs=104.2

Q ss_pred             cccCCCCHHHHHHHHh-CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          34 FDNMGLREDLLRGIYA-YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        34 f~~~~l~~~i~~~l~~-~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      +.++++++.+.+.|++ +||..|+++|.++|+.+++|+|+++.+|||+|||++|++|++.      ...++|||+|+++|
T Consensus        23 ~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~------~~g~~lVisP~~~L   96 (591)
T 2v1x_A           23 KEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALC------SDGFTLVICPLISL   96 (591)
T ss_dssp             CSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHT------SSSEEEEECSCHHH
T ss_pred             cccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHH------cCCcEEEEeCHHHH
Confidence            3458899999999987 6999999999999999999999999999999999999999986      34699999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh------cCCCcEEEeChHHHH
Q psy9277         113 AVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL------DYGQHVVSGTPGRVF  162 (178)
Q Consensus       113 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~------~~~~~IlV~TP~~l~  162 (178)
                      +.|+++.+..+    ++.+..+.|+....+....+      ..+++|+|+||++|.
T Consensus        97 ~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~  148 (591)
T 2v1x_A           97 MEDQLMVLKQL----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIA  148 (591)
T ss_dssp             HHHHHHHHHHH----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHH
T ss_pred             HHHHHHHHHhc----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhh
Confidence            99999999887    78888889888776554332      346899999999874

>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=99.86  E-value=2e-21  Score=163.73  Aligned_cols=121  Identities=17%  Similarity=0.229  Sum_probs=106.0

Q ss_pred             cccccCCCCHHHHHHHHh-CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          32 STFDNMGLREDLLRGIYA-YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~-~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ..|++++|++.+.+.|++ +||..|+++|.++|+.+++|+|+++++|||+|||++|++|++.      ....+||++|++
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 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL------LNGLTVVVSPLI   75 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH------SSSEEEEECSCH
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHH------hCCCEEEECChH
Confidence            579999999999999987 8999999999999999999999999999999999999999985      245899999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH----hcCCCcEEEeChHHHH
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK----LDYGQHVVSGTPGRVF  162 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~----~~~~~~IlV~TP~~l~  162 (178)
                      +|+.|+++.++.+    ++.+..+.++....+....    ....++|+++||++|.
T Consensus        76 aL~~q~~~~l~~~----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~  127 (523)
T 1oyw_A           76 SLMKDQVDQLQAN----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLM  127 (523)
T ss_dssp             HHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHT
T ss_pred             HHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh
Confidence            9999999999876    7788888888776654322    2346899999999984

>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=99.86  E-value=2.3e-21  Score=170.49  Aligned_cols=122  Identities=15%  Similarity=0.163  Sum_probs=102.5

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC--CceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR--ETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      -+|+..|+++|.++++.++.|+++++++|||+|||++|++|+++.+.....  +.++|||+|+++|+.|+++.++.++..
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            457889999999999999999999999999999999999999998876432  679999999999999999999999888


Q ss_pred             CCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         127 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       127 ~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      .++++..++|+.....+...+..+++|+|+||++|.+++.++.+
T Consensus       323 ~~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~  366 (797)
T 4a2q_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTL  366 (797)
T ss_dssp             GTCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSC
T ss_pred             CCceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccc
Confidence            89999999999987776666667899999999999999987766

>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=99.86  E-value=1.7e-22  Score=175.42  Aligned_cols=130  Identities=12%  Similarity=0.189  Sum_probs=111.3

Q ss_pred             ccccCC--CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          33 TFDNMG--LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        33 ~f~~~~--l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      +|++++  |++++.+.+++.||.+|+++|.++++.+.+++++++++|||||||++|.+++++.+..   +.+++|++|++
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            688999  9999999999999999999999999999999999999999999999999999988763   56999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +|+.|+++.++.+ ...|+++..++|+....+.   ...+++|+|+||+++..++++..
T Consensus        79 ~La~q~~~~~~~~-~~~g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~  133 (702)
T 2p6r_A           79 ALAGEKYESFKKW-EKIGLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRA  133 (702)
T ss_dssp             HHHHHHHHHHTTT-TTTTCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHH-HhcCCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcCh
Confidence            9999999999655 3458999999998765432   12368999999999999988754

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.86  E-value=3.5e-21  Score=173.84  Aligned_cols=115  Identities=17%  Similarity=0.120  Sum_probs=101.9

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      ...|| +||++|.++++.+++|+|++++||||||||++|+++++..+   ..+.++||++||++||.|+++.++.++ ..
T Consensus        73 ~~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~---~~~~~~Lil~PtreLa~Q~~~~l~~l~-~~  147 (1104)
T 4ddu_A           73 KKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA---RKGKKSALVFPTVTLVKQTLERLQKLA-DE  147 (1104)
T ss_dssp             HHSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH---TTTCCEEEEESSHHHHHHHHHHHHTTS-CT
T ss_pred             HhcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH---hcCCeEEEEechHHHHHHHHHHHHHhh-CC
Confidence            35788 59999999999999999999999999999999998888876   356799999999999999999999987 77


Q ss_pred             CceEEEEEcCccH---HHHHHHhcCC-CcEEEeChHHHHHHHHc
Q psy9277         128 NVQCHACIGGTNL---SEDLRKLDYG-QHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       128 ~~~~~~~~g~~~~---~~~~~~~~~~-~~IlV~TP~~l~~~l~~  167 (178)
                      ++++..++|+.+.   ..+...+..+ ++|+|+||++|.+++..
T Consensus       148 ~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~  191 (1104)
T 4ddu_A          148 KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK  191 (1104)
T ss_dssp             TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH
T ss_pred             CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh
Confidence            8999999999987   5666667666 99999999999887653

>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=99.86  E-value=5.3e-22  Score=184.90  Aligned_cols=124  Identities=16%  Similarity=0.267  Sum_probs=102.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhc--------CCCceEEEEcCc
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQ--------LRETQVLCLSPT  109 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~--------~~~~~~lil~Pt  109 (178)
                      |+++...++  .||++++++|++++|.++. ++|++++||||||||++|.+++++.+...        ..+.++||++|+
T Consensus        66 Lp~~~~~~f--~g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~  143 (1724)
T 4f92_B           66 LPKYAQAGF--EGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPM  143 (1724)
T ss_dssp             SCGGGSTTC--TTCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSS
T ss_pred             cCHHHHHhc--CCCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCH
Confidence            444444443  2799999999999999875 89999999999999999999999998652        235689999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      ++||.|+++.+.+.+...|+++..++|+.+...+   ...+++|+|+|||++..++++
T Consensus       144 kALa~e~~~~l~~~~~~~gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~  198 (1724)
T 4f92_B          144 RSLVQEMVGSFGKRLATYGITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRK  198 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTTTCCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHHHhhCCCEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcC
Confidence            9999999999998888899999999999876432   123689999999998555544

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.85  E-value=3.9e-21  Score=167.15  Aligned_cols=112  Identities=19%  Similarity=0.263  Sum_probs=99.0

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+|| +|+++|..++|.++.|+  +..++||+|||++|.+|++....   .+..++||+||++||.|.++.+..+++.+|
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL---~g~~vlVltptreLA~qd~e~~~~l~~~lg  152 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL---TGKGVHVVTVNEYLASRDAEQMGKIFEFLG  152 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT---TSSCEEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHH---cCCCEEEEeCCHHHHHHHHHHHHHHHhhcC
Confidence            5799 89999999999999999  99999999999999999985433   356899999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      +++.+++||.+...+..  ..+|||+||||++| .|+|+..
T Consensus       153 l~v~~i~gg~~~~~r~~--~~~~dIv~gTpgrlgfD~L~D~  191 (844)
T 1tf5_A          153 LTVGLNLNSMSKDEKRE--AYAADITYSTNNELGFDYLRDN  191 (844)
T ss_dssp             CCEEECCTTSCHHHHHH--HHHSSEEEEEHHHHHHHHHHHT
T ss_pred             CeEEEEeCCCCHHHHHH--hcCCCEEEECchhhhHHHHHHh
Confidence            99999999998765533  34799999999999 7777654

>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=1.5e-20  Score=175.28  Aligned_cols=127  Identities=22%  Similarity=0.269  Sum_probs=108.7

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~  117 (178)
                      |++...+++...+|..++|+|+++|+.++. +.|++++||||||||++|.+|+++.+... .+.++||++|+++||.|++
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            667888888888999999999999999986 67999999999999999999999988764 4568999999999999999


Q ss_pred             HHHHH-hccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         118 KVVLA-LGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       118 ~~~~~-~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      +.+.+ +....|+++..++|+...+....   .+++|+|+|||++..++++..
T Consensus       990 ~~~~~~f~~~~g~~V~~ltGd~~~~~~~~---~~~~IiV~TPEkld~llr~~~ 1039 (1724)
T 4f92_B          990 MDWYEKFQDRLNKKVVLLTGETSTDLKLL---GKGNIIISTPEKWDILSRRWK 1039 (1724)
T ss_dssp             HHHHHHHTTTSCCCEEECCSCHHHHHHHH---HHCSEEEECHHHHHHHHTTTT
T ss_pred             HHHHHHhchhcCCEEEEEECCCCcchhhc---CCCCEEEECHHHHHHHHhCcc
Confidence            99864 66678999999999877654422   357999999999987777543

>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=99.84  E-value=9.8e-21  Score=170.51  Aligned_cols=117  Identities=21%  Similarity=0.219  Sum_probs=102.4

Q ss_pred             HHH-HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          45 RGI-YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        45 ~~l-~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      +.+ +.+||. | ++|.++|+.+++|+|++++||||||||+ |.+|++..+..  .++++||++||++||.|+++.++.+
T Consensus        48 ~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~--~~~~~lil~PtreLa~Q~~~~l~~l  122 (1054)
T 1gku_B           48 EFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL--KGKRCYVIFPTSLLVIQAAETIRKY  122 (1054)
T ss_dssp             HHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT--TSCCEEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh--cCCeEEEEeccHHHHHHHHHHHHHH
Confidence            444 458999 9 9999999999999999999999999998 88888887764  5679999999999999999999999


Q ss_pred             ccCCCc----eEEEEEcCccHHHH---HHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         124 GDFMNV----QCHACIGGTNLSED---LRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       124 ~~~~~~----~~~~~~g~~~~~~~---~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      +...++    ++..++|+.+...+   ...+.+ ++|+|+||++|++++.+
T Consensus       123 ~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~  172 (1054)
T 1gku_B          123 AEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE  172 (1054)
T ss_dssp             HTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT
T ss_pred             HhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH
Confidence            988888    89999999887763   344455 99999999999998765

>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=99.83  E-value=1.7e-20  Score=167.30  Aligned_cols=122  Identities=15%  Similarity=0.163  Sum_probs=100.8

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC--CceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR--ETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~--~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      -.|+..|+++|.++++.+++|+++++++|||+|||++|++|+++.+.....  +.++|||+|+++|+.|+++.++.++..
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            346778999999999999999999999999999999999999987765421  568999999999999999999999888


Q ss_pred             CCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         127 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       127 ~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      .++++..++|+.+...+...+..+++|+|+||++|.+++.++.+
T Consensus       323 ~~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~  366 (936)
T 4a2w_A          323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTL  366 (936)
T ss_dssp             TTCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSC
T ss_pred             cCceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCcc
Confidence            89999999999877665555555789999999999999987665

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.83  E-value=2.1e-20  Score=162.45  Aligned_cols=113  Identities=19%  Similarity=0.236  Sum_probs=98.9

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .+|. +|+++|..+++.++.|+  +..++||+|||++|++|++....   .+.+++||+||++||.|+++.+..+++.++
T Consensus        70 ~lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l---~g~~vlVltPTreLA~Q~~e~~~~l~~~lg  143 (853)
T 2fsf_A           70 VFGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNAL---TGKGVHVVTVNDYLAQRDAENNRPLFEFLG  143 (853)
T ss_dssp             HHSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHT---TSSCCEEEESSHHHHHHHHHHHHHHHHHTT
T ss_pred             HcCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHH---cCCcEEEEcCCHHHHHHHHHHHHHHHHhcC
Confidence            3565 79999999999999998  99999999999999999986543   356899999999999999999999999999


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQ  169 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~  169 (178)
                      +++.+++||.+...+  .+..++||+||||++| .|+|+.+.
T Consensus       144 l~v~~i~GG~~~~~r--~~~~~~dIvvgTpgrl~fDyLrd~~  183 (853)
T 2fsf_A          144 LTVGINLPGMPAPAK--REAYAADITYGTNNEYGFDYLRDNM  183 (853)
T ss_dssp             CCEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTT
T ss_pred             CeEEEEeCCCCHHHH--HHhcCCCEEEECCchhhHHHHHhhh
Confidence            999999999987544  3334799999999999 79988653

>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=99.82  E-value=2.6e-20  Score=138.89  Aligned_cols=119  Identities=16%  Similarity=0.131  Sum_probs=93.7

Q ss_pred             CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCcHHHHHH-HHHHHHHhcc
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPTRELAVQ-IQKVVLALGD  125 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt~~L~~q-~~~~~~~~~~  125 (178)
                      .+...|+++|.++++.+++++++++.+|||+|||++|++++++.+...   ..+.+++|++|+++|+.| ..+.+..+..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L~~q~~~~~~~~~~~  108 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLK  108 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHTHHHHHT
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHHHHHHHHHHHHHHhc
Confidence            344579999999999999999999999999999999999998876542   235689999999999999 6777888765


Q ss_pred             CCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         126 FMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       126 ~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      . ++++..+.|+.........+..+++|+|+||++|.+++....
T Consensus       109 ~-~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~  151 (216)
T 3b6e_A          109 K-WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLE  151 (216)
T ss_dssp             T-TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC--
T ss_pred             c-CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccC
Confidence            5 678888888765544333333468999999999999988653

>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=99.82  E-value=5.4e-20  Score=166.18  Aligned_cols=126  Identities=20%  Similarity=0.174  Sum_probs=108.2

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ...|..+++++.+...+...++..|+++|.++++.+.+|++++++||||||||++|.+|++..+.   .+.+++|++|++
T Consensus       161 ~~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~---~g~rvlvl~Ptr  237 (1108)
T 3l9o_A          161 PPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK---NKQRVIYTSPIK  237 (1108)
T ss_dssp             SSCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHH---TTCEEEEEESSH
T ss_pred             CCCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHh---cCCeEEEEcCcH
Confidence            45677788888887777666777899999999999999999999999999999999999998874   467999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      +|+.|+++.+..+..    .+..++|+.+.       ..+++|+|+||++|.+++.++..
T Consensus       238 aLa~Q~~~~l~~~~~----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~~~~  286 (1108)
T 3l9o_A          238 ALSNQKYRELLAEFG----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGSE  286 (1108)
T ss_dssp             HHHHHHHHHHHHHTS----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHHCSS
T ss_pred             HHHHHHHHHHHHHhC----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHcCcc
Confidence            999999999988765    46667887763       34689999999999999887643

>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=99.80  E-value=3.7e-19  Score=155.65  Aligned_cols=118  Identities=26%  Similarity=0.306  Sum_probs=101.3

Q ss_pred             HHHHH-HHhCCCCCCcHHHHHHHHHHHcC------CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHH
Q psy9277          42 DLLRG-IYAYGFEKPSAIQQRSIKPIVKG------RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAV  114 (178)
Q Consensus        42 ~i~~~-l~~~g~~~~~~~Q~~~i~~i~~g------~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~  114 (178)
                      ..++. +.+++| .||++|.++++.++++      +++++++|||||||++|++|++..+..   +.+++|++||++||.
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---g~qvlvlaPtr~La~  431 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSILAI  431 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHHHH
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---CCeEEEEeCcHHHHH
Confidence            44444 588999 8999999999999875      699999999999999999999988763   579999999999999


Q ss_pred             HHHHHHHHhccCCCceEEEEEcCccHHHHHH---HhcC-CCcEEEeChHHHHH
Q psy9277         115 QIQKVVLALGDFMNVQCHACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVFD  163 (178)
Q Consensus       115 q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~~  163 (178)
                      |+++.+.++....++++..++|+.+..++..   .+.. .++|+|+||+.|.+
T Consensus       432 Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~  484 (780)
T 1gm5_A          432 QHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE  484 (780)
T ss_dssp             HHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH
T ss_pred             HHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh
Confidence            9999999999888999999999988776433   3334 48999999998855

>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=99.80  E-value=2.5e-19  Score=156.17  Aligned_cols=113  Identities=19%  Similarity=0.240  Sum_probs=98.9

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +.+|+ +|+++|..+++.++.|+  +..++||+|||++|.+|++....   .+..++||+||++||.|.++.+..+++.+
T Consensus       106 R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL---~g~~v~VvTpTreLA~Qdae~m~~l~~~l  179 (922)
T 1nkt_A          106 RVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNAL---AGNGVHIVTVNDYLAKRDSEWMGRVHRFL  179 (922)
T ss_dssp             HHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHT---TTSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             HHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHH---hCCCeEEEeCCHHHHHHHHHHHHHHHhhc
Confidence            35788 89999999999999998  99999999999999999975433   24589999999999999999999999999


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSS  168 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~  168 (178)
                      |+++.+++||.+...+..  ..+|||++|||++| .|+|+.+
T Consensus       180 GLsv~~i~gg~~~~~r~~--~y~~DIvygTpgrlgfDyLrD~  219 (922)
T 1nkt_A          180 GLQVGVILATMTPDERRV--AYNADITYGTNNEFGFDYLRDN  219 (922)
T ss_dssp             TCCEEECCTTCCHHHHHH--HHHSSEEEEEHHHHHHHHHHHT
T ss_pred             CCeEEEEeCCCCHHHHHH--hcCCCEEEECchHhhHHHHHhh
Confidence            999999999998655433  34699999999999 8888765

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.80  E-value=4.5e-19  Score=154.50  Aligned_cols=114  Identities=17%  Similarity=0.163  Sum_probs=99.9

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +-+|+ +|+++|..+++.++.|+  +..+.||+|||++|.+|++....   .+.+++||+||++||.|.+..+..+++.+
T Consensus        74 R~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL---~G~qv~VvTPTreLA~Qdae~m~~l~~~l  147 (997)
T 2ipc_A           74 RYLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNAL---TGKGVHVVTVNDYLARRDAEWMGPVYRGL  147 (997)
T ss_dssp             HHTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHT---TCSCCEEEESSHHHHHHHHHHHHHHHHTT
T ss_pred             HHhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHH---hCCCEEEEeCCHHHHHHHHHHHHHHHHhc
Confidence            34799 89999999999999998  99999999999999999964333   34589999999999999999999999999


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQ  169 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~  169 (178)
                      |+++.+++|+.+...+..  ..++||+||||++| .|+|+.+.
T Consensus       148 GLsv~~i~Gg~~~~~r~~--ay~~DIvyGTpgrlgfDyLrd~m  188 (997)
T 2ipc_A          148 GLSVGVIQHASTPAERRK--AYLADVTYVTNSELGFDYLRDNM  188 (997)
T ss_dssp             TCCEEECCTTCCHHHHHH--HHTSSEEEEEHHHHHHHHHHHTS
T ss_pred             CCeEEEEeCCCCHHHHHH--HcCCCEEEECchhhhhHHHHHhh
Confidence            999999999998655433  34699999999999 89998764

>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=99.76  E-value=3.6e-19  Score=153.97  Aligned_cols=112  Identities=17%  Similarity=0.170  Sum_probs=93.6

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCcHHHHHHH-HHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPTRELAVQI-QKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt~~L~~q~-~~~~~~~~~~~~~  129 (178)
                      .|+++|.++++.+++|+++++.+|||+|||++|++|+++.+...   ..+.++|||+|+++|+.|+ ++.++.++.. ++
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~-~~   85 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK-WY   85 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHHHHHHHHHTHHHHHTT-TS
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHHHHHHHHHHHHHHcCc-Cc
Confidence            69999999999999999999999999999999999999887653   2236899999999999999 9999998765 58


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      ++..++|+.........+..+++|+|+||++|.+.+.
T Consensus        86 ~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~  122 (699)
T 4gl2_A           86 RVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLL  122 (699)
T ss_dssp             CEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC
T ss_pred             eEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHh
Confidence            8899999877665445555679999999999998884

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.74  E-value=1.5e-17  Score=149.23  Aligned_cols=108  Identities=23%  Similarity=0.277  Sum_probs=93.0

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      ...+|. |+++|.++++.+.+|+++++++|||+|||++|.++++..+.   .+.+++|++|+++|+.|+++.+..+..  
T Consensus        81 ~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~---~g~rvL~l~PtkaLa~Q~~~~l~~~~~--  154 (1010)
T 2xgj_A           81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK---NKQRVIYTSPIKALSNQKYRELLAEFG--  154 (1010)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHH---TTCEEEEEESSHHHHHHHHHHHHHHHS--
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhc---cCCeEEEECChHHHHHHHHHHHHHHhC--
Confidence            455775 99999999999999999999999999999999999988774   457999999999999999999988765  


Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                        .+..++|+.+..       .+++|+|+||++|.+++.++..
T Consensus       155 --~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~~~~  188 (1010)
T 2xgj_A          155 --DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYRGSE  188 (1010)
T ss_dssp             --CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHHTCT
T ss_pred             --CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHcCcc
Confidence              567778877643       3579999999999999876543

>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=99.73  E-value=5.8e-17  Score=132.89  Aligned_cols=114  Identities=18%  Similarity=0.161  Sum_probs=97.1

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA  133 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  133 (178)
                      .|+++|.++++.++.+ ++++.+|||+|||++++++++..+.  ..+.++||++|+++|+.|+++.+.++....+.++..
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~--~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~   85 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLT--KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVA   85 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHH--HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEE
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHh--cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEE
Confidence            6999999999999999 9999999999999999999988776  245699999999999999999999887544568888


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      +.|+.......... .+++|+|+||+.|.+.+.++...
T Consensus        86 ~~g~~~~~~~~~~~-~~~~ivv~T~~~l~~~~~~~~~~  122 (494)
T 1wp9_A           86 LTGEKSPEERSKAW-ARAKVIVATPQTIENDLLAGRIS  122 (494)
T ss_dssp             ECSCSCHHHHHHHH-HHCSEEEECHHHHHHHHHTTSCC
T ss_pred             eeCCcchhhhhhhc-cCCCEEEecHHHHHHHHhcCCcc
Confidence            89888777554333 36899999999999988866543

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.72  E-value=3.7e-17  Score=146.52  Aligned_cols=109  Identities=17%  Similarity=0.218  Sum_probs=92.4

Q ss_pred             hCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCC
Q psy9277          49 AYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMN  128 (178)
Q Consensus        49 ~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~  128 (178)
                      .++| .|+++|.++++.+++|+++++++|||+|||++|++++...+.   .+.+++|++|+++|+.|+++.+..+..  +
T Consensus        35 ~~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~---~g~~vlvl~PtraLa~Q~~~~l~~~~~--~  108 (997)
T 4a4z_A           35 SWPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHR---NMTKTIYTSPIKALSNQKFRDFKETFD--D  108 (997)
T ss_dssp             CCSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHH---TTCEEEEEESCGGGHHHHHHHHHTTC----
T ss_pred             hCCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHh---cCCeEEEEeCCHHHHHHHHHHHHHHcC--C
Confidence            4567 489999999999999999999999999999999999887654   457999999999999999999987653  6


Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      +++..++|+.+..       ..++|+|+||++|.+++.....
T Consensus       109 ~~v~~l~G~~~~~-------~~~~IlV~Tpe~L~~~l~~~~~  143 (997)
T 4a4z_A          109 VNIGLITGDVQIN-------PDANCLIMTTEILRSMLYRGAD  143 (997)
T ss_dssp             CCEEEECSSCEEC-------TTSSEEEEEHHHHHHHHHHTCS
T ss_pred             CeEEEEeCCCccC-------CCCCEEEECHHHHHHHHHhCch
Confidence            7888888887533       3579999999999999876543

>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=99.70  E-value=5.5e-17  Score=126.39  Aligned_cols=105  Identities=20%  Similarity=0.234  Sum_probs=87.5

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA  133 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  133 (178)
                      .|+++|.++++.++++.+.++++|||+|||++++.++...+..  ...+++|++|+++|+.|+++.+.++....+..+..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~--~~~~~lil~Pt~~L~~q~~~~l~~~~~~~~~~~~~  190 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH--CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHc--CCCeEEEEECCHHHHHHHHHHHHHhcccccceEEE
Confidence            7999999999999998889999999999999998887776553  33489999999999999999999997766777888


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHH
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~  163 (178)
                      +.++.....   ....+++|+|+||+++..
T Consensus       191 ~~~~~~~~~---~~~~~~~I~v~T~~~l~~  217 (282)
T 1rif_A          191 IGGGASKDD---KYKNDAPVVVGTWQTVVK  217 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTT
T ss_pred             EeCCCcchh---hhccCCcEEEEchHHHHh
Confidence            877765432   222468999999998754

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.70  E-value=4.9e-17  Score=136.01  Aligned_cols=106  Identities=19%  Similarity=0.215  Sum_probs=90.9

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEE
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCH  132 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  132 (178)
                      ..|+++|.++++.+++++++++++|||+|||++|+.++...+..  .+.+++||+|+++|+.|+++.+.++....+..+.
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~--~~~~vlvl~P~~~L~~Q~~~~~~~~~~~~~~~v~  189 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN--YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIK  189 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHH--CSSEEEEEESSHHHHHHHHHHHHHTTSSCGGGEE
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhC--CCCeEEEEECcHHHHHHHHHHHHHhhcCCccceE
Confidence            37999999999999999999999999999999999988887653  3359999999999999999999998766677888


Q ss_pred             EEEcCccHHHHHHHhcCCCcEEEeChHHHHH
Q psy9277         133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       133 ~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~  163 (178)
                      .+.|+.+..++   +..+++|+|+||+.|..
T Consensus       190 ~~~~~~~~~~~---~~~~~~I~i~T~~~l~~  217 (510)
T 2oca_A          190 KIGGGASKDDK---YKNDAPVVVGTWQTVVK  217 (510)
T ss_dssp             ECGGGCCTTGG---GCTTCSEEEEEHHHHTT
T ss_pred             EEecCCccccc---cccCCcEEEEeHHHHhh
Confidence            88888766543   44578999999997643

>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=99.68  E-value=1.4e-16  Score=121.11  Aligned_cols=123  Identities=17%  Similarity=0.166  Sum_probs=89.5

Q ss_pred             CHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCC--CceEEEEcCcHHHHHHHH
Q psy9277          40 REDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLR--ETQVLCLSPTRELAVQIQ  117 (178)
Q Consensus        40 ~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~--~~~~lil~Pt~~L~~q~~  117 (178)
                      ++...+.+...+...++++|.++++.+.+|++++++||||||||.++.++++........  ..++++++|+++++.|++
T Consensus        47 ~~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~la~q~~  126 (235)
T 3llm_A           47 DHDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVA  126 (235)
T ss_dssp             CHHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHHHHHHHH
T ss_pred             CHHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchHHHHHHH
Confidence            333333333333345799999999999999999999999999999999998887655433  458999999999999999


Q ss_pred             HHHHHhcc-CCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         118 KVVLALGD-FMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       118 ~~~~~~~~-~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                      +.+..... ..+..+.........     ....+++|+|+||++|++++.+
T Consensus       127 ~~~~~~~~~~~~~~~g~~~~~~~~-----~~~~~~~Ivv~Tpg~l~~~l~~  172 (235)
T 3llm_A          127 ERVAFERGEEPGKSCGYSVRFESI-----LPRPHASIMFCTVGVLLRKLEA  172 (235)
T ss_dssp             HHHHHTTTCCTTSSEEEEETTEEE-----CCCSSSEEEEEEHHHHHHHHHH
T ss_pred             HHHHHHhccccCceEEEeechhhc-----cCCCCCeEEEECHHHHHHHHHh
Confidence            88865433 344444433222111     1114589999999999999876

>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=99.68  E-value=1.1e-15  Score=138.86  Aligned_cols=122  Identities=18%  Similarity=0.134  Sum_probs=99.7

Q ss_pred             CCCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHc----CC--cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          37 MGLREDLLRGI-YAYGFEKPSAIQQRSIKPIVK----GR--DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        37 ~~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~----g~--~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      ++.+....+.+ ..++|+ +|++|.++++.+++    |+  ++++++|||+|||++|+.+++..+.   .+.+++|++||
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            45667777776 567885 79999999999987    65  9999999999999999988877554   45699999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH---HhcC-CCcEEEeChHHHH
Q psy9277         110 RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR---KLDY-GQHVVSGTPGRVF  162 (178)
Q Consensus       110 ~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~~-~~~IlV~TP~~l~  162 (178)
                      ++|+.|+++.+.++....++++..+.+.....+...   .+.. .++|+|+||+.|.
T Consensus       662 ~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~  718 (1151)
T 2eyq_A          662 TLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ  718 (1151)
T ss_dssp             HHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH
T ss_pred             HHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh
Confidence            999999999999888888899988887766554433   3334 4899999997663

>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=99.63  E-value=1.9e-15  Score=125.20  Aligned_cols=94  Identities=16%  Similarity=0.120  Sum_probs=81.9

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce-EE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ-CH  132 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~-~~  132 (178)
                      .|+++|.++++.++++.++++++|||+|||++|+.++...      +.++||++|+++|+.|.++.+.++    ++. +.
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------~~~~Lvl~P~~~L~~Q~~~~~~~~----~~~~v~  162 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------CSCEEEEESSHHHHHHHHHHGGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEECCHHHHHHHHHHHHhC----CCcceE
Confidence            5899999999999999999999999999999999988763      468999999999999999998774    677 77


Q ss_pred             EEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       133 ~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      .+.|+...         .++|+|+||+.+...+.
T Consensus       163 ~~~g~~~~---------~~~Ivv~T~~~l~~~~~  187 (472)
T 2fwr_A          163 EFSGRIKE---------LKPLTVSTYDSAYVNAE  187 (472)
T ss_dssp             EBSSSCBC---------CCSEEEEEHHHHHHTHH
T ss_pred             EECCCcCC---------cCCEEEEEcHHHHHHHH
Confidence            77776642         47899999999977664

>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=99.59  E-value=1.9e-14  Score=109.67  Aligned_cols=94  Identities=16%  Similarity=0.120  Sum_probs=79.6

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCce-EE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQ-CH  132 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~-~~  132 (178)
                      .++++|.+++..++++.++++++|||+|||.+++.++...      +.+++|++|+++|+.|.++.+.++    ++. +.
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------~~~~liv~P~~~L~~q~~~~~~~~----~~~~v~  162 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------STPTLIVVPTLALAEQWKERLGIF----GEEYVG  162 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------CSCEEEEESSHHHHHHHHHHHGGG----CGGGEE
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------CCCEEEEeCCHHHHHHHHHHHHhC----CCCeEE
Confidence            6899999999999999999999999999999998877652      468999999999999999998774    677 77


Q ss_pred             EEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       133 ~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      .+.|+..         ...+|+|+||+.+...+.
T Consensus       163 ~~~g~~~---------~~~~i~v~T~~~l~~~~~  187 (237)
T 2fz4_A          163 EFSGRIK---------ELKPLTVSTYDSAYVNAE  187 (237)
T ss_dssp             EESSSCB---------CCCSEEEEEHHHHHHTHH
T ss_pred             EEeCCCC---------CcCCEEEEeHHHHHhhHH
Confidence            7766653         257899999999876654

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.58  E-value=8.4e-15  Score=124.05  Aligned_cols=80  Identities=19%  Similarity=0.144  Sum_probs=69.7

Q ss_pred             CCCCCcHHHHHHHHHH----HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          51 GFEKPSAIQQRSIKPI----VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i----~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      || ++++.|.+++..+    ..|+++++.+|||+|||++|++|++.      .+.+++|++||++|+.|+.+.+..+.+.
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 5899999988754    46999999999999999999999998      3569999999999999999999988777


Q ss_pred             CCceEEEEEcC
Q psy9277         127 MNVQCHACIGG  137 (178)
Q Consensus       127 ~~~~~~~~~g~  137 (178)
                      .+++++.+.|.
T Consensus        74 ~~~~~~~l~gr   84 (551)
T 3crv_A           74 RNITFSFLVGK   84 (551)
T ss_dssp             SCCCEEECCCH
T ss_pred             cCccEEEEccc
Confidence            78888877663

>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=99.53  E-value=4.5e-15  Score=122.85  Aligned_cols=104  Identities=18%  Similarity=0.147  Sum_probs=79.6

Q ss_pred             CCCCCcHHHHHHHHHHHcCCcE-EEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          51 GFEKPSAIQQRSIKPIVKGRDV-IAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~g~~v-~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      |+..++++|. ++|.+++++++ ++++|||||||++|++|++..+..  .+.+++|++||++|+.|+++.+.      +.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~------g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL--RRLRTLILAPTRVVAAEMEEALR------GL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT------TS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh--cCCcEEEECCCHHHHHHHHHHhc------Cc
Confidence            6788999985 79999998887 999999999999999999987665  45799999999999999999874      23


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      .+....+....     ....+..|.++|++.+...+.+.
T Consensus        72 ~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~  105 (451)
T 2jlq_A           72 PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS  105 (451)
T ss_dssp             CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC
T ss_pred             eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc
Confidence            32221111111     11234579999999998777654

>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=99.52  E-value=6.4e-14  Score=122.81  Aligned_cols=131  Identities=18%  Similarity=0.194  Sum_probs=95.1

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-CCcEEEEcCCCChHHHHHHHHHHHHhh--hcCCCceEEE
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-GRDVIAQAQSGTGKTATFSISILQSLD--TQLRETQVLC  105 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-g~~v~v~aptGsGKTl~~ll~il~~l~--~~~~~~~~li  105 (178)
                      .+..+|+++++++.+.+.+.+.+ ..|++.|.++|+.++. +++++++||||||||+  ++|++....  ....+.++++
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            45778999999999999998877 6899999999998776 6789999999999998  455552221  1222567999


Q ss_pred             EcCcHHHHHHHHHHHHHhc-cCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcC
Q psy9277         106 LSPTRELAVQIQKVVLALG-DFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       106 l~Pt~~L~~q~~~~~~~~~-~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~  168 (178)
                      ++|+++|+.|+++.+.... ...+..+........      ....+.+|+++|||++.+.+...
T Consensus       146 l~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~  203 (773)
T 2xau_A          146 TQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED  203 (773)
T ss_dssp             EESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS
T ss_pred             cCchHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC
Confidence            9999999999998764432 223333332211111      11246789999999999887654

>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=99.47  E-value=1.4e-14  Score=124.38  Aligned_cols=91  Identities=14%  Similarity=0.122  Sum_probs=73.2

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEE
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHAC  134 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~  134 (178)
                      ++..|..+++.+..+++++++||||||||++|.+++++      ++.+++|++|||+||.|+++.+.+..   +..+...
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~------~g~~vLVl~PTReLA~Qia~~l~~~~---g~~vg~~  288 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAH---GIDPNIR  288 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHH------TTCCEEEEESCHHHHHHHHHHHHHHH---SCCCEEE
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHH------CCCeEEEEcchHHHHHHHHHHHHHHh---CCCeeEE
Confidence            45566666666778899999999999999999999886      35699999999999999999775543   4455566


Q ss_pred             EcCccHHHHHHHhcCCCcEEEeChHHH
Q psy9277         135 IGGTNLSEDLRKLDYGQHVVSGTPGRV  161 (178)
Q Consensus       135 ~g~~~~~~~~~~~~~~~~IlV~TP~~l  161 (178)
                      +|+..       ...+++|+|+||++|
T Consensus       289 vG~~~-------~~~~~~IlV~TPGrL  308 (666)
T 3o8b_A          289 TGVRT-------ITTGAPVTYSTYGKF  308 (666)
T ss_dssp             CSSCE-------ECCCCSEEEEEHHHH
T ss_pred             ECcEe-------ccCCCCEEEECcHHH
Confidence            66654       346789999999997

>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=99.46  E-value=1.4e-13  Score=123.56  Aligned_cols=108  Identities=16%  Similarity=0.107  Sum_probs=83.9

Q ss_pred             CCcHHHHHHHHHHHc--------------CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVK--------------GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~--------------g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      .|+++|.+|++.++.              +++.++.++||||||+++ ++++..+.......++|||+|+++|+.|+.+.
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              368999999999999997 56665554333346999999999999999999


Q ss_pred             HHHhccCCCceEEEEEcCccHHHHHHHhc-CCCcEEEeChHHHHHHHHcC
Q psy9277         120 VLALGDFMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTPGRVFDMIRSS  168 (178)
Q Consensus       120 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP~~l~~~l~~~  168 (178)
                      +..+....      +.++.+.......+. .+++|+|+||++|.+++...
T Consensus       350 f~~f~~~~------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~  393 (1038)
T 2w00_A          350 YQRFSPDS------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAE  393 (1038)
T ss_dssp             HHTTSTTC------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHC
T ss_pred             HHHhcccc------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcc
Confidence            98876431      234444555545553 46899999999999988754

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.41  E-value=3.4e-13  Score=113.95  Aligned_cols=67  Identities=21%  Similarity=0.254  Sum_probs=54.7

Q ss_pred             CCCCCCcHHHHHHHHH----HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          50 YGFEKPSAIQQRSIKP----IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~----i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .|| .|+++|.+++..    +..|+++++.+|||+|||++|++|++..      +.+++|++||++|+.|+.+.+..+
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 799999998765    4568999999999999999999998763      469999999999999999888664

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.41  E-value=1.7e-13  Score=116.61  Aligned_cols=100  Identities=23%  Similarity=0.224  Sum_probs=61.6

Q ss_pred             CCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHHHHHHHHhhhcC-------CCceEEEEcCcHHHHHHHH-HHH
Q psy9277          54 KPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFSISILQSLDTQL-------RETQVLCLSPTRELAVQIQ-KVV  120 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~ll~il~~l~~~~-------~~~~~lil~Pt~~L~~q~~-~~~  120 (178)
                      .|+++|.++++.+++     ++++++++|||+|||++++. ++..+....       ...++|||+|+++|+.|.+ +.+
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     46799999999999999654 444444433       5679999999999999999 766


Q ss_pred             HHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHH
Q psy9277         121 LALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       121 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~  166 (178)
                      +.+.    ..+..+.++        ....+.+|+|+||++|...+.
T Consensus       257 ~~~~----~~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~  290 (590)
T 3h1t_A          257 TPFG----DARHKIEGG--------KVVKSREIYFAIYQSIASDER  290 (590)
T ss_dssp             TTTC----SSEEECCC----------CCSSCSEEEEEGGGC-----
T ss_pred             Hhcc----hhhhhhhcc--------CCCCCCcEEEEEhhhhccccc
Confidence            6553    333333322        233468999999999988754

>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=99.39  E-value=1.6e-14  Score=123.88  Aligned_cols=82  Identities=22%  Similarity=0.208  Sum_probs=66.8

Q ss_pred             CCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          37 MGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        37 ~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +++++..++++... ...++|+|..+++.+++|+++++++|||||||++|++|+++.+..  .+.++||++||++||.|+
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            56777777777553 478899988899999999999999999999999999999998865  457999999999999999


Q ss_pred             HHHHH
Q psy9277         117 QKVVL  121 (178)
Q Consensus       117 ~~~~~  121 (178)
                      ++.+.
T Consensus       232 ~~~l~  236 (618)
T 2whx_A          232 EEALR  236 (618)
T ss_dssp             HHHTT
T ss_pred             HHHhc
Confidence            98875

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.35  E-value=1.3e-12  Score=112.02  Aligned_cols=84  Identities=26%  Similarity=0.265  Sum_probs=71.5

Q ss_pred             CCcHHHHHHHHHH----HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPI----VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i----~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      +|++.|.+++..+    .+|+++++.||||+|||++|++|++..+..  .+.+++|++||++++.|+.+.+..+....++
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~--~~~kvli~t~T~~l~~Qi~~el~~l~~~~~~   80 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSE--RKLKVLYLVRTNSQEEQVIKELRSLSSTMKI   80 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHH--HTCEEEEEESSHHHHHHHHHHHHHHHHHSCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhh--cCCeEEEECCCHHHHHHHHHHHHHHhhccCe
Confidence            5899999998644    569999999999999999999999998765  3469999999999999999999988877788


Q ss_pred             eEEEEEcCcc
Q psy9277         130 QCHACIGGTN  139 (178)
Q Consensus       130 ~~~~~~g~~~  139 (178)
                      +++.+.|..+
T Consensus        81 ~~~~l~gr~~   90 (620)
T 4a15_A           81 RAIPMQGRVN   90 (620)
T ss_dssp             CEEECCCHHH
T ss_pred             EEEEEECCCc
Confidence            8888877653

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.32  E-value=6.9e-14  Score=120.87  Aligned_cols=76  Identities=25%  Similarity=0.364  Sum_probs=64.0

Q ss_pred             HHHhCCCC-----CCcHHHH-----HHHHHHH------cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          46 GIYAYGFE-----KPSAIQQ-----RSIKPIV------KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        46 ~l~~~g~~-----~~~~~Q~-----~~i~~i~------~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      ++...||.     +|+++|.     .+||.++      +++|+++++|||||||++|++|+++.+..  .+.+++|++||
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            44556776     8999999     9999988      89999999999999999999999988765  45799999999


Q ss_pred             HHHHHHHHHHHHHh
Q psy9277         110 RELAVQIQKVVLAL  123 (178)
Q Consensus       110 ~~L~~q~~~~~~~~  123 (178)
                      ++||.|+++.+..+
T Consensus       280 r~La~Q~~~~l~~~  293 (673)
T 2wv9_A          280 RVVAAEMAEALRGL  293 (673)
T ss_dssp             HHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHhcC
Confidence            99999999988644

>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=99.22  E-value=1.3e-11  Score=102.30  Aligned_cols=92  Identities=14%  Similarity=0.136  Sum_probs=64.1

Q ss_pred             HHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHH
Q psy9277          63 IKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE  142 (178)
Q Consensus        63 i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~  142 (178)
                      ...+.+++++++++|||||||++|++|+++.+..  .+.++||++||++||.|+++.+.      +..+....+..... 
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~--~~~~~lvl~Ptr~La~Q~~~~l~------g~~v~~~~~~~~~~-   85 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ--QRLRTAVLAPTRVVAAEMAEALR------GLPVRYQTSAVQRE-   85 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH--TTCCEEEEECSHHHHHHHHHHTT------TSCEEECC-------
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEECchHHHHHHHHHHhc------CceEeEEecccccC-
Confidence            3445668999999999999999999999998765  45799999999999999999886      22222211111110 


Q ss_pred             HHHHhcCCCcEEEeChHHHHHHHHc
Q psy9277         143 DLRKLDYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       143 ~~~~~~~~~~IlV~TP~~l~~~l~~  167 (178)
                          -..+..+.+.|.+.+...+.+
T Consensus        86 ----~t~~~~i~~~~~~~l~~~l~~  106 (459)
T 2z83_A           86 ----HQGNEIVDVMCHATLTHRLMS  106 (459)
T ss_dssp             ------CCCSEEEEEHHHHHHHHHS
T ss_pred             ----CCCCcEEEEEchHHHHHHhhc
Confidence                112345677888887665544

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.19  E-value=4.7e-11  Score=98.25  Aligned_cols=87  Identities=13%  Similarity=0.081  Sum_probs=60.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL  147 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~  147 (178)
                      +|+++++++|||||||++|++|+++.+..  .+.+++|++||++|+.|+++.+.      ++.+....|+...     .-
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~--~g~~~lvl~Pt~~La~Q~~~~~~------~~~v~~~~~~~~~-----~~   67 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK--KRLRTVILAPTRVVASEMYEALR------GEPIRYMTPAVQS-----ER   67 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT------TSCEEEC-------------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh--CCCCEEEECcHHHHHHHHHHHhC------CCeEEEEecCccc-----cC
Confidence            37899999999999999999999976654  45699999999999999998775      4444444443221     11


Q ss_pred             cCCCcEEEeChHHHHHHHHc
Q psy9277         148 DYGQHVVSGTPGRVFDMIRS  167 (178)
Q Consensus       148 ~~~~~IlV~TP~~l~~~l~~  167 (178)
                      ..+..+.+.|.+.+...+.+
T Consensus        68 ~~~~~~~~~~~~~l~~~l~~   87 (431)
T 2v6i_A           68 TGNEIVDFMCHSTFTMKLLQ   87 (431)
T ss_dssp             -CCCSEEEEEHHHHHHHHHH
T ss_pred             CCCceEEEEchHHHHHHHhc
Confidence            12345667788887655544

>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=99.16  E-value=1.1e-10  Score=97.29  Aligned_cols=102  Identities=10%  Similarity=0.031  Sum_probs=76.3

Q ss_pred             CCcHHHHHHHHHH----HcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPI----VKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i----~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      .|+++|.++++.+    ..+.++++..+||+|||+.++..+ ..+.......++||||| .+|+.|..+.++++..  +.
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i-~~~~~~~~~~~~LIv~P-~~l~~qw~~e~~~~~~--~~  112 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKENELTPSLVICP-LSVLKNWEEELSKFAP--HL  112 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCT--TS
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHH-HHHHhcCCCCCEEEEcc-HHHHHHHHHHHHHHCC--Cc
Confidence            6999999998766    358899999999999999975544 44444444568999999 5699999999998865  45


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDM  164 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~  164 (178)
                      ++..+.|+...     ......+|+|+||+.+...
T Consensus       113 ~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~  142 (500)
T 1z63_A          113 RFAVFHEDRSK-----IKLEDYDIILTTYAVLLRD  142 (500)
T ss_dssp             CEEECSSSTTS-----CCGGGSSEEEEEHHHHTTC
T ss_pred             eEEEEecCchh-----ccccCCcEEEeeHHHHhcc
Confidence            56666555422     1123579999999998543

>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=99.15  E-value=1.8e-11  Score=100.99  Aligned_cols=57  Identities=28%  Similarity=0.426  Sum_probs=50.5

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .+++|+|+++++|||||||++|++|+++.+..  .+.+++|++||++||.|+++.+..+
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~--~~~~~lil~Ptr~La~Q~~~~l~~~   60 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFHGL   60 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh--cCCeEEEEcchHHHHHHHHHHHhcC
Confidence            45679999999999999999999999997765  4579999999999999999988643

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.07  E-value=2e-10  Score=99.31  Aligned_cols=105  Identities=19%  Similarity=0.160  Sum_probs=69.4

Q ss_pred             CHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          40 REDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        40 ~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      ..+.++++.+++.  |.  |.......++|++++++||||||||+    ++++.+...   ..++|++||++||.|+++.
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--PP--NWYPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSA---KSGVYCGPLKLLAHEIFEK  198 (677)
T ss_dssp             CHHHHHHHTBCCC--GG--GGCHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHS---SSEEEEESSHHHHHHHHHH
T ss_pred             CHHHHHHHhhccC--hh--hhCHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhc---CCeEEEeCHHHHHHHHHHH
Confidence            3344455544433  32  22223345679999999999999998    444444432   3459999999999999999


Q ss_pred             HHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH
Q psy9277         120 VLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV  161 (178)
Q Consensus       120 ~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l  161 (178)
                      +...    ++.+..++|+......  .-....+++++|++.+
T Consensus       199 l~~~----g~~v~lltG~~~~iv~--TpGr~~~il~~T~e~~  234 (677)
T 3rc3_A          199 SNAA----GVPCDLVTGEERVTVQ--PNGKQASHVSCTVEMC  234 (677)
T ss_dssp             HHHT----TCCEEEECSSCEECCS--TTCCCCSEEEEEGGGC
T ss_pred             HHhc----CCcEEEEECCeeEEec--CCCcccceeEecHhHh
Confidence            9876    7788888888655100  0001257888888654

>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=99.04  E-value=5.2e-10  Score=100.28  Aligned_cols=104  Identities=15%  Similarity=0.035  Sum_probs=75.7

Q ss_pred             CCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceE
Q psy9277          54 KPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQC  131 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~  131 (178)
                      .|+++|.+++..++.  +.+++++++||+|||+.++..+...+.. ....++|||||+ +|+.|..+.+.+..   ++.+
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~-g~~~rvLIVvP~-sLl~Qw~~E~~~~f---~l~v  227 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLS-GAAERVLIIVPE-TLQHQWLVEMLRRF---NLRF  227 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHT-SSCCCEEEECCT-TTHHHHHHHHHHHS---CCCC
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHh-CCCCeEEEEeCH-HHHHHHHHHHHHHh---CCCE
Confidence            689999999998877  4589999999999999997777665543 334589999999 99999999886554   5555


Q ss_pred             EEEEcCccHHHHHH--HhcCCCcEEEeChHHHH
Q psy9277         132 HACIGGTNLSEDLR--KLDYGQHVVSGTPGRVF  162 (178)
Q Consensus       132 ~~~~g~~~~~~~~~--~~~~~~~IlV~TP~~l~  162 (178)
                      ..+.++........  ......+|+|+|++.+.
T Consensus       228 ~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~  260 (968)
T 3dmq_A          228 ALFDDERYAEAQHDAYNPFDTEQLVICSLDFAR  260 (968)
T ss_dssp             EECCHHHHHHHHHTTCSSSTTCSEEEECHHHHH
T ss_pred             EEEccchhhhhhhhcccccccCCEEEEcHHHHh
Confidence            55544332221111  11135699999998884

>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=99.02  E-value=2.9e-09  Score=91.94  Aligned_cols=83  Identities=17%  Similarity=0.171  Sum_probs=72.7

Q ss_pred             HhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCC
Q psy9277          48 YAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM  127 (178)
Q Consensus        48 ~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~  127 (178)
                      +-+|. +|+++|....-.+..|+  +..+.||+|||+++.+|++-...   .+..+.+|+|+..||.|-++.+..+.+.+
T Consensus        70 R~lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL---~G~~vhVvT~ndyLA~rdae~m~~l~~~L  143 (822)
T 3jux_A           70 RTLGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNAL---IGKGVHLVTVNDYLARRDALWMGPVYLFL  143 (822)
T ss_dssp             HHTSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHT---TSSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             HHhCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHh---cCCceEEEeccHHHHHhHHHHHHHHHHHh
Confidence            34576 69999999998888887  99999999999999999874433   35679999999999999999999999999


Q ss_pred             CceEEEEEc
Q psy9277         128 NVQCHACIG  136 (178)
Q Consensus       128 ~~~~~~~~g  136 (178)
                      |+++.+++.
T Consensus       144 glsvg~i~~  152 (822)
T 3jux_A          144 GLRVGVINS  152 (822)
T ss_dssp             TCCEEEEET
T ss_pred             CCEEEEEcC
Confidence            999999887

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.95  E-value=4.1e-09  Score=92.77  Aligned_cols=108  Identities=15%  Similarity=0.152  Sum_probs=82.3

Q ss_pred             CCcHHHHHHHHHHH----cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPIV----KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~----~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      .++++|.+++..+.    .+.+.++..++|.|||+..+..+...+........+||||| .+|+.|..+.+.++..  ++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P-~sll~qW~~E~~~~~p--~~  312 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVP-LSTMPAWLDTFEKWAP--DL  312 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECC-TTTHHHHHHHHHHHST--TC
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEEC-chHHHHHHHHHHHHCC--Cc
Confidence            68899999997655    68999999999999999987766655544445567899999 7888999999988864  56


Q ss_pred             eEEEEEcCccHHHHHHHh------------cCCCcEEEeChHHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRKL------------DYGQHVVSGTPGRVFDM  164 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~------------~~~~~IlV~TP~~l~~~  164 (178)
                      ++..+.|+..........            ...++|+|+|++.+...
T Consensus       313 ~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~  359 (800)
T 3mwy_W          313 NCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKD  359 (800)
T ss_dssp             CEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHT
T ss_pred             eEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhh
Confidence            777777776554433321            23568999999998653

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=98.83  E-value=3.7e-08  Score=84.83  Aligned_cols=109  Identities=19%  Similarity=0.085  Sum_probs=77.8

Q ss_pred             CCcHHHHHHHHHHH---------cCCcEEEEcCCCChHHHHHHHHHHHHhhhcC----CCceEEEEcCcHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIV---------KGRDVIAQAQSGTGKTATFSISILQSLDTQL----RETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~---------~g~~v~v~aptGsGKTl~~ll~il~~l~~~~----~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      .++|+|.+++..+.         .+.+.++..++|.|||+..+..+...+....    ...++|||+|+ +|+.|..+.+
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            68999999998764         4578999999999999998776665443321    12468999997 8889999999


Q ss_pred             HHhccCCCceEEEEEcCccHHHH--HHH-hc-----CCCcEEEeChHHHHHH
Q psy9277         121 LALGDFMNVQCHACIGGTNLSED--LRK-LD-----YGQHVVSGTPGRVFDM  164 (178)
Q Consensus       121 ~~~~~~~~~~~~~~~g~~~~~~~--~~~-~~-----~~~~IlV~TP~~l~~~  164 (178)
                      .++... .+.++.+.++......  ... ..     ...+|+|+|++.+...
T Consensus       134 ~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~  184 (644)
T 1z3i_X          134 GKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLH  184 (644)
T ss_dssp             HHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHH
T ss_pred             HHHcCC-CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhh
Confidence            888654 4666666666543221  111 11     1368999999998654

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.45  E-value=3.7e-07  Score=78.09  Aligned_cols=66  Identities=17%  Similarity=0.170  Sum_probs=55.8

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHH--HHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHH
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKT--ATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLA  122 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKT--l~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~  122 (178)
                      ++.|..+++.++.++.+++.|++|+|||  ++++++.+..+.. ..+.++++++||...|.++.+.+..
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~-~~~~~vll~APTg~AA~~L~e~~~~  218 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-GERCRIRLAAPTGKAAARLTESLGK  218 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-SCCCCEEEEBSSHHHHHHHHHHHTH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh-cCCCeEEEEeCChhHHHHHHHHHHH
Confidence            7899999999999999999999999999  6677777765432 2456899999999999999887754

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.96  E-value=3.4e-05  Score=66.35  Aligned_cols=67  Identities=22%  Similarity=0.278  Sum_probs=54.2

Q ss_pred             CCcHHHHHHHHHHHcCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          54 KPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .+++-|.+|+..++..+ -.+|.||+|||||.+.+-.+.+.+.   .+.++|+++||..-|.++.+.+...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~---~~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVK---QGLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEcCchHHHHHHHHHHHhc
Confidence            47899999999988765 5689999999999886555544433   4568999999999999999888654

>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=97.87  E-value=5.3e-05  Score=65.46  Aligned_cols=69  Identities=32%  Similarity=0.385  Sum_probs=53.3

Q ss_pred             CCCCCcHHHHHHHHHHHc----CC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          51 GFEKPSAIQQRSIKPIVK----GR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~----g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      +| .|+..|..++..+..    |. ..++.+.||||||+++.-.+ ...     +..+|||+|+..+|.|+++.++.|..
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~-~~~-----~~~~lvv~~~~~~A~ql~~el~~~~~   78 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVI-EAL-----GRPALVLAPNKILAAQLAAEFRELFP   78 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHH-HHH-----TCCEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHH-HHh-----CCCEEEEecCHHHHHHHHHHHHHHCC
Confidence            56 799999999887654    33 57789999999997764322 222     22589999999999999999999964


Q ss_pred             C
Q psy9277         126 F  126 (178)
Q Consensus       126 ~  126 (178)
                      .
T Consensus        79 ~   79 (664)
T 1c4o_A           79 E   79 (664)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=97.85  E-value=6.6e-05  Score=64.37  Aligned_cols=69  Identities=23%  Similarity=0.256  Sum_probs=55.1

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..+++.|.+++..++.+..++|.||+|+|||....- ++..+... .+.++++++||..-+.++.+.+...
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~~-~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHHH-HHHHHHTS-SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHHH-HHHHHHHc-CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            457899999999999888899999999999987543 33333322 4568999999999999999887654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.83  E-value=7.3e-05  Score=65.90  Aligned_cols=69  Identities=17%  Similarity=0.258  Sum_probs=55.2

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..+++.|.+|+..++.+.-++|.||+|+|||....--+ ..+... .+.++++++||..-+.++.+.+...
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~~i-~~l~~~-~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIV-YHLSKI-HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHHHH-HHHHHH-HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHH-HHHHhC-CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            45789999999999888889999999999998754333 333321 3458999999999999999988765

>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=97.74  E-value=0.0001  Score=62.99  Aligned_cols=70  Identities=14%  Similarity=0.212  Sum_probs=55.7

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC-CCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL-RETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~-~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      ..+++-|.+++..  .+..++|.|+.|||||.+.+--+.+.+.... ...+++++++|+..+.++.+.+..+.
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            4689999999973  3678999999999999887665655554322 33589999999999999999997764

>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=97.68  E-value=0.00018  Score=63.43  Aligned_cols=69  Identities=23%  Similarity=0.266  Sum_probs=55.0

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      ..+++.|.+++..++.+.-.+|.||+|+|||.... .++..+... .+.++++++||..-|.++.+.+...
T Consensus       355 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~~-~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHTT-CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHHc-CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            35789999999999988889999999999998754 333444332 4568999999999999998887654

>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=97.62  E-value=0.00021  Score=58.97  Aligned_cols=72  Identities=21%  Similarity=0.258  Sum_probs=52.1

Q ss_pred             HHhCCCCCCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          47 IYAYGFEKPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        47 l~~~g~~~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      ...+.|..+++-|.+++..++.     ...+++.|+.|||||... ..++..+... ....+++++||...+..+...+
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~-~~~~il~~a~T~~Aa~~l~~~~   94 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALIST-GETGIILAAPTHAAKKILSKLS   94 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHT-TCCCEEEEESSHHHHHHHHHHH
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhc-CCceEEEecCcHHHHHHHHhhh
Confidence            3456788999999999987754     239999999999999654 3444444443 2247899999999888776544

>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=97.56  E-value=0.00032  Score=59.55  Aligned_cols=63  Identities=22%  Similarity=0.228  Sum_probs=51.1

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      .+++.|.+++..++.+..+++.|++|+|||... ..++..+..  .+.++++++||...+..+.+.
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~--~g~~Vl~~ApT~~Aa~~L~e~  251 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES--LGLEVGLCAPTGKAARRLGEV  251 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH--TTCCEEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh--cCCeEEEecCcHHHHHHhHhh
Confidence            589999999999999999999999999999663 334443333  456899999999999888764

>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=97.51  E-value=0.00028  Score=60.85  Aligned_cols=70  Identities=16%  Similarity=0.150  Sum_probs=55.9

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+++-|.+++..  .+..++|.|+.|||||.+.+--+.+.+... ....++++|+.|+..|.++.+.+.....
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            478999998875  367899999999999988766665555442 2345899999999999999999977754

>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=97.31  E-value=0.00057  Score=62.90  Aligned_cols=68  Identities=19%  Similarity=0.300  Sum_probs=55.8

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcC---CCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQL---RETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~---~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .+|+-|.+++..-  +.+++|.|..|||||.+.+--++..+....   ...+++++++|++.|.++.+.+...
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            5899999998754  889999999999999887766776665432   3358999999999999999988653

>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=97.24  E-value=0.0012  Score=57.41  Aligned_cols=70  Identities=19%  Similarity=0.250  Sum_probs=55.7

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhc
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALG  124 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~  124 (178)
                      ..+++-|.+++..  .+..++|.|+.|||||.+.+--+.+.+... -...++++|+.|+..|.++.+.+..+.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            4689999998865  357899999999999988776666655432 234589999999999999999887764

>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=97.20  E-value=0.0019  Score=55.69  Aligned_cols=67  Identities=25%  Similarity=0.322  Sum_probs=50.7

Q ss_pred             CCcHHHHHHHHHHHc----CC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          54 KPSAIQQRSIKPIVK----GR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      .|+..|..++..+..    |. ...+.+-||||||++..-. +...    + ..+|||+|+..+|.|.+..++.|...
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~-~~~~----~-~~~lvv~~~~~~A~~l~~el~~~~~~   83 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNL-IKEV----N-KPTLVIAHNKTLAGQLYSEFKEFFPN   83 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHH-HHHH----C-CCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHH-HHHh----C-CCEEEEECCHHHHHHHHHHHHHHcCC
Confidence            688899888876553    43 4778899999999765422 2221    2 25899999999999999999999643

>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=96.88  E-value=0.0065  Score=51.67  Aligned_cols=72  Identities=13%  Similarity=0.133  Sum_probs=57.9

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      .++++|...+..+...+.+++..+-++|||.+....++..+... .+..+++++|+.+.|..+++.++.+.+.
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~-~~~~i~~va~t~~qA~~~~~~i~~~i~~  234 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN-KDKAVGILAHKGSMSAEVLDRTKQAIEL  234 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS-SSCEEEEEESSHHHHHHHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC-CCCeEEEEECCHHHHHHHHHHHHHHHHh
Confidence            47999999998876678899999999999998776555554433 3458999999999999999888776543

>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=96.85  E-value=0.0061  Score=49.24  Aligned_cols=71  Identities=13%  Similarity=0.108  Sum_probs=56.8

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .++++|...+..+...+.+++..+-+.|||.+....++..+.. ..+..+++++|+++.|..+++.+..+.+
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~-~~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-NKDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS-SSSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh-CCCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            6899999999877666779999999999999877666654443 2456899999999999988887766543

>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=96.30  E-value=0.026  Score=39.86  Aligned_cols=58  Identities=14%  Similarity=0.080  Sum_probs=45.1

Q ss_pred             cCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          97 QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        97 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .....++||.++++..+..++..+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus        31 ~~~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~   92 (175)
T 2rb4_A           31 SITIGQAIIFCQTRRNAKWLTVEMIQD----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN   92 (175)
T ss_dssp             TSCCSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC
T ss_pred             hCCCCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec
Confidence            334569999999999999999888654    788899999988776655442    3578999993

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=96.24  E-value=0.027  Score=39.36  Aligned_cols=55  Identities=15%  Similarity=0.203  Sum_probs=44.1

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      .+.++||.++++..+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|
T Consensus        34 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T   92 (163)
T 2hjv_A           34 NPDSCIIFCRTKEHVNQLTDELDDL----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVAT   92 (163)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEC
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEC
Confidence            4568999999999999999988765    788899999988776554442    346899999

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=96.05  E-value=0.039  Score=38.57  Aligned_cols=56  Identities=13%  Similarity=0.050  Sum_probs=44.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.+++++.+..++..+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus        29 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~   88 (165)
T 1fuk_A           29 SVTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD   88 (165)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC
Confidence            4568999999999999999888764    678889999988776654442    3568999993

>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=96.02  E-value=0.048  Score=38.50  Aligned_cols=56  Identities=14%  Similarity=0.247  Sum_probs=44.7

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++++..+..+++.+...    ++.+..++|+.+..++...+.    ....|+|+|.
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~   89 (172)
T 1t5i_A           30 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN   89 (172)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC
Confidence            4568999999999999999988765    788889999988776554443    3578999994

>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=95.89  E-value=0.047  Score=39.99  Aligned_cols=56  Identities=20%  Similarity=0.195  Sum_probs=45.1

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++++.-+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus        30 ~~~~~lVF~~~~~~~~~l~~~L~~~----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~   89 (212)
T 3eaq_A           30 SPDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD   89 (212)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHHH----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHc----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC
Confidence            4569999999999999999988765    788899999988776655443    3468999993

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.78  E-value=0.0041  Score=50.99  Aligned_cols=57  Identities=16%  Similarity=0.235  Sum_probs=37.3

Q ss_pred             ccccccccccCCCCHHHHHHHHhCC---CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYG---FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g---~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+..+|++++--+...+.|.+.=   +..|..++..   -+.-.+.+++.||+|+|||+.+
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~---g~~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDM---GIRAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHH---CCCCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCeeEEECcCCCCHHHHH
Confidence            3467789999987777777775421   1122222221   1222589999999999999775

>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=95.58  E-value=0.16  Score=42.18  Aligned_cols=52  Identities=12%  Similarity=0.222  Sum_probs=39.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+....+.+-+|||||++..-.+     .. .+..+|+|+|+...|.|+++.++.+..
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a~l~-----~~-~~~p~lvv~~~~~~A~~l~~~l~~~~~   64 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVAEIA-----ER-HAGPVVLIAPDMQNALRLHDEISQFTD   64 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHHHHH-----HH-SSSCEEEEESSHHHHHHHHHHHHHTCS
T ss_pred             CCCeEEEeCCCchHHHHHHHHHH-----HH-hCCCEEEEeCCHHHHHHHHHHHHhhCC
Confidence            46678999999999996542211     11 233589999999999999999998864

>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=95.28  E-value=0.022  Score=40.32  Aligned_cols=49  Identities=16%  Similarity=0.299  Sum_probs=28.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      .|+.+++.||+|+|||...-. +...+... .+..+++ .+..++...+...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~~~-i~~~~~~~-~g~~~~~-~~~~~~~~~~~~~   85 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLAVA-TLKAIYEK-KGIRGYF-FDTKDLIFRLKHL   85 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHHHH-HHHHHHHH-SCCCCCE-EEHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHH-HHHHHHHH-cCCeEEE-EEHHHHHHHHHHH
Confidence            378999999999999976532 33333212 2323333 4555565555443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.17  E-value=0.017  Score=46.83  Aligned_cols=57  Identities=25%  Similarity=0.281  Sum_probs=34.5

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHH-HHHHH--HHcCCcEEEEcCCCChHHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ-RSIKP--IVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~-~~i~~--i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..|..+|++.+=-+...+.|++. +.  +|... +.+..  +.-.+.+++.||+|+|||+.+-
T Consensus       141 ~~p~v~~~dIgGl~~~k~~l~e~-v~--~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAk  200 (405)
T 4b4t_J          141 KVPDSTYDMVGGLTKQIKEIKEV-IE--LPVKHPELFESLGIAQPKGVILYGPPGTGKTLLAR  200 (405)
T ss_dssp             CSCSCCGGGSCSCHHHHHHHHHH-TH--HHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHH
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHH-HH--HHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHH
Confidence            34678899997556666666542 11  22111 11111  2225899999999999997753

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.07  E-value=0.011  Score=48.40  Aligned_cols=57  Identities=25%  Similarity=0.306  Sum_probs=34.1

Q ss_pred             cccccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+..+|++++=-+...+.|++.   -+..|-.++..   -+.-.+.+++.||+|+|||+.+-
T Consensus       174 ~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~---g~~~prGvLL~GPPGtGKTllAk  233 (437)
T 4b4t_L          174 EQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRV---GIKPPKGVLLYGPPGTGKTLLAK  233 (437)
T ss_dssp             ESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTSSHHHHHH
T ss_pred             cCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCeEEEECCCCCcHHHHHH
Confidence            45677899997555555555432   01111111111   11225899999999999997753

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.91  E-value=0.018  Score=47.55  Aligned_cols=56  Identities=18%  Similarity=0.230  Sum_probs=35.9

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHH-HHHHHH--HHcCCcEEEEcCCCChHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQ-QRSIKP--IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q-~~~i~~--i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|..+|++.+=-+.+.+.|++. +.  +|.. -+.+..  +.-.+.+++.||+|+|||+.+
T Consensus       202 e~P~vt~~DIgGl~~~k~~L~e~-V~--~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          202 EKPDVTYSDVGGCKDQIEKLREV-VE--LPLLSPERFATLGIDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SSCSCCCSSCTTCHHHHHHHHHH-TH--HHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCCCCHHHhccHHHHHHHHHHH-HH--HHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHH
Confidence            35668899998777777777643 11  1111 122222  223689999999999999765

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=94.85  E-value=0.22  Score=35.81  Aligned_cols=54  Identities=20%  Similarity=0.266  Sum_probs=44.0

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      +.++||.+++++-+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT  111 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT  111 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc
Confidence            458999999999999999988765    788889999988776655443    357899999

>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=94.83  E-value=0.38  Score=40.03  Aligned_cols=77  Identities=6%  Similarity=0.024  Sum_probs=53.9

Q ss_pred             hHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEe
Q psy9277          81 GKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSG  156 (178)
Q Consensus        81 GKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~  156 (178)
                      .+....+-.+...+.....+.++||.++++.-+..+++.+..... .++.+..++|+.+..++...+.    ...+|||+
T Consensus       320 ~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~~l~~~L~~~~~-~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLva  398 (563)
T 3i5x_A          320 NSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVC  398 (563)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEE
T ss_pred             hhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHHHHHHHHHHhcc-CCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEE
Confidence            333333333444444434567999999999999999999877643 2678888999988776655443    45799999


Q ss_pred             Ch
Q psy9277         157 TP  158 (178)
Q Consensus       157 TP  158 (178)
                      |.
T Consensus       399 T~  400 (563)
T 3i5x_A          399 TD  400 (563)
T ss_dssp             CG
T ss_pred             cc
Confidence            94

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.69  E-value=0.029  Score=38.36  Aligned_cols=21  Identities=10%  Similarity=0.099  Sum_probs=17.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ...+.++++.|++|+|||..+
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHH
T ss_pred             hCCCCcEEEECCCCccHHHHH
Confidence            345789999999999999654

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.67  E-value=0.018  Score=47.17  Aligned_cols=57  Identities=21%  Similarity=0.166  Sum_probs=33.6

Q ss_pred             cccccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+..+|++.+=-+.+.+.|.+.   -+..|-.++..   -+.-.+.+++.||+|+|||+.+-
T Consensus       165 ~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~---g~~~prGiLL~GPPGtGKT~lak  224 (428)
T 4b4t_K          165 EKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQI---GIDPPRGVLLYGPPGTGKTMLVK  224 (428)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHH---CCCCCCEEEEESCTTTTHHHHHH
T ss_pred             CCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCceEEEECCCCCCHHHHHH
Confidence            45667899987555555555431   01111111111   12235789999999999997753

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=94.65  E-value=0.036  Score=37.95  Aligned_cols=21  Identities=19%  Similarity=0.158  Sum_probs=17.8

Q ss_pred             HcCCcEEEEcCCCChHHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+.++++.||+|+|||..+-
T Consensus        22 ~~~~~vll~G~~GtGKt~lA~   42 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGAR   42 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHHH
Confidence            357899999999999997663

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=94.51  E-value=0.039  Score=45.34  Aligned_cols=44  Identities=25%  Similarity=0.308  Sum_probs=33.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      +-.++.|+.|+|||....-    .+.    ....++++||++++.++.+.+.
T Consensus       162 ~v~~I~G~aGsGKTt~I~~----~~~----~~~~lVlTpT~~aa~~l~~kl~  205 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEILS----RVN----FEEDLILVPGRQAAEMIRRRAN  205 (446)
T ss_dssp             EEEEEEECTTSCHHHHHHH----HCC----TTTCEEEESCHHHHHHHHHHHT
T ss_pred             cEEEEEcCCCCCHHHHHHH----Hhc----cCCeEEEeCCHHHHHHHHHHhh
Confidence            4568999999999976532    111    1356999999999999888875

>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=94.50  E-value=0.12  Score=36.98  Aligned_cols=71  Identities=14%  Similarity=0.240  Sum_probs=43.2

Q ss_pred             CChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEE
Q psy9277          79 GTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVV  154 (178)
Q Consensus        79 GsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~Il  154 (178)
                      .+.|-. .+.-++..   ...+.++||.++++.-+..+++.+...    ++.+..++|+.+..++...+.    ....|+
T Consensus        29 ~~~K~~-~L~~ll~~---~~~~~k~lVF~~~~~~~~~l~~~L~~~----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vL  100 (185)
T 2jgn_A           29 ESDKRS-FLLDLLNA---TGKDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPIL  100 (185)
T ss_dssp             GGGHHH-HHHHHHHH---C-CCSCEEEEESCHHHHHHHHHHHHHT----TCCEEEEC--------CHHHHHHHHTSSSEE
T ss_pred             cHHHHH-HHHHHHHh---cCCCCeEEEEECCHHHHHHHHHHHHHc----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEE
Confidence            455643 33334332   224568999999999999999988764    788888998876655433332    357899


Q ss_pred             EeC
Q psy9277         155 SGT  157 (178)
Q Consensus       155 V~T  157 (178)
                      |+|
T Consensus       101 vaT  103 (185)
T 2jgn_A          101 VAT  103 (185)
T ss_dssp             EEE
T ss_pred             EEc
Confidence            999

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=94.42  E-value=0.14  Score=39.68  Aligned_cols=55  Identities=18%  Similarity=0.199  Sum_probs=43.7

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      .+.++||.+++++-+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|
T Consensus        27 ~~~~~LVF~~t~~~~~~l~~~L~~~----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT   85 (300)
T 3i32_A           27 SPDRAMVFTRTKAETEEIAQGLLRL----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVAT   85 (300)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHTT----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEEC
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEe
Confidence            3569999999999999888887544    788999999988766655443    357899999

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=94.35  E-value=0.52  Score=39.57  Aligned_cols=67  Identities=6%  Similarity=0.047  Sum_probs=49.6

Q ss_pred             HHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          91 LQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        91 l~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ...+.....+.++||.++++.-+..+++.+..... .++.+..++|+.+..++...+.    ...+|||+|-
T Consensus       279 ~~~~~~~~~~~~~iVF~~t~~~~~~l~~~L~~~~~-~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~  349 (579)
T 3sqw_A          279 KKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFK-KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD  349 (579)
T ss_dssp             HHHHHHTTTCCEEEEECSSHHHHHHHHHHHHHHHT-TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG
T ss_pred             HHHHhhcCCCCcEEEECCcHHHHHHHHHHHHHhhc-CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc
Confidence            33333334567999999999999999999977643 2678888999988776554443    4578999994

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.23  E-value=0.019  Score=43.63  Aligned_cols=57  Identities=19%  Similarity=0.243  Sum_probs=34.8

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH--HHcCCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP--IVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~--i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|+++.-.+...+.+.+.- ..+ ....+.+..  +..+.++++.||+|+|||...-
T Consensus        11 ~~~~~~~~i~G~~~~~~~l~~~~-~~~-~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~   69 (285)
T 3h4m_A           11 RPNVRYEDIGGLEKQMQEIREVV-ELP-LKHPELFEKVGIEPPKGILLYGPPGTGKTLLAK   69 (285)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHT-HHH-HHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHH
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHH-HHH-hhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHH
Confidence            44567888887777777775421 100 011122222  2346789999999999997653

>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=94.01  E-value=0.34  Score=38.19  Aligned_cols=56  Identities=9%  Similarity=0.070  Sum_probs=44.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ...++||.+++++-+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       257 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~  316 (400)
T 1s2m_A          257 QINQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD  316 (400)
T ss_dssp             CCSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS
T ss_pred             CCCcEEEEEecHHHHHHHHHHHHhc----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC
Confidence            4568999999999999999988776    678888999988766554442    3468999993

>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=93.84  E-value=0.24  Score=39.09  Aligned_cols=56  Identities=14%  Similarity=0.073  Sum_probs=44.9

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++++..+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       265 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~  324 (412)
T 3fht_A          265 TIAQAMIFCHTRKTASWLAAELSKE----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN  324 (412)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhC----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC
Confidence            4468999999999999999998766    678888999988776655442    3578999994

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=93.73  E-value=0.34  Score=38.38  Aligned_cols=56  Identities=13%  Similarity=0.202  Sum_probs=44.9

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.+++++.+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~  334 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA  334 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC
Confidence            4568999999999999999988764    788899999988776654443    3578999994

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=93.70  E-value=0.03  Score=45.87  Aligned_cols=57  Identities=23%  Similarity=0.300  Sum_probs=33.9

Q ss_pred             ccccccccccCCCCHHHHHHHHhC---CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAY---GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~---g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+..+|++++=-+.+.+.|++.   -+..|--++..   -+.-.+.+++.||+|+|||+.+
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~---Gi~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEM---GIKPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHH---TCCCCSEEEEESSTTTTHHHHH
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhC---CCCCCCCCceECCCCchHHHHH
Confidence            345678999987444444444331   11222222221   1222589999999999999765

>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=93.62  E-value=0.097  Score=41.29  Aligned_cols=42  Identities=12%  Similarity=-0.014  Sum_probs=26.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt~  110 (178)
                      |.-+++.||+|+|||...+-.+.......   ..+..++|+.-..
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            45689999999999987655444322211   0244777776543

>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=93.58  E-value=0.36  Score=37.73  Aligned_cols=56  Identities=14%  Similarity=0.049  Sum_probs=44.4

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ...++||.++++.-+..+++.++..    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       242 ~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~  301 (395)
T 3pey_A          242 TIGSSIIFVATKKTANVLYGKLKSE----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN  301 (395)
T ss_dssp             TSSEEEEECSCHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHhc----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC
Confidence            4568999999999999999988765    678888999988776555442    3468999994

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=93.57  E-value=0.099  Score=38.44  Aligned_cols=52  Identities=19%  Similarity=0.189  Sum_probs=32.2

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      +..|.-+++.||+|+|||...+--+.... .  .+..++|+.-.. ...++.+.+.
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~~~~~~~~-~--~~~~v~~~~~e~-~~~~~~~~~~   71 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQQFLWNGL-K--MGEPGIYVALEE-HPVQVRQNMA   71 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHHH-H--TTCCEEEEESSS-CHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHH-h--cCCeEEEEEccC-CHHHHHHHHH
Confidence            34578899999999999987554333332 2  344677776432 2345554444

>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=93.54  E-value=0.023  Score=43.97  Aligned_cols=55  Identities=18%  Similarity=0.294  Sum_probs=33.0

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHH-HHHHH--HHcCCcEEEEcCCCChHHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQ-RSIKP--IVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~-~~i~~--i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+|++++-.+.+.+.|.+. +.  ++... +.+..  +..++.+++.||+|+|||...-
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~-v~--~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~   67 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQEL-VQ--YPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAK   67 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHH-HH--HHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHH-HH--HHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHH
Confidence            456788887667666666542 10  11100 11111  2346789999999999997653

>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=93.31  E-value=0.12  Score=41.84  Aligned_cols=44  Identities=16%  Similarity=0.327  Sum_probs=32.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAV  114 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~  114 (178)
                      ...++++.|+||||||... ..++..+..  .+..++|+=|..++..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~--~g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLL--RGDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHH--TTCEEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHH--CCCcEEEEeCCCchhH
Confidence            4679999999999999874 334444333  3457888888888764

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=93.30  E-value=0.55  Score=36.78  Aligned_cols=56  Identities=14%  Similarity=0.247  Sum_probs=44.2

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.+++++.+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       249 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~  308 (391)
T 1xti_A          249 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN  308 (391)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhC----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC
Confidence            4568999999999999999988765    778888999988766544443    3468999994

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.23  E-value=0.15  Score=39.78  Aligned_cols=52  Identities=13%  Similarity=0.099  Sum_probs=32.8

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+|++++=.+.+.+.|++.=   -+|.+   .|.+..     .+.+++.||+|+|||...-
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v---~~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la~   63 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAV---ILPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLAK   63 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHH---HHHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHH---HHHHh---CHHHHhCCCCCCceEEEECCCCccHHHHHH
Confidence            4568999877777777765420   01111   122222     3789999999999997653

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=93.14  E-value=0.12  Score=37.03  Aligned_cols=18  Identities=22%  Similarity=0.377  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      .++++.||+|+|||....
T Consensus        55 ~~~~l~G~~GtGKT~la~   72 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA   72 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            789999999999997643

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=93.04  E-value=0.16  Score=42.30  Aligned_cols=43  Identities=16%  Similarity=0.183  Sum_probs=30.2

Q ss_pred             HHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHH
Q psy9277          43 LLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        43 i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +.+.+. ..+..-...-..+...+..+.++++.||+|+|||...
T Consensus        16 l~~~l~-~~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           16 LSSSLE-KGLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             HHHHHH-TTCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             HHHHHH-hhhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            334443 2454555555566666777999999999999999765

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=92.86  E-value=0.46  Score=40.30  Aligned_cols=56  Identities=11%  Similarity=0.044  Sum_probs=45.4

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++++.-+.++++.+...    ++.+..++|+.+..++...+.    ...+|||+|-
T Consensus       266 ~~~~~IVf~~sr~~~e~la~~L~~~----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~  325 (591)
T 2v1x_A          266 KGQSGIIYCFSQKDSEQVTVSLQNL----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV  325 (591)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT
T ss_pred             cCCCeEEEeCcHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec
Confidence            4568999999999999999998765    788999999998776654443    3578999994

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=92.82  E-value=0.19  Score=42.01  Aligned_cols=41  Identities=17%  Similarity=0.125  Sum_probs=27.0

Q ss_pred             HHHHHhCCCCCCcHHHHHHH-HHHHcCCcEEEEcCCCChHHHHH
Q psy9277          44 LRGIYAYGFEKPSAIQQRSI-KPIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        44 ~~~l~~~g~~~~~~~Q~~~i-~~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|.+.|.  +++.+..-+ -.+..|.+++++||||||||...
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTlL  277 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTTL  277 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHHH
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            444556663  233333333 34567999999999999999653

>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=92.74  E-value=0.45  Score=37.66  Aligned_cols=56  Identities=14%  Similarity=0.077  Sum_probs=44.1

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ...++||.++++..+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~  334 (410)
T 2j0s_A          275 TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD  334 (410)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG
T ss_pred             CCCcEEEEEcCHHHHHHHHHHHHhC----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC
Confidence            3458999999999999999888765    678888999988766554443    3578999994

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=92.67  E-value=0.12  Score=38.54  Aligned_cols=56  Identities=20%  Similarity=0.236  Sum_probs=31.7

Q ss_pred             ccccccccCCCCHHHHHHHHhCC--CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYG--FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g--~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|+++.-.+.+.+.+.+.-  +..+..++..   .....+++++.||+|+|||...-
T Consensus         6 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~vll~G~~GtGKT~la~   63 (257)
T 1lv7_A            6 QIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLAK   63 (257)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHc---CCCCCCeEEEECcCCCCHHHHHH
Confidence            34568888877777776664320  0000000000   01124679999999999997653

>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=92.47  E-value=0.23  Score=39.12  Aligned_cols=20  Identities=20%  Similarity=0.338  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.++++.||+|+|||..+-
T Consensus        50 ~~~~vll~GppGtGKT~la~   69 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAE   69 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            35789999999999998753

>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=92.37  E-value=0.38  Score=36.47  Aligned_cols=19  Identities=21%  Similarity=0.426  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus        50 ~~~vll~G~~GtGKT~la~   68 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIAR   68 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            6789999999999997653

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=92.33  E-value=0.36  Score=37.42  Aligned_cols=44  Identities=14%  Similarity=0.282  Sum_probs=26.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhh-hcCCCceEEEEcCcHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLD-TQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~-~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +.++++.||+|+|||.... .+...+. .  .+..++++. ..+++.++
T Consensus       152 ~~~lll~G~~GtGKT~La~-aia~~~~~~--~g~~v~~~~-~~~l~~~l  196 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA-AMAHELSEK--KGVSTTLLH-FPSFAIDV  196 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH-HHHHHHHHH--SCCCEEEEE-HHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH-HHHHHHHHh--cCCcEEEEE-HHHHHHHH
Confidence            5899999999999997654 3333333 3  233444443 23454443

>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=92.26  E-value=0.7  Score=38.47  Aligned_cols=56  Identities=11%  Similarity=0.050  Sum_probs=44.8

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++++.-+..+++.++..    ++.+..++|+.+..++.....    ...+|+|+|.
T Consensus       235 ~~~~~IVf~~sr~~~e~l~~~L~~~----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~  294 (523)
T 1oyw_A          235 RGKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV  294 (523)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHC----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec
Confidence            4568999999999999999988765    788899999988766544332    3578999995

>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=91.48  E-value=0.025  Score=39.79  Aligned_cols=56  Identities=11%  Similarity=0.064  Sum_probs=42.0

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++++..+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus        29 ~~~~~iVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~   88 (170)
T 2yjt_D           29 EATRSIVFVRKRERVHELANWLREA----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD   88 (170)
Confidence            4468999999999999988887654    677888888877665544443    2468999983

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.24  E-value=0.14  Score=37.51  Aligned_cols=33  Identities=21%  Similarity=0.179  Sum_probs=27.2

Q ss_pred             CcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          55 PSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      -+.-|..++..+..|.-+.+.||+|+|||..+-
T Consensus         8 k~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl~   40 (208)
T 3b85_A            8 KTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLAM   40 (208)
T ss_dssp             CSHHHHHHHHHHHHCSEEEEECCTTSSTTHHHH
T ss_pred             CCHhHHHHHHhccCCCEEEEECCCCCCHHHHHH
Confidence            345567788888889999999999999997653

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=92.20  E-value=0.17  Score=39.64  Aligned_cols=49  Identities=29%  Similarity=0.245  Sum_probs=29.7

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHH
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++..+|+++--.+...+.+..            ....+..    ++++++.||+|+|||...-
T Consensus        36 ~~~p~~~~~~ivG~~~~~~~l~~------------l~~~~~~~~~~~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           36 ALEPRQASQGMVGQLAARRAAGV------------VLEMIREGKIAGRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             TSCBCSEETTEESCHHHHHHHHH------------HHHHHHTTCCTTCEEEEEESTTSSHHHHHH
T ss_pred             ccCcCcchhhccChHHHHHHHHH------------HHHHHHcCCCCCCEEEEECCCCCCHHHHHH
Confidence            34555557766555555444321            1122222    4689999999999997654

>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=92.10  E-value=0.085  Score=39.38  Aligned_cols=56  Identities=14%  Similarity=0.062  Sum_probs=33.3

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~   86 (178)
                      ..+..+|+++.-.+.....+++.-..  . -....+..+--  .+.+++.||+|+|||...
T Consensus         9 ~~~~~~~~~i~g~~~~~~~l~~l~~~--~-~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~   66 (254)
T 1ixz_A            9 EAPKVTFKDVAGAEEAKEELKEIVEF--L-KNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   66 (254)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHH--H-HCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHH--H-HCHHHHHHcCCCCCCeEEEECCCCCCHHHHH
Confidence            34567888887777666666543110  0 01122322211  356999999999999664

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=92.07  E-value=0.028  Score=42.98  Aligned_cols=55  Identities=18%  Similarity=0.216  Sum_probs=28.7

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHH-HHHHHHHH--cCCcEEEEcCCCChHHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQ-QRSIKPIV--KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q-~~~i~~i~--~g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+|++++--+.+.+.|++.=   .+++. ..++..+-  -.+.+++.||+|+|||...-
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i---~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLak   62 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAI---LAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAK   62 (274)
T ss_dssp             -------CCHHHHHHHHHHHHH---THHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH---HHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHH
Confidence            4567899887777777775421   12221 12232221  14569999999999997653

>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=92.07  E-value=0.031  Score=43.61  Aligned_cols=53  Identities=11%  Similarity=0.116  Sum_probs=34.0

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|+++.-.+.+.+.|++.= .  ++.   ..|.+..     .+++++.||+|+|||...-
T Consensus        12 ~~~~~~~di~G~~~~~~~l~~~i-~--~~~---~~~~~~~~~~~~~~~vLl~GppGtGKT~la~   69 (322)
T 3eie_A           12 KPNVKWEDVAGLEGAKEALKEAV-I--LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLAK   69 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHT-H--HHH---HCGGGCCTTCCCCCEEEEECSSSSCHHHHHH
T ss_pred             CCCCCHHHhcChHHHHHHHHHHH-H--HHH---hCHHHHhcCCCCCCeEEEECCCCCcHHHHHH
Confidence            34567899887777877776431 0  111   1122222     4689999999999997753

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=92.05  E-value=0.28  Score=35.03  Aligned_cols=39  Identities=15%  Similarity=0.183  Sum_probs=25.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      |+-.++.||.|+|||...+--+. ++..  .+.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~-~~~~--~g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVE-IYKL--GKKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH-HHHH--TTCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHHHHHH-HHHH--CCCeEEEEeecc
Confidence            55678999999999987653333 2222  344677777763

>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=91.96  E-value=0.61  Score=37.21  Aligned_cols=75  Identities=17%  Similarity=0.214  Sum_probs=48.0

Q ss_pred             CChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEc--------CccHHHHHHHhc--
Q psy9277          79 GTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG--------GTNLSEDLRKLD--  148 (178)
Q Consensus        79 GsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g--------~~~~~~~~~~~~--  148 (178)
                      .++|... +.-++........+.++||.++++.-+..+++.+...    ++.+..++|        +.+..++...+.  
T Consensus       341 ~~~k~~~-l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F  415 (494)
T 1wp9_A          341 DHPKMDK-LKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDEF  415 (494)
T ss_dssp             SCHHHHH-HHHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHHH
T ss_pred             CChHHHH-HHHHHHHHhccCCCCeEEEEEccHHHHHHHHHHHHHc----CCCcEEEeccccccccccCCHHHHHHHHHHH
Confidence            4455432 3344444332235679999999999999999988766    788888888        555444433332  


Q ss_pred             --CCCcEEEeCh
Q psy9277         149 --YGQHVVSGTP  158 (178)
Q Consensus       149 --~~~~IlV~TP  158 (178)
                        ..++|+|+|.
T Consensus       416 ~~~~~~vLv~T~  427 (494)
T 1wp9_A          416 ARGEFNVLVATS  427 (494)
T ss_dssp             HHTSCSEEEECG
T ss_pred             hcCCceEEEECC
Confidence              3578999993

>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=91.95  E-value=0.57  Score=36.18  Aligned_cols=56  Identities=13%  Similarity=0.141  Sum_probs=44.2

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.+++++-+..+++.++..    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       237 ~~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~  296 (367)
T 1hv8_A          237 KEFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD  296 (367)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHhc----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC
Confidence            4568999999999999999988765    778888999988766554432    3568999994

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=91.88  E-value=0.088  Score=36.69  Aligned_cols=19  Identities=26%  Similarity=0.408  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +.++++.||+|+|||...-
T Consensus        43 ~~~~ll~G~~G~GKT~l~~   61 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIVE   61 (195)
T ss_dssp             SCEEEEECCTTSCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            4789999999999997653

>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=91.74  E-value=0.25  Score=36.66  Aligned_cols=39  Identities=21%  Similarity=0.219  Sum_probs=26.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      |.-+++.|++|+|||...+-.+. ++..  .+.+++++.|..
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~-r~~~--~g~kVli~~~~~   50 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLH-RLEY--ADVKYLVFKPKI   50 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHH-HHHH--TTCCEEEEEECC
T ss_pred             cEEEEEECCCCCcHHHHHHHHHH-HHHh--cCCEEEEEEecc
Confidence            66788899999999977654433 3332  345677776654

>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=91.73  E-value=1.3  Score=31.34  Aligned_cols=17  Identities=41%  Similarity=0.524  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      .++++.||+|+|||...
T Consensus        39 ~~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATA   55 (226)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999764

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=91.71  E-value=0.3  Score=39.59  Aligned_cols=54  Identities=11%  Similarity=-0.026  Sum_probs=40.3

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh-cCCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL-DYGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~IlV~TP  158 (178)
                      +.+++|++|+++-+..+++.++..    ++++..++|+.... ..... ....+|||+|-
T Consensus       171 ~~~~lVF~~~~~~~~~l~~~L~~~----~~~v~~lhg~~r~~-~~~~f~~g~~~vLVaT~  225 (431)
T 2v6i_A          171 DGRTVWFVHSIKQGAEIGTCLQKA----GKKVLYLNRKTFES-EYPKCKSEKWDFVITTD  225 (431)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTTHHH-HTTHHHHSCCSEEEECG
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCeEEEeCCccHHH-HHHhhcCCCCeEEEECc
Confidence            458999999999999999988776    77888888874332 22222 24579999994

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=91.61  E-value=0.22  Score=36.52  Aligned_cols=50  Identities=20%  Similarity=0.268  Sum_probs=30.1

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      .|.-+++.|++|+|||...+--+.+....  .+..++|++-. .-..++.+.+
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            46789999999999997765444443332  23356666533 2234444444

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=91.49  E-value=0.37  Score=37.30  Aligned_cols=43  Identities=19%  Similarity=0.208  Sum_probs=27.9

Q ss_pred             ccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHH----cCCcEEEEcCCCChHHHHHH
Q psy9277          33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV----KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        33 ~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~----~g~~v~v~aptGsGKTl~~l   87 (178)
                      +|+++--.+..++.+..            ++....    ...++++.||+|+|||...-
T Consensus        27 ~~~~iiG~~~~~~~l~~------------~l~~~~~~~~~~~~vll~G~~GtGKT~la~   73 (338)
T 3pfi_A           27 NFDGYIGQESIKKNLNV------------FIAAAKKRNECLDHILFSGPAGLGKTTLAN   73 (338)
T ss_dssp             SGGGCCSCHHHHHHHHH------------HHHHHHHTTSCCCCEEEECSTTSSHHHHHH
T ss_pred             CHHHhCChHHHHHHHHH------------HHHHHHhcCCCCCeEEEECcCCCCHHHHHH
Confidence            67777666666655532            111211    23589999999999997754

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=91.45  E-value=0.19  Score=38.93  Aligned_cols=31  Identities=19%  Similarity=0.319  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          57 AIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        57 ~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..-..+...+..+.++++.||+|+|||...-
T Consensus        34 ~~~~~l~~~l~~~~~vll~G~pGtGKT~la~   64 (331)
T 2r44_A           34 YMINRLLIGICTGGHILLEGVPGLAKTLSVN   64 (331)
T ss_dssp             HHHHHHHHHHHHTCCEEEESCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCeEEEECCCCCcHHHHHH
Confidence            3333344455568999999999999997653

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=91.43  E-value=0.1  Score=36.97  Aligned_cols=20  Identities=10%  Similarity=0.242  Sum_probs=16.7

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|+-++++||+|+|||...-
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~   23 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKN   23 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            47789999999999997653

>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=91.41  E-value=0.62  Score=35.54  Aligned_cols=44  Identities=11%  Similarity=0.121  Sum_probs=32.3

Q ss_pred             HHHHHHHHhCCCCCCcHHH-HHHHHHHHcCC-----cEEEEcCCCChHHHHHH
Q psy9277          41 EDLLRGIYAYGFEKPSAIQ-QRSIKPIVKGR-----DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        41 ~~i~~~l~~~g~~~~~~~Q-~~~i~~i~~g~-----~v~v~aptGsGKTl~~l   87 (178)
                      .++.+-|+-.||.   +++ ..++..+++++     .+++.||+|+|||+.+.
T Consensus        73 n~i~~~l~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKILELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHHHHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            3788888877874   444 33455666654     59999999999998876

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=91.41  E-value=0.62  Score=37.62  Aligned_cols=27  Identities=7%  Similarity=0.160  Sum_probs=21.7

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCC
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEK   54 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~   54 (178)
                      +.++..+...|+++..++.|++.||..
T Consensus        80 ~~~~~~l~~~gi~~~~~~~L~~ag~~t  106 (400)
T 3lda_A           80 FVPIEKLQVNGITMADVKKLRESGLHT  106 (400)
T ss_dssp             SCBGGGGCCTTCCHHHHHHHHHTTCCB
T ss_pred             ccCHHHHHhCCCCHHHHHHHHHcCCCc
Confidence            345667777889999999999999854

>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=91.40  E-value=0.19  Score=37.62  Aligned_cols=19  Identities=26%  Similarity=0.356  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+.++++.||+|+|||...
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            4789999999999999664

>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=91.37  E-value=0.94  Score=37.11  Aligned_cols=86  Identities=17%  Similarity=0.175  Sum_probs=45.0

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHH----H
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE----D  143 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~----~  143 (178)
                      .-+++.+++|+|||....--+ ..+..  .+.+++++.  |.+.-+.++   ++.+....++.+.....+.+...    .
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA-~~l~~--~G~kVllv~~D~~R~aa~eq---L~~~~~~~gvpv~~~~~~~dp~~i~~~a  174 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLA-RYFQK--RGYKVGVVCSDTWRPGAYHQ---LRQLLDRYHIEVFGNPQEKDAIKLAKEG  174 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH-HHHHT--TTCCEEEEECCCSSTHHHHH---HHHHHGGGTCEEECCTTCCCHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHH-HHHHH--CCCeEEEEeCCCcchhHHHH---HHHHHHhcCCcEEecCCCCCHHHHHHHH
Confidence            368899999999998764322 22332  345666665  445544333   33444455665543333322211    1


Q ss_pred             HHHh-cCCCc-EEEeChHHH
Q psy9277         144 LRKL-DYGQH-VVSGTPGRV  161 (178)
Q Consensus       144 ~~~~-~~~~~-IlV~TP~~l  161 (178)
                      .... .+++| |+|=||+++
T Consensus       175 l~~a~~~~~DvVIIDTaGrl  194 (443)
T 3dm5_A          175 VDYFKSKGVDIIIVDTAGRH  194 (443)
T ss_dssp             HHHHHHTTCSEEEEECCCCS
T ss_pred             HHHHHhCCCCEEEEECCCcc
Confidence            1121 23465 456788764

>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=91.25  E-value=0.18  Score=36.34  Aligned_cols=17  Identities=35%  Similarity=0.663  Sum_probs=14.2

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +-++++||+|+|||...
T Consensus         2 RpIVi~GPSG~GK~Tl~   18 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45899999999999653

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.25  E-value=0.13  Score=40.97  Aligned_cols=22  Identities=23%  Similarity=0.484  Sum_probs=18.6

Q ss_pred             HHHcCCcEEEEcCCCChHHHHH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      .+..|..+.++||||||||...
T Consensus       171 ~i~~G~~i~ivG~sGsGKSTll  192 (361)
T 2gza_A          171 AVQLERVIVVAGETGSGKTTLM  192 (361)
T ss_dssp             HHHTTCCEEEEESSSSCHHHHH
T ss_pred             HHhcCCEEEEECCCCCCHHHHH
Confidence            4556999999999999999654

>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=91.24  E-value=0.11  Score=37.82  Aligned_cols=20  Identities=10%  Similarity=0.094  Sum_probs=17.1

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+++.||+|+|||....
T Consensus        51 ~~~~~ll~G~~G~GKT~la~   70 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLIH   70 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            46899999999999997653

>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=91.19  E-value=0.041  Score=41.60  Aligned_cols=19  Identities=26%  Similarity=0.244  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus        64 ~~~vLl~G~~GtGKT~la~   82 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAA   82 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            3589999999999997754

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=91.02  E-value=0.56  Score=47.20  Aligned_cols=48  Identities=17%  Similarity=0.170  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHH-HHH---HHHcCCcEEEEcCCCChHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQR-SIK---PIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~-~i~---~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      |...+.+.+.+.|+. +++.+.. +++   .+.....+++.||||||||.++-
T Consensus       873 l~~ai~~~~~~~~L~-~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          873 LRKKIQEIAKQRHLV-TKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             HHHHHHHHHHHTTCC-CCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHH
T ss_pred             HHHHHHHHHHHcCCc-cCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHH
Confidence            445677777888885 5555443 332   23347899999999999999974

>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=90.99  E-value=0.36  Score=38.16  Aligned_cols=59  Identities=19%  Similarity=0.103  Sum_probs=39.4

Q ss_pred             hcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc---C-CCcEEEeCh
Q psy9277          96 TQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD---Y-GQHVVSGTP  158 (178)
Q Consensus        96 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~---~-~~~IlV~TP  158 (178)
                      ......++||.+++++.+..+++.+...    ++.+..++|+.+..++...+.   + ..+|+|+|.
T Consensus       276 ~~~~~~~~lvf~~~~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~  338 (414)
T 3eiq_A          276 ETLTITQAVIFINTRRKVDWLTEKMHAR----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTD  338 (414)
T ss_dssp             HSSCCSSCEEECSCHHHHHHHHHHHHTT----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECS
T ss_pred             HhCCCCcEEEEeCCHHHHHHHHHHHHhc----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECC
Confidence            3334568999999999999998888654    678888899887766544442   2 468999984

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=90.93  E-value=0.13  Score=36.91  Aligned_cols=21  Identities=19%  Similarity=0.091  Sum_probs=17.4

Q ss_pred             HcCCcEEEEcCCCChHHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++.++++|++|||||...-
T Consensus        23 ~~~~~i~l~G~~GsGKsTl~~   43 (199)
T 3vaa_A           23 NAMVRIFLTGYMGAGKTTLGK   43 (199)
T ss_dssp             -CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCEEEEEcCCCCCHHHHHH
Confidence            357899999999999997753

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=90.86  E-value=0.2  Score=39.22  Aligned_cols=26  Identities=8%  Similarity=0.084  Sum_probs=19.5

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      +.++++.||+|+|||.+.- .++..+.
T Consensus        45 ~~~lli~GpPGTGKT~~v~-~v~~~L~   70 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVN-DVMDELI   70 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            5789999999999997754 3444443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=90.83  E-value=0.091  Score=36.58  Aligned_cols=19  Identities=32%  Similarity=0.415  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||....
T Consensus        43 ~~~vll~G~~G~GKT~la~   61 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVE   61 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHH
Confidence            5689999999999997653

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=90.78  E-value=0.12  Score=39.54  Aligned_cols=19  Identities=26%  Similarity=0.244  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +.++++.||+|+|||...-
T Consensus        67 ~~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CCEEEEEECTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4579999999999997753

>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=90.75  E-value=1.2  Score=35.99  Aligned_cols=53  Identities=13%  Similarity=0.058  Sum_probs=42.8

Q ss_pred             eEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277         102 QVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus       102 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+||.++++.-+..+++.+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus       302 ~~lVF~~t~~~a~~l~~~L~~~----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~  358 (434)
T 2db3_A          302 GTIVFVETKRGADFLASFLSEK----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS  358 (434)
T ss_dssp             TEEEECSSHHHHHHHHHHHHHT----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG
T ss_pred             CEEEEEeCcHHHHHHHHHHHhC----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch
Confidence            4999999999999999888765    788889999988776655443    3478999994

>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=90.66  E-value=0.31  Score=38.88  Aligned_cols=42  Identities=24%  Similarity=0.407  Sum_probs=29.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      .+.++++.|+||+|||...-.-+.+. ..  .+.+++++=|..+.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~-~~--~~~~~~~~D~~~~~   75 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLRE-YM--QGSRVIIIDPEREY   75 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHH-HT--TTCCEEEEESSCCS
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHH-HH--CCCEEEEEeCCcCH
Confidence            56799999999999997654433332 22  45577777777553

>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=90.65  E-value=0.72  Score=35.96  Aligned_cols=33  Identities=24%  Similarity=0.352  Sum_probs=24.0

Q ss_pred             cHHHHHHHHHHH----cCC---cEEEEcCCCChHHHHHHH
Q psy9277          56 SAIQQRSIKPIV----KGR---DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        56 ~~~Q~~~i~~i~----~g~---~v~v~aptGsGKTl~~ll   88 (178)
                      .|+|.+++..+.    +|+   .+++.||.|+|||.....
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~   43 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA   43 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHH
Confidence            567777766554    343   489999999999977643

>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=90.63  E-value=0.37  Score=37.34  Aligned_cols=24  Identities=21%  Similarity=0.135  Sum_probs=18.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      |.-+++.|++|+|||...+-.+.+
T Consensus        98 g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           98 QSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            467999999999999876654443

>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=90.63  E-value=0.83  Score=45.44  Aligned_cols=48  Identities=23%  Similarity=0.211  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHH-HH---HHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQR-SI---KPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~-~i---~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +...+.+.+.+.|+. +++.+.. ++   ..+.....+++.||||||||.++-
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            445677777788875 5665532 22   334458899999999999999874

>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=90.62  E-value=0.38  Score=39.19  Aligned_cols=54  Identities=9%  Similarity=-0.042  Sum_probs=38.2

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc-CCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP  158 (178)
                      +.+++|++|+++-+..+++.++..    ++++..++|+...... .... ...+|+|+|.
T Consensus       177 ~~~~lVF~~s~~~a~~l~~~L~~~----~~~v~~lhg~~R~~~~-~~F~~g~~~vLVaT~  231 (440)
T 1yks_A          177 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREY-PTIKQKKPDFILATD  231 (440)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC---------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHHc----CCCEEEecchhHHHHH-hhhcCCCceEEEECC
Confidence            468999999999999999988765    6788888885433322 3333 3479999994

>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=90.50  E-value=0.14  Score=38.03  Aligned_cols=53  Identities=13%  Similarity=0.168  Sum_probs=29.5

Q ss_pred             cccccCCCCHHHHHHHHhCC--CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYG--FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g--~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+|+++.-.+.+.+.+++.-  +..+..+...   .+...+++++.||+|+|||...-
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---g~~~~~~vll~G~~GtGKT~la~   57 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQL---GAKVPKGALLLGPPGCGKTLLAK   57 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHc---CCCCCceEEEECCCCCCHHHHHH
Confidence            56777765666666664320  1111111110   11235789999999999997653

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=90.47  E-value=0.14  Score=39.10  Aligned_cols=55  Identities=7%  Similarity=0.054  Sum_probs=32.7

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHH-HHHHHHHH-cCCcEEEEcCCCChHHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQ-QRSIKPIV-KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q-~~~i~~i~-~g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+|+++.=.+...+.+.+.= .  .+.. .+.+..+. .++.+++.||+|+|||...-
T Consensus        16 ~~~~~~~i~G~~~~~~~l~~~i-~--~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~   72 (297)
T 3b9p_A           16 AKVEWTDIAGQDVAKQALQEMV-I--LPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLAR   72 (297)
T ss_dssp             SCCCGGGSCCCHHHHHHHHHHT-H--HHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHH-H--hhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHH
Confidence            4567888876777777765421 0  1110 00011111 36799999999999997653

>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=90.45  E-value=0.42  Score=34.50  Aligned_cols=39  Identities=10%  Similarity=0.171  Sum_probs=26.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      |+=.++.||.|+|||...+-- +.+...  .+.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~-a~r~~~--~g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRR-IRRAKI--AKQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHH-HHHHHH--TTCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHHHH-HHHHHH--CCCEEEEEEecc
Confidence            556788999999999776533 333332  456788888874

>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=90.43  E-value=0.12  Score=36.24  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=17.7

Q ss_pred             HcCCcEEEEcCCCChHHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++.++++|++|||||...-
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~   29 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGK   29 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHH
T ss_pred             ccCCeEEEEeCCCCCHHHHHH
Confidence            356789999999999997654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=90.40  E-value=0.18  Score=34.82  Aligned_cols=20  Identities=20%  Similarity=0.418  Sum_probs=17.3

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|..+++.||+|+|||...-
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~   54 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQ   54 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            68899999999999996643

>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=90.37  E-value=0.74  Score=37.61  Aligned_cols=86  Identities=21%  Similarity=0.170  Sum_probs=43.3

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHH----HH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS----ED  143 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~----~~  143 (178)
                      .-+++.|++|+|||....--+ ..+..  .+.+++++.  +.+.-+.++   +..+....++.+.....+.+..    ..
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA-~~l~~--~G~kVllv~~D~~r~~a~eq---L~~~~~~~gv~~~~~~~~~dp~~i~~~a  171 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLA-YFYKK--RGYKVGLVAADVYRPAAYDQ---LLQLGNQIGVQVYGEPNNQNPIEIAKKG  171 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHH-HHHHH--TTCCEEEEEECCSCHHHHHH---HHHHHHTTTCCEECCTTCSCHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH-HHHHH--cCCeEEEEecCccchhHHHH---HHHHHHhcCCceeeccccCCHHHHHHHH
Confidence            468899999999997754322 22222  345666655  334433333   3333344455443332222221    11


Q ss_pred             HHHhc-CCCc-EEEeChHHH
Q psy9277         144 LRKLD-YGQH-VVSGTPGRV  161 (178)
Q Consensus       144 ~~~~~-~~~~-IlV~TP~~l  161 (178)
                      ..... .+++ |+|=||+++
T Consensus       172 l~~a~~~~~DvvIIDTaGr~  191 (433)
T 3kl4_A          172 VDIFVKNKMDIIIVDTAGRH  191 (433)
T ss_dssp             HHHTTTTTCSEEEEEECCCS
T ss_pred             HHHHHhcCCCEEEEECCCCc
Confidence            22222 3454 567888874

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=90.37  E-value=0.16  Score=36.67  Aligned_cols=20  Identities=30%  Similarity=0.488  Sum_probs=15.7

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|+-+.++||+|+|||...-
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~   22 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLK   22 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            47789999999999997653

>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=90.37  E-value=0.34  Score=39.61  Aligned_cols=52  Identities=19%  Similarity=0.116  Sum_probs=31.1

Q ss_pred             cccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+...|+++.-.+...+.+...       + ..+-.....++++++.||+|+|||..+-
T Consensus        30 ~~~~~~~~~iiG~~~~~~~l~~~-------~-~~~~~~~~~~~~iLl~GppGtGKT~la~   81 (456)
T 2c9o_A           30 GLAKQAASGLVGQENAREACGVI-------V-ELIKSKKMAGRAVLLAGPPGTGKTALAL   81 (456)
T ss_dssp             SCBCSEETTEESCHHHHHHHHHH-------H-HHHHTTCCTTCEEEEECCTTSSHHHHHH
T ss_pred             cChhhchhhccCHHHHHHHHHHH-------H-HHHHhCCCCCCeEEEECCCcCCHHHHHH
Confidence            44556677776666666555321       0 0000111234789999999999997764

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=90.35  E-value=0.11  Score=39.35  Aligned_cols=21  Identities=24%  Similarity=0.347  Sum_probs=17.9

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|.-+.+.||||||||...
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            456888999999999999764

>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=90.27  E-value=0.33  Score=44.42  Aligned_cols=40  Identities=25%  Similarity=0.281  Sum_probs=31.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      -+|.|..|||||.+.+--+.+.+.....+.++++++|...
T Consensus         4 ~lV~agAGSGKT~~l~~ri~~ll~~~~~~~~il~lVP~q~   43 (1166)
T 3u4q_B            4 EFLVGRSGSGKTKLIINSIQDELRRAPFGKPIIFLVPDQM   43 (1166)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHHCTTSSCEEEECCGGG
T ss_pred             EEEEeCCCCChHHHHHHHHHHHHHhCCCCCcEEEEecCcc
Confidence            3789999999999887777666655444568999999764

>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=90.20  E-value=0.16  Score=39.88  Aligned_cols=20  Identities=40%  Similarity=0.645  Sum_probs=17.4

Q ss_pred             HHcCCcEEEEcCCCChHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTAT   85 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~   85 (178)
                      +..|..+.+.||||||||..
T Consensus       168 i~~g~~v~i~G~~GsGKTTl  187 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTY  187 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHH
Confidence            44699999999999999964

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=90.19  E-value=0.17  Score=35.65  Aligned_cols=19  Identities=26%  Similarity=0.212  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ++.++++|++|||||...-
T Consensus         5 ~~~i~l~G~~GsGKst~a~   23 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGS   23 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            5689999999999997764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=90.17  E-value=0.15  Score=36.41  Aligned_cols=21  Identities=29%  Similarity=0.308  Sum_probs=17.1

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|.-+.+.||+|||||...
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            345788999999999999765

>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=90.16  E-value=0.23  Score=35.81  Aligned_cols=36  Identities=17%  Similarity=0.073  Sum_probs=24.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      +..|.-+++.+|+|+|||.....-+.    .  .+..++++.
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~~l~~----~--~~~~v~~i~   52 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLALQTGL----L--SGKKVAYVD   52 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHHHHHH----H--HCSEEEEEE
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHH----H--cCCcEEEEE
Confidence            33477899999999999977654333    1  234566665

>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=89.99  E-value=0.11  Score=36.82  Aligned_cols=21  Identities=19%  Similarity=0.363  Sum_probs=17.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|.-+++.||+|||||...
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~   26 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIA   26 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHH
Confidence            445788999999999999764

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=89.90  E-value=0.3  Score=39.73  Aligned_cols=29  Identities=17%  Similarity=0.441  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHc--CCcEEEEcCCCChHHHHH
Q psy9277          58 IQQRSIKPIVK--GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        58 ~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~   86 (178)
                      -+..++..++.  |.-+++.||||||||...
T Consensus       154 ~~~~~L~~l~~~~ggii~I~GpnGSGKTTlL  184 (418)
T 1p9r_A          154 HNHDNFRRLIKRPHGIILVTGPTGSGKSTTL  184 (418)
T ss_dssp             HHHHHHHHHHTSSSEEEEEECSTTSCHHHHH
T ss_pred             HHHHHHHHHHHhcCCeEEEECCCCCCHHHHH
Confidence            34445544443  557899999999999653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=89.86  E-value=0.32  Score=35.19  Aligned_cols=23  Identities=30%  Similarity=0.257  Sum_probs=18.2

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll   88 (178)
                      +..|.-+++.||+|+|||.....
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~~   42 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSLH   42 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHH
T ss_pred             CcCCCEEEEEcCCCCCHHHHHHH
Confidence            34578899999999999966543

>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=89.84  E-value=0.18  Score=35.13  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ++-++++|++|||||.+.-
T Consensus         3 ~~~i~l~G~~GsGKST~a~   21 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVR   21 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            4668999999999997753

>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=89.80  E-value=0.19  Score=36.47  Aligned_cols=19  Identities=26%  Similarity=0.413  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|+-++++||+|+|||...
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            4677999999999999764

>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=89.74  E-value=4.4  Score=29.31  Aligned_cols=35  Identities=17%  Similarity=0.148  Sum_probs=27.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      .-.+++..++|.|||.+++-..+..+.   .+.+++++
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g---~G~rV~~v   62 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVG---HGKNVGVV   62 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHH---TTCCEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEE
Confidence            458999999999999998877776654   45566666

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=89.74  E-value=0.2  Score=34.72  Aligned_cols=18  Identities=22%  Similarity=0.361  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      ++.+.+.|++|||||...
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            567999999999999764

>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=89.72  E-value=0.76  Score=35.42  Aligned_cols=44  Identities=18%  Similarity=0.221  Sum_probs=26.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQI  116 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~  116 (178)
                      +..+++.||+|+|||...- .+...+...  +..++++. ..++..+.
T Consensus        37 ~~~lll~G~~GtGKT~la~-~i~~~~~~~--~~~~~~i~-~~~~~~~~   80 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLLQ-AAGNEAKKR--GYRVIYSS-ADDFAQAM   80 (324)
T ss_dssp             CSSEEEECSSSSSHHHHHH-HHHHHHHHT--TCCEEEEE-HHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHC--CCEEEEEE-HHHHHHHH
Confidence            4689999999999997653 333333322  33455554 33344333

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=89.71  E-value=0.17  Score=36.51  Aligned_cols=21  Identities=19%  Similarity=0.317  Sum_probs=17.6

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      ...|+-++++||+|||||...
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHH
T ss_pred             cccCCEEEEECCCCCCHHHHH
Confidence            345788999999999999754

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.68  E-value=0.82  Score=35.42  Aligned_cols=40  Identities=23%  Similarity=0.069  Sum_probs=27.2

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..|.-+++.|++|+|||...+--+.+...   .+..++|++-
T Consensus        65 l~~G~l~li~G~pG~GKTtl~l~ia~~~a~---~g~~vl~~sl  104 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTAFALKQAKNMSD---NDDVVNLHSL  104 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHHHHHHHHHHHHT---TTCEEEEEES
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEEC
Confidence            444778999999999999766544444332   2356777763

>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=89.68  E-value=0.2  Score=36.23  Aligned_cols=22  Identities=32%  Similarity=0.517  Sum_probs=17.3

Q ss_pred             HHHcCCcEEEEcCCCChHHHHH
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~   86 (178)
                      .+..|+-+.+.||+|+|||...
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            6777999999999999999765

>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=89.60  E-value=0.59  Score=39.06  Aligned_cols=25  Identities=20%  Similarity=0.368  Sum_probs=19.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      .+.+++|.|+||||||.+.-..++.
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~s  190 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILS  190 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHH
Confidence            3679999999999999875444433

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=89.52  E-value=2.7  Score=34.07  Aligned_cols=34  Identities=18%  Similarity=0.243  Sum_probs=26.6

Q ss_pred             CCcHHHHHHHHHHHc---CCcEEEEcCCCChHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVK---GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~---g~~v~v~aptGsGKTl~~l   87 (178)
                      +|-..-..+|...+.   |+.+.+.+|+|+|||....
T Consensus       156 ~~~~tGiraID~~~pi~rGQr~~IvG~sG~GKTtLl~  192 (422)
T 3ice_A          156 STEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQ  192 (422)
T ss_dssp             CTTHHHHHHHHHHSCCBTTCEEEEECCSSSSHHHHHH
T ss_pred             CcccccceeeeeeeeecCCcEEEEecCCCCChhHHHH
Confidence            455666677776554   8999999999999997764

>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=89.48  E-value=0.19  Score=34.61  Aligned_cols=17  Identities=18%  Similarity=0.337  Sum_probs=14.3

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -++++|++|||||...-
T Consensus         3 ~I~l~G~~GsGKsT~a~   19 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAK   19 (179)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            57899999999997653

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=89.41  E-value=0.23  Score=36.39  Aligned_cols=21  Identities=19%  Similarity=0.222  Sum_probs=16.9

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|+-+.+.||+|+|||...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl   40 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLI   40 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            346889999999999999764

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=89.38  E-value=0.21  Score=35.62  Aligned_cols=19  Identities=42%  Similarity=0.480  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
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            5778999999999999765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=89.28  E-value=0.13  Score=38.96  Aligned_cols=54  Identities=15%  Similarity=0.066  Sum_probs=33.4

Q ss_pred             cccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHH--cCCcEEEEcCCCChHHHHH
Q psy9277          30 VVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        30 ~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~--~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+|+++.-.+.+.+.++..-..  . -....+..+-  -.+.+++.+|+|+|||...
T Consensus        35 ~~~~~~~i~g~~~~~~~l~~l~~~--~-~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~   90 (278)
T 1iy2_A           35 PKVTFKDVAGAEEAKEELKEIVEF--L-KNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   90 (278)
T ss_dssp             CCCCGGGSSSCHHHHHHHHHHHHH--H-HCHHHHHHTTCCCCCEEEEECCTTSSHHHHH
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHH--H-HCHHHHHHcCCCCCCeEEEECCCcChHHHHH
Confidence            567899988777777777543210  0 0112222221  1356999999999999664

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.19  E-value=1.1  Score=43.54  Aligned_cols=41  Identities=20%  Similarity=0.150  Sum_probs=30.2

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      ++++++.+|+|+|||......+....   .++.+++++.....+
T Consensus      1427 g~~vll~GppGtGKT~LA~ala~ea~---~~G~~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1427 GRIVEIYGPESSGKTTLTLQVIAAAQ---REGKTCAFIDAEHAL 1467 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHHHHH---TTTCCEEEECTTSCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH---HcCCcEEEEEccccc
Confidence            78999999999999988765544432   256688888766444

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=89.17  E-value=0.32  Score=37.56  Aligned_cols=19  Identities=32%  Similarity=0.441  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+.++++.|++|+|||..+
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            4679999999999999765

>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=89.01  E-value=0.65  Score=36.12  Aligned_cols=42  Identities=10%  Similarity=-0.051  Sum_probs=26.8

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhc---CCCceEEEEcCcH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQ---LRETQVLCLSPTR  110 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~---~~~~~~lil~Pt~  110 (178)
                      |.-+++.||+|+|||...+-.+.+.....   ..+..++|+.-..
T Consensus       107 G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          107 RTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            57899999999999977655444322110   0144777776543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=88.96  E-value=0.19  Score=35.26  Aligned_cols=20  Identities=25%  Similarity=0.243  Sum_probs=17.1

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|.-+.++||+|||||..+-
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            46778999999999997765

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=88.86  E-value=0.19  Score=38.58  Aligned_cols=19  Identities=16%  Similarity=0.017  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.+++.||+|+|||...-
T Consensus        36 p~~lLl~GppGtGKT~la~   54 (293)
T 3t15_A           36 PLILGIWGGKGQGKSFQCE   54 (293)
T ss_dssp             CSEEEEEECTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4679999999999997653

>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=88.62  E-value=0.26  Score=34.86  Aligned_cols=20  Identities=35%  Similarity=0.591  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..++++|++|||||.+.-
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~   28 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAE   28 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            46789999999999997753

>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=88.53  E-value=0.26  Score=34.63  Aligned_cols=18  Identities=22%  Similarity=0.396  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      +..+++.|++|||||...
T Consensus         3 ~~~I~i~G~~GsGKsT~~   20 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSS   20 (192)
T ss_dssp             CCEEEEECCTTSCHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567999999999999764

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=88.46  E-value=0.83  Score=33.62  Aligned_cols=50  Identities=14%  Similarity=0.169  Sum_probs=31.1

Q ss_pred             HHHHHHHhCCCCCCcHHHHHHHHHHHcC----CcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          42 DLLRGIYAYGFEKPSAIQQRSIKPIVKG----RDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        42 ~i~~~l~~~g~~~~~~~Q~~~i~~i~~g----~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .|.+-|+=.|+ .+... ...+..++++    ..+++.||+|+|||..+ ..++..+
T Consensus        29 ~I~~~l~yq~~-~~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~l   82 (212)
T 1tue_A           29 PIVQFLRYQQI-EFITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHFI   82 (212)
T ss_dssp             HHHHHHHHTTC-CHHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHHH
T ss_pred             HHHHHHHHcCc-CHHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHHh
Confidence            56666654454 34444 4455555554    36999999999999765 3444443

>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=88.42  E-value=1.6  Score=37.53  Aligned_cols=56  Identities=13%  Similarity=0.197  Sum_probs=43.9

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.++|+..+..+.+.+...    ++.+..++|+.+..++...+.    ...+|+|||-
T Consensus       444 ~~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~  503 (661)
T 2d7d_A          444 RNERVLVTTLTKKMSEDLTDYLKEI----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN  503 (661)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHhc----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc
Confidence            4569999999999999999988775    778888888887766655432    3478999983

>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=88.42  E-value=0.26  Score=38.95  Aligned_cols=53  Identities=11%  Similarity=0.137  Sum_probs=31.0

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc-----CCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK-----GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~-----g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|+++.-.+.+.+.|.+. +.  ++.   -.|.+..     .+++++.||+|+|||...-
T Consensus        45 ~~~~~~~di~G~~~~~~~l~~~-v~--~~~---~~~~~~~~~~~~~~~iLL~GppGtGKT~la~  102 (355)
T 2qp9_X           45 KPNVKWEDVAGLEGAKEALKEA-VI--LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLAK  102 (355)
T ss_dssp             --CCCGGGSCCGGGHHHHHHHH-TH--HHH---HCGGGGCSSCCCCCCEEEECSTTSCHHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHH-HH--HHH---hCHHHHhcCCCCCceEEEECCCCCcHHHHHH
Confidence            3456788887666666666432 10  111   1122222     4689999999999997754

>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=88.34  E-value=0.25  Score=38.70  Aligned_cols=17  Identities=24%  Similarity=0.290  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -++++||||||||....
T Consensus        12 ~i~i~GptgsGKt~la~   28 (316)
T 3foz_A           12 AIFLMGPTASGKTALAI   28 (316)
T ss_dssp             EEEEECCTTSCHHHHHH
T ss_pred             EEEEECCCccCHHHHHH
Confidence            47899999999997654

>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=88.32  E-value=0.48  Score=34.00  Aligned_cols=17  Identities=24%  Similarity=0.341  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      ..+++.||+|+|||...
T Consensus        46 ~~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           46 HAYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             SEEEEECSTTSCHHHHH
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            36899999999999764

>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=88.31  E-value=4.9  Score=34.48  Aligned_cols=55  Identities=9%  Similarity=0.059  Sum_probs=43.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---c-CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---D-YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~-~~~~IlV~T  157 (178)
                      .+.++||.++|+..+..+.+.+...    ++.+..++|+.+..++...+   . ...+|+|||
T Consensus       438 ~~~~vlVf~~t~~~ae~L~~~L~~~----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT  496 (664)
T 1c4o_A          438 RGERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI  496 (664)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEES
T ss_pred             cCCEEEEEECCHHHHHHHHHHHHhc----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEcc
Confidence            4569999999999999999988765    67888888888776665543   2 346899988

>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=88.25  E-value=0.25  Score=38.75  Aligned_cols=18  Identities=28%  Similarity=0.222  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +-++|.||||||||....
T Consensus         4 ~~i~i~GptgsGKt~la~   21 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSV   21 (322)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCcCCHHHHHH
Confidence            347899999999997654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=88.23  E-value=0.26  Score=39.02  Aligned_cols=19  Identities=21%  Similarity=0.288  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ++-+++.||||+|||....
T Consensus        40 ~~lIvI~GPTgsGKTtLa~   58 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSI   58 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3469999999999997654

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=88.17  E-value=0.25  Score=37.14  Aligned_cols=17  Identities=18%  Similarity=0.059  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -++++||+|||||....
T Consensus         3 li~I~G~~GSGKSTla~   19 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAI   19 (253)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCcCHHHHHH
Confidence            47899999999997654

>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=88.14  E-value=0.23  Score=36.43  Aligned_cols=19  Identities=37%  Similarity=0.518  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |+-+++.+|||+|||...+
T Consensus        34 g~~ilI~GpsGsGKStLA~   52 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETAL   52 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            6779999999999985543

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.05  E-value=0.3  Score=35.04  Aligned_cols=20  Identities=35%  Similarity=0.469  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|.-+++.||+|||||...-
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~   47 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAH   47 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            47889999999999997653

>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=88.03  E-value=0.3  Score=35.50  Aligned_cols=21  Identities=14%  Similarity=0.272  Sum_probs=17.4

Q ss_pred             HcCCcEEEEcCCCChHHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..|+-++++||+|+|||...-
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~~   37 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIKN   37 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHHH
T ss_pred             CCCCEEEEECcCCCCHHHHHH
Confidence            367889999999999997643

>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=87.99  E-value=0.91  Score=34.97  Aligned_cols=19  Identities=26%  Similarity=0.538  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ++-+++.+++|+|||....
T Consensus       105 g~vi~lvG~~GsGKTTl~~  123 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLA  123 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5678999999999997654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=87.98  E-value=0.27  Score=34.14  Aligned_cols=16  Identities=19%  Similarity=0.283  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -++++|++|||||...
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            4789999999999765

>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=87.93  E-value=0.25  Score=34.46  Aligned_cols=19  Identities=32%  Similarity=0.319  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |..++++|++|||||...-
T Consensus         8 g~~i~l~G~~GsGKSTl~~   26 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVAS   26 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHH
Confidence            5679999999999997653

>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=87.74  E-value=0.3  Score=38.64  Aligned_cols=19  Identities=21%  Similarity=0.387  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus        72 ~~~ill~Gp~GtGKT~la~   90 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQ   90 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHH
Confidence            5689999999999997653

>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=87.72  E-value=0.28  Score=33.75  Aligned_cols=17  Identities=12%  Similarity=0.018  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.|++|||||...-
T Consensus         3 ~i~l~G~~GsGKsT~~~   19 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAA   19 (173)
T ss_dssp             EEEEECSSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            57899999999997653

>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=87.67  E-value=0.84  Score=37.16  Aligned_cols=54  Identities=11%  Similarity=0.028  Sum_probs=40.0

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc-CCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP  158 (178)
                      +.++||.+|++.-+.++++.+...    ++.+..+++..... ...... ...+|||+|-
T Consensus       188 ~~~~lVF~~s~~~a~~l~~~L~~~----g~~~~~lh~~~~~~-~~~~f~~g~~~vLVaT~  242 (451)
T 2jlq_A          188 QGKTVWFVPSIKAGNDIANCLRKS----GKRVIQLSRKTFDT-EYPKTKLTDWDFVVTTD  242 (451)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECTTTHHH-HGGGGGSSCCSEEEECG
T ss_pred             CCCEEEEcCCHHHHHHHHHHHHHc----CCeEEECCHHHHHH-HHHhhccCCceEEEECC
Confidence            458999999999999999888654    67888888776533 223333 3479999994

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=87.61  E-value=0.8  Score=39.52  Aligned_cols=55  Identities=7%  Similarity=0.030  Sum_probs=40.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcC-CCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDY-GQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~-~~~IlV~TP  158 (178)
                      .+.++||++|+++-+..+++.++..    ++++..++|.. .........+ ..+|||+|-
T Consensus       409 ~~~~~lVF~~s~~~~e~la~~L~~~----g~~v~~lHg~e-R~~v~~~F~~g~~~VLVaTd  464 (673)
T 2wv9_A          409 YAGKTVWFVASVKMSNEIAQCLQRA----GKRVIQLNRKS-YDTEYPKCKNGDWDFVITTD  464 (673)
T ss_dssp             CCSCEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSS-HHHHGGGGGTCCCSEEEECG
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHhC----CCeEEEeChHH-HHHHHHHHHCCCceEEEECc
Confidence            3468999999999999988888654    78888888853 3333333333 479999993

>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=87.58  E-value=0.32  Score=35.79  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=17.3

Q ss_pred             HHcCCcEEEEcCCCChHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ...|+-+++.||+|+|||...-
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk   34 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQ   34 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHH
Confidence            4568889999999999997653

>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=87.49  E-value=0.54  Score=34.28  Aligned_cols=26  Identities=23%  Similarity=0.111  Sum_probs=20.0

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISIL   91 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il   91 (178)
                      +..|.-+.+.+|+|+|||.....-+.
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHH
Confidence            33578899999999999987654443

>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=87.44  E-value=3.2  Score=36.33  Aligned_cols=60  Identities=13%  Similarity=0.122  Sum_probs=46.9

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhc-------cCCCceEEEEEcCccHHHHHHHhcC---------CCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALG-------DFMNVQCHACIGGTNLSEDLRKLDY---------GQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~-------~~~~~~~~~~~g~~~~~~~~~~~~~---------~~~IlV~TP  158 (178)
                      .+.++||.+|++.-+..+++.+....       ...++.+..++|+.+..++...+..         ...|||+|.
T Consensus       302 ~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~  377 (773)
T 2xau_A          302 EAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTN  377 (773)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECT
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCc
Confidence            45699999999999999999887532       2347889999999998877665532         348999994

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=87.34  E-value=0.36  Score=36.78  Aligned_cols=18  Identities=22%  Similarity=0.292  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      ..+++.||+|+|||..+-
T Consensus        48 ~~~ll~G~~GtGKt~la~   65 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAK   65 (311)
T ss_dssp             EEEEEESCSSSSHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHH
Confidence            479999999999997754

>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=87.31  E-value=0.23  Score=39.71  Aligned_cols=21  Identities=24%  Similarity=0.347  Sum_probs=17.4

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|..+++.||||||||...
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll  153 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI  153 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH
Confidence            345788999999999999764

>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=87.24  E-value=0.15  Score=38.23  Aligned_cols=19  Identities=32%  Similarity=0.389  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+++++.||+|+|||...-
T Consensus        44 ~~~vll~G~~GtGKT~la~   62 (268)
T 2r62_A           44 PKGVLLVGPPGTGKTLLAK   62 (268)
T ss_dssp             CSCCCCBCSSCSSHHHHHH
T ss_pred             CceEEEECCCCCcHHHHHH
Confidence            5679999999999997754

>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=87.22  E-value=0.31  Score=38.46  Aligned_cols=19  Identities=26%  Similarity=0.326  Sum_probs=16.6

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+++++.||+|+|||...-
T Consensus       117 ~~~vLl~GppGtGKT~la~  135 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGK  135 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5789999999999997754

>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=87.07  E-value=0.28  Score=39.04  Aligned_cols=19  Identities=26%  Similarity=0.457  Sum_probs=15.9

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+..+++.||||||||...
T Consensus       122 ~~g~i~I~GptGSGKTTlL  140 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTL  140 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4568999999999999664

>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=87.02  E-value=0.92  Score=36.94  Aligned_cols=48  Identities=15%  Similarity=0.174  Sum_probs=28.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      ...+++.||+|+|||...- .+...+.....+..++++.. ..+..+...
T Consensus       130 ~~~lll~Gp~G~GKTtLa~-aia~~l~~~~~~~~v~~v~~-~~~~~~~~~  177 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQ-SIGNYVVQNEPDLRVMYITS-EKFLNDLVD  177 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHH-HHHHHHHHHCCSSCEEEEEH-HHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHHHhCCCCeEEEeeH-HHHHHHHHH
Confidence            3689999999999997653 33344433323445555543 334444443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=87.00  E-value=0.32  Score=38.77  Aligned_cols=19  Identities=26%  Similarity=0.387  Sum_probs=16.6

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+++++.||+|+|||...-
T Consensus       148 ~~~vLL~GppGtGKT~la~  166 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLAK  166 (389)
T ss_dssp             CSEEEEESSTTSCHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5799999999999997654

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=86.96  E-value=0.75  Score=37.59  Aligned_cols=40  Identities=23%  Similarity=0.071  Sum_probs=28.0

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..|.-+++.|++|+|||...+--+.+....   +..++|++-
T Consensus       194 l~~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSl  233 (444)
T 3bgw_A          194 YKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSL  233 (444)
T ss_dssp             BCSSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECS
T ss_pred             CCCCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEEC
Confidence            3446789999999999997766555444332   457777763

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=86.96  E-value=2.2  Score=34.94  Aligned_cols=78  Identities=18%  Similarity=0.123  Sum_probs=43.2

Q ss_pred             ChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEc--------CccHHHHHHHh---c
Q psy9277          80 TGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG--------GTNLSEDLRKL---D  148 (178)
Q Consensus        80 sGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g--------~~~~~~~~~~~---~  148 (178)
                      ++|... +.-++..........++||.++++..+..+++.+.......++++..++|        +.+..++...+   .
T Consensus       370 ~~k~~~-l~~~l~~~~~~~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~  448 (555)
T 3tbk_A          370 NPKLRD-LYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFR  448 (555)
T ss_dssp             CHHHHH-HHHHHHHHHHHCTTCCEEEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC-----------------------
T ss_pred             CHHHHH-HHHHHHHHhccCCCceEEEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHh
Confidence            455433 33444444333455799999999999999999998765333344444443        55554443333   2


Q ss_pred             C--CCcEEEeCh
Q psy9277         149 Y--GQHVVSGTP  158 (178)
Q Consensus       149 ~--~~~IlV~TP  158 (178)
                      +  ..+|+|+|-
T Consensus       449 ~~g~~~vLvaT~  460 (555)
T 3tbk_A          449 ASGDNNILIATS  460 (555)
T ss_dssp             ---CCSEEEECC
T ss_pred             cCCCeeEEEEcc
Confidence            3  368999994

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=86.94  E-value=1.7  Score=34.29  Aligned_cols=40  Identities=30%  Similarity=0.352  Sum_probs=27.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..|.-+++.|++|+|||...+-.+.+...   .+..++|++.
T Consensus        43 l~~G~LiiIaG~pG~GKTt~al~ia~~~a~---~g~~Vl~fSl   82 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKTSLMMNMVLSALN---DDRGVAVFSL   82 (338)
T ss_dssp             BCTTCEEEEEECTTSCHHHHHHHHHHHHHH---TTCEEEEEES
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHH---cCCeEEEEeC
Confidence            444678999999999999776554444333   4457777763

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=86.91  E-value=0.31  Score=38.14  Aligned_cols=19  Identities=32%  Similarity=0.389  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +.++++.||+|+|||...-
T Consensus        44 ~~~vll~G~~G~GKT~l~~   62 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVAR   62 (387)
T ss_dssp             CCCEEECBCTTSSHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            5789999999999997653

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=86.90  E-value=0.25  Score=34.72  Aligned_cols=20  Identities=35%  Similarity=0.446  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|..+++.|++|||||...-
T Consensus         3 ~g~~I~l~G~~GsGKST~~~   22 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQAS   22 (186)
T ss_dssp             CEEEEEEECCTTSCHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            45679999999999997653

>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=86.88  E-value=1.2  Score=34.82  Aligned_cols=18  Identities=28%  Similarity=0.180  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      ...+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            457999999999999765

>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=86.85  E-value=0.91  Score=35.86  Aligned_cols=37  Identities=14%  Similarity=0.161  Sum_probs=24.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      .|.-+++.+|+|+|||...+..+.....   .+..++|+.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~---~g~~vlyi~   96 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQA---AGGIAAFID   96 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHH---TTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh---CCCeEEEEE
Confidence            4678999999999999876554443322   234555554

>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=86.81  E-value=1.7  Score=39.95  Aligned_cols=54  Identities=22%  Similarity=0.255  Sum_probs=41.4

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhc---------CCCceEEEEcCcHHHHHHHHHHHHHh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQ---------LRETQVLCLSPTRELAVQIQKVVLAL  123 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~---------~~~~~~lil~Pt~~L~~q~~~~~~~~  123 (178)
                      .+.+|.|+-|||||.+..-=++..+...         ....+.|+|+=|++=|.++.++++..
T Consensus        17 g~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~   79 (1180)
T 1w36_B           17 GERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN   79 (1180)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHH
Confidence            3459999999999988777777766532         12347999999999999888887544

>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=86.68  E-value=0.82  Score=34.76  Aligned_cols=40  Identities=23%  Similarity=0.199  Sum_probs=25.3

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      +..|.-+++.||+|+|||.....-+.. +... .+..++++.
T Consensus        32 l~~G~~~~i~G~~G~GKTTl~~~ia~~-~~~~-~G~~v~~~~   71 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTFVRQQALQ-WGTA-MGKKVGLAM   71 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHHHHHHHHH-HHHT-SCCCEEEEE
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHH-HHHH-cCCeEEEEe
Confidence            445889999999999999765443322 2222 233566654

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=86.55  E-value=0.91  Score=41.08  Aligned_cols=32  Identities=9%  Similarity=-0.000  Sum_probs=24.4

Q ss_pred             ceEEEEEcCccHHHHHHHhcCCCcEEEeChHH
Q psy9277         129 VQCHACIGGTNLSEDLRKLDYGQHVVSGTPGR  160 (178)
Q Consensus       129 ~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~  160 (178)
                      -++.++.++.....+...+..++.|||||=.+
T Consensus       236 ~~~LlvlDd~~~~~~~~~~~~~~~ilvTtR~~  267 (1249)
T 3sfz_A          236 PRSLLILDDVWDPWVLKAFDNQCQILLTTRDK  267 (1249)
T ss_dssp             CSCEEEEESCCCHHHHTTTCSSCEEEEEESST
T ss_pred             CCEEEEEecCCCHHHHHhhcCCCEEEEEcCCH
Confidence            37788888887777777777789999999533

>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=86.39  E-value=0.58  Score=36.23  Aligned_cols=18  Identities=33%  Similarity=0.455  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      .++++.||+|+|||...-
T Consensus        59 ~~~ll~G~~G~GKT~la~   76 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTIL   76 (353)
T ss_dssp             CCEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            469999999999997653

>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=86.35  E-value=1.1  Score=35.64  Aligned_cols=38  Identities=18%  Similarity=0.127  Sum_probs=26.0

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      .|.-+++.+++|+|||...+-.+.+...   .+..++|+..
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~---~g~~vlyid~   99 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQR---EGKTCAFIDA   99 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHH---TTCCEEEEES
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH---CCCeEEEEeC
Confidence            4678999999999999877654443322   2345666664

>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=86.31  E-value=1.2  Score=37.65  Aligned_cols=26  Identities=19%  Similarity=0.372  Sum_probs=20.0

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      ..+++|.|.||||||.+.-..++..+
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl  239 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSIL  239 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHH
Confidence            46899999999999987655555444

>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=86.19  E-value=0.28  Score=37.65  Aligned_cols=19  Identities=21%  Similarity=0.218  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus        38 ~~~vll~G~~GtGKT~la~   56 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLAH   56 (324)
T ss_dssp             CCCCEEECCTTCCCHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHH
Confidence            4789999999999997653

>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=86.14  E-value=0.65  Score=39.70  Aligned_cols=59  Identities=15%  Similarity=0.170  Sum_probs=40.6

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHh--ccCCCceEEEEEcC--------ccHHHHHHHhc---C-CCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLAL--GDFMNVQCHACIGG--------TNLSEDLRKLD---Y-GQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~--~~~~~~~~~~~~g~--------~~~~~~~~~~~---~-~~~IlV~TP  158 (178)
                      +.++||.++++..+..+++.+...  ....|+++..++|+        .+..++...+.   + ..+|||+|-
T Consensus       400 ~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~  472 (699)
T 4gl2_A          400 SARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATT  472 (699)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEEC
T ss_pred             CCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEcc
Confidence            579999999999999999988754  22337888888888        77766655443   2 468999983

>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=86.09  E-value=0.36  Score=34.55  Aligned_cols=20  Identities=30%  Similarity=0.370  Sum_probs=17.0

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~   42 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLA   42 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHH
Confidence            34788999999999999765

>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=86.03  E-value=0.69  Score=36.30  Aligned_cols=23  Identities=35%  Similarity=0.618  Sum_probs=17.8

Q ss_pred             HHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          64 KPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      ..++.|.|  ++..|+||||||...
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            44556765  788999999999775

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=85.89  E-value=0.63  Score=33.74  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=16.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~   92 (178)
                      -.+++|++|||||...+--++.
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~   28 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMAN   28 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            5789999999999876443333

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=85.89  E-value=1.4  Score=38.06  Aligned_cols=61  Identities=18%  Similarity=0.260  Sum_probs=44.9

Q ss_pred             CCcHHHHHHHHHHHc--CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVK--GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVV  120 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~--g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~  120 (178)
                      .+|.-|.+++..+..  ..-.++.|+-|.|||.+.-+.+-. +.     ..+++.+|+.+-+..+.+..
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~-~~-----~~~~vtAP~~~a~~~l~~~~  237 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISR-IA-----GRAIVTAPAKASTDVLAQFA  237 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHH-SS-----SCEEEECSSCCSCHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHH-HH-----hCcEEECCCHHHHHHHHHHh
Confidence            679999999988877  345799999999999554443332 22     24689999988887666654

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=85.83  E-value=0.57  Score=35.26  Aligned_cols=21  Identities=29%  Similarity=0.423  Sum_probs=18.1

Q ss_pred             HcCCcEEEEcCCCChHHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.|+.+++.|++|||||...-
T Consensus        46 l~g~~i~l~G~~GsGKSTl~~   66 (250)
T 3nwj_A           46 LNGRSMYLVGMMGSGKTTVGK   66 (250)
T ss_dssp             HTTCCEEEECSTTSCHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHH
Confidence            349999999999999997753

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=85.80  E-value=0.58  Score=39.76  Aligned_cols=16  Identities=19%  Similarity=0.437  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      ++++.||+|+|||..+
T Consensus       329 ~vLL~GppGtGKT~LA  344 (595)
T 3f9v_A          329 HILIIGDPGTAKSQML  344 (595)
T ss_dssp             CEEEEESSCCTHHHHH
T ss_pred             ceEEECCCchHHHHHH
Confidence            8999999999999764

>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=85.78  E-value=6.8  Score=29.84  Aligned_cols=71  Identities=15%  Similarity=0.147  Sum_probs=37.4

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC---CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG---RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g---~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      .+|+++--++.+.+.+.+               .+..+   .-+++.+|+|+|||...-. +...+     +...+.+.+
T Consensus        23 ~~~~~ivg~~~~~~~l~~---------------~l~~~~~~~~~L~~G~~G~GKT~la~~-la~~l-----~~~~~~i~~   81 (324)
T 3u61_B           23 STIDECILPAFDKETFKS---------------ITSKGKIPHIILHSPSPGTGKTTVAKA-LCHDV-----NADMMFVNG   81 (324)
T ss_dssp             CSTTTSCCCHHHHHHHHH---------------HHHTTCCCSEEEECSSTTSSHHHHHHH-HHHHT-----TEEEEEEET
T ss_pred             CCHHHHhCcHHHHHHHHH---------------HHHcCCCCeEEEeeCcCCCCHHHHHHH-HHHHh-----CCCEEEEcc
Confidence            467777666666655532               11122   2456777799999977543 22322     234555554


Q ss_pred             cHHHHHHHHHHHHHh
Q psy9277         109 TRELAVQIQKVVLAL  123 (178)
Q Consensus       109 t~~L~~q~~~~~~~~  123 (178)
                      ...-...+.+.+..+
T Consensus        82 ~~~~~~~i~~~~~~~   96 (324)
T 3u61_B           82 SDCKIDFVRGPLTNF   96 (324)
T ss_dssp             TTCCHHHHHTHHHHH
T ss_pred             cccCHHHHHHHHHHH
Confidence            433233343334333

>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=85.77  E-value=0.67  Score=33.43  Aligned_cols=31  Identities=13%  Similarity=0.138  Sum_probs=22.5

Q ss_pred             cHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          56 SAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +..++.. ..+..|..+++.|++|||||...-
T Consensus        13 ~~~~r~~-~~~~~~~~i~~~G~~GsGKsT~~~   43 (211)
T 1m7g_A           13 TRSERTE-LRNQRGLTIWLTGLSASGKSTLAV   43 (211)
T ss_dssp             CHHHHHH-HHTSSCEEEEEECSTTSSHHHHHH
T ss_pred             CHHHhhc-ccCCCCCEEEEECCCCCCHHHHHH
Confidence            4555554 345568889999999999997653

>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=85.73  E-value=0.41  Score=39.06  Aligned_cols=56  Identities=13%  Similarity=0.054  Sum_probs=32.5

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHH-HHH-HHHcCCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQR-SIK-PIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~-~i~-~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|+++.=.+.+.+.|.+.-.   ++.... .+. .....+.+++.||+|+|||...-
T Consensus       128 ~~~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~  185 (444)
T 2zan_A          128 RPNVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAK  185 (444)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHT---HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHH
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHhhccCCCCceEEEECCCCCCHHHHHH
Confidence            345678888766666666653210   111100 000 11224789999999999997653

>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=85.71  E-value=1.5  Score=33.95  Aligned_cols=44  Identities=14%  Similarity=0.181  Sum_probs=28.9

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+|+++--++.+.+.|+..-...            -...++++.||+|+|||...-
T Consensus        11 ~~~~~~vg~~~~~~~l~~~~~~~------------~~~~~~ll~Gp~G~GKTtl~~   54 (354)
T 1sxj_E           11 KSLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRCM   54 (354)
T ss_dssp             CSGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHHHhhC------------CCCCeEEEECCCCCCHHHHHH
Confidence            45777666777777776431110            123359999999999997653

>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=85.69  E-value=0.89  Score=36.13  Aligned_cols=39  Identities=21%  Similarity=0.166  Sum_probs=24.8

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      .|.-+++.+|+|+|||...+..+ ..+..  .+..++|+...
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la-~~~~~--~gg~VlyId~E   98 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAI-AEAQK--MGGVAAFIDAE   98 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHH-HHHHH--TTCCEEEEESS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH-HHHHh--cCCeEEEEecc
Confidence            36789999999999997654333 33322  33456666543

>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=85.66  E-value=0.37  Score=35.84  Aligned_cols=20  Identities=30%  Similarity=0.429  Sum_probs=16.6

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        29 ~~Ge~~~iiG~nGsGKSTLl   48 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKSTML   48 (235)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            34788999999999999653

>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=85.63  E-value=0.44  Score=42.01  Aligned_cols=56  Identities=20%  Similarity=0.243  Sum_probs=34.6

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHH--HHcCCcEEEEcCCCChHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKP--IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~--i~~g~~v~v~aptGsGKTl~~   86 (178)
                      .+..+|++++.-++..+.|++.= ..|... .+.+..  +...+.+++.||+|+|||+.+
T Consensus       471 ~p~v~w~diggl~~~k~~l~e~v-~~p~~~-p~~f~~~g~~~~~gvLl~GPPGtGKT~lA  528 (806)
T 3cf2_A          471 VPQVTWEDIGGLEDVKRELQELV-QYPVEH-PDKFLKFGMTPSKGVLFYGPPGCGKTLLA  528 (806)
T ss_dssp             CCCCCSTTCCSCHHHHHHHTTTT-TTTTTC-SGGGSSSCCCCCSCCEEESSTTSSHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHH-HhhhhC-HHHHHhcCCCCCceEEEecCCCCCchHHH
Confidence            34567999988888888886542 111110 000100  112468999999999999665

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=85.55  E-value=0.43  Score=37.44  Aligned_cols=18  Identities=17%  Similarity=0.198  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +.++++||||||||....
T Consensus         6 ~~i~i~GptGsGKTtla~   23 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAM   23 (323)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            368999999999997654

>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=85.48  E-value=0.31  Score=34.39  Aligned_cols=18  Identities=28%  Similarity=0.418  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      .-+++.||+|+|||...-
T Consensus         3 ~ii~l~G~~GaGKSTl~~   20 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCK   20 (189)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            457899999999997653

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=85.47  E-value=4.3  Score=32.98  Aligned_cols=86  Identities=17%  Similarity=0.171  Sum_probs=42.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc--CcHHHHHHHHHHHHHhccCCCceEEEEEcCccHH----HH
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS--PTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS----ED  143 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~--Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~----~~  143 (178)
                      +-+++.+++|+|||.....-+. .+..  .+.+++++.  +.+..+.++...+.   ...++.+.....+.+..    +.
T Consensus        99 ~vi~i~G~~GsGKTT~~~~LA~-~l~~--~g~~Vllvd~D~~r~aa~~qL~~~~---~~~gv~v~~~~~~~~p~~i~~~~  172 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAAKLAL-YYKG--KGRRPLLVAADTQRPAAREQLRLLG---EKVGVPVLEVMDGESPESIRRRV  172 (425)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH-HHHT--TTCCEEEEECCSSCHHHHHHHHHHH---HHHTCCEEECCTTCCHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-HHHH--cCCeEEEeeccccCchhHHHHHHhc---ccCCccEEecCCCCCHHHHHHHH
Confidence            3577889999999976543222 2222  344565554  33444443333222   22245443322222211    12


Q ss_pred             HHHh-cCCCc-EEEeChHHH
Q psy9277         144 LRKL-DYGQH-VVSGTPGRV  161 (178)
Q Consensus       144 ~~~~-~~~~~-IlV~TP~~l  161 (178)
                      .... ..++| |||=||+++
T Consensus       173 l~~~~~~~~DvVIIDTaG~l  192 (425)
T 2ffh_A          173 EEKARLEARDLILVDTAGRL  192 (425)
T ss_dssp             HHHHHHTTCSEEEEECCCCS
T ss_pred             HHHHHHCCCCEEEEcCCCcc
Confidence            2223 24565 778899875

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=85.42  E-value=0.44  Score=34.03  Aligned_cols=19  Identities=21%  Similarity=0.351  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+-++++|++|||||...-
T Consensus        18 ~~~I~l~G~~GsGKSTla~   36 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGE   36 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3579999999999997653

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=85.23  E-value=0.38  Score=34.73  Aligned_cols=19  Identities=21%  Similarity=0.240  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
T Consensus        21 ~g~~v~I~G~sGsGKSTl~   39 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLS   39 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4678899999999999654

>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=85.22  E-value=0.4  Score=33.69  Aligned_cols=18  Identities=28%  Similarity=0.278  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      +.-++++|++|||||...
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            457899999999999765

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=85.15  E-value=0.47  Score=37.51  Aligned_cols=17  Identities=18%  Similarity=0.200  Sum_probs=14.5

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -++|+||||||||....
T Consensus         9 lI~I~GptgSGKTtla~   25 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSI   25 (340)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             eEEEECCCcCcHHHHHH
Confidence            58899999999997653

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=85.13  E-value=0.41  Score=33.59  Aligned_cols=19  Identities=21%  Similarity=0.228  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+++.|++|||||...-
T Consensus         3 ~~~I~l~G~~GsGKsT~a~   21 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCA   21 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            4568999999999997753

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=85.07  E-value=1.6  Score=35.52  Aligned_cols=41  Identities=20%  Similarity=0.116  Sum_probs=27.1

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..|.-+++.|++|+|||...+--+......  .+..++|+..
T Consensus       200 l~~G~liiI~G~pG~GKTtl~l~ia~~~~~~--~g~~Vl~~s~  240 (454)
T 2r6a_A          200 FQRSDLIIVAARPSVGKTAFALNIAQNVATK--TNENVAIFSL  240 (454)
T ss_dssp             BCTTCEEEEECCTTSCHHHHHHHHHHHHHHH--SSCCEEEEES
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEEEC
Confidence            3447789999999999997765444433322  2346777763

>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=85.03  E-value=0.49  Score=33.55  Aligned_cols=16  Identities=31%  Similarity=0.578  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      .+.+.||+|+|||...
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            4789999999999765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=85.01  E-value=1.6  Score=35.52  Aligned_cols=41  Identities=22%  Similarity=0.024  Sum_probs=26.8

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..|.-+++.|++|+|||...+--+.+....  .+..++|+..
T Consensus       197 l~~G~l~ii~G~pg~GKT~lal~ia~~~a~~--~g~~vl~~sl  237 (444)
T 2q6t_A          197 LGPGSLNIIAARPAMGKTAFALTIAQNAALK--EGVGVGIYSL  237 (444)
T ss_dssp             CCTTCEEEEEECTTSCHHHHHHHHHHHHHHT--TCCCEEEEES
T ss_pred             cCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEEC
Confidence            3346789999999999997665444443322  2346777664

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=84.98  E-value=0.53  Score=32.75  Aligned_cols=18  Identities=17%  Similarity=0.364  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +.+++.+++|||||...-
T Consensus         5 ~~i~i~G~~GsGKsTla~   22 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLAR   22 (175)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHH
Confidence            368999999999997653

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=84.87  E-value=0.42  Score=36.63  Aligned_cols=18  Identities=28%  Similarity=0.357  Sum_probs=15.1

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      +.-++++||+|||||...
T Consensus        33 ~~livl~G~sGsGKSTla   50 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLR   50 (287)
T ss_dssp             CEEEEEECCTTSCTHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            356899999999999765

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=84.75  E-value=0.5  Score=33.36  Aligned_cols=19  Identities=21%  Similarity=0.317  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+.-++++|++|||||...
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            4678999999999999765

>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=84.69  E-value=0.78  Score=35.72  Aligned_cols=19  Identities=32%  Similarity=0.473  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+++.||+|+|||...-
T Consensus        45 ~~~vli~G~~G~GKTtl~~   63 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVVK   63 (386)
T ss_dssp             CCCEEEEECTTSSHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            6789999999999997653

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=84.67  E-value=0.54  Score=33.09  Aligned_cols=19  Identities=21%  Similarity=0.314  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+..+++.|++|||||...
T Consensus         8 ~~~~I~l~G~~GsGKsT~~   26 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQC   26 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999765

>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=84.67  E-value=0.61  Score=32.64  Aligned_cols=18  Identities=17%  Similarity=0.250  Sum_probs=15.2

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++|++|||||...-
T Consensus         3 ~~I~l~G~~GsGKsT~a~   20 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGR   20 (184)
T ss_dssp             CSEEEECSTTSSHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH
Confidence            468999999999997753

>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=84.63  E-value=1.3  Score=38.15  Aligned_cols=53  Identities=19%  Similarity=0.208  Sum_probs=42.1

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP  158 (178)
                      .+.++||.+++++-+.++++.+++.    ++.+..++|+.+..+.   .+.+.+|||+|.
T Consensus       395 ~~~~vLVFv~Tr~~ae~la~~L~~~----g~~v~~lHG~l~q~er---~~~~~~VLVATd  447 (666)
T 3o8b_A          395 RGGRHLIFCHSKKKCDELAAKLSGL----GINAVAYYRGLDVSVI---PTIGDVVVVATD  447 (666)
T ss_dssp             SSSEEEEECSCHHHHHHHHHHHHTT----TCCEEEECTTSCGGGS---CSSSCEEEEECT
T ss_pred             cCCcEEEEeCCHHHHHHHHHHHHhC----CCcEEEecCCCCHHHH---HhCCCcEEEECC
Confidence            3458999999999999999888754    7889999999876642   234569999994

>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=84.63  E-value=1.7  Score=32.88  Aligned_cols=43  Identities=26%  Similarity=0.394  Sum_probs=28.4

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+|+++--++...+.+.+. +..            -...++++.||+|+|||....
T Consensus        14 ~~~~~~~g~~~~~~~l~~~-l~~------------~~~~~~ll~G~~G~GKt~la~   56 (319)
T 2chq_A           14 RTLDEVVGQDEVIQRLKGY-VER------------KNIPHLLFSGPPGTGKTATAI   56 (319)
T ss_dssp             SSGGGSCSCHHHHHHHHTT-TTT------------TCCCCEEEESSSSSSHHHHHH
T ss_pred             CCHHHHhCCHHHHHHHHHH-HhC------------CCCCeEEEECcCCcCHHHHHH
Confidence            4577766677777777543 111            122369999999999997653

>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=84.55  E-value=1.7  Score=37.01  Aligned_cols=54  Identities=11%  Similarity=0.000  Sum_probs=39.9

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh-cCCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL-DYGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~IlV~TP  158 (178)
                      +.++||.++++.-+..+++.++..    ++.+..++|+.... ..... ....+|||+|.
T Consensus       355 ~~~~LVF~~s~~~a~~l~~~L~~~----g~~v~~lhg~~R~~-~l~~F~~g~~~VLVaTd  409 (618)
T 2whx_A          355 QGKTVWFVPSIKAGNDIANCLRKS----GKRVIQLSRKTFDT-EYPKTKLTDWDFVVTTD  409 (618)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTTHHH-HTTHHHHSCCSEEEECG
T ss_pred             CCCEEEEECChhHHHHHHHHHHHc----CCcEEEEChHHHHH-HHHhhcCCCcEEEEECc
Confidence            458999999999999999998765    67788888754332 22222 24578999995

>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=84.50  E-value=0.45  Score=34.41  Aligned_cols=23  Identities=22%  Similarity=0.101  Sum_probs=18.4

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll   88 (178)
                      +..|.-+.+.+|+|+|||.....
T Consensus        22 i~~G~~~~l~G~nGsGKSTll~~   44 (231)
T 4a74_A           22 IETQAITEVFGEFGSGKTQLAHT   44 (231)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHH
Confidence            34578899999999999976543

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=84.49  E-value=0.53  Score=33.90  Aligned_cols=17  Identities=18%  Similarity=0.391  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.|++|||||...-
T Consensus         2 ~I~l~G~~GsGKsT~a~   18 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAE   18 (216)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999997653

>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=84.49  E-value=0.73  Score=36.08  Aligned_cols=17  Identities=35%  Similarity=0.483  Sum_probs=15.0

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.||+|+|||...-
T Consensus        46 ~~li~G~~G~GKTtl~~   62 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLR   62 (389)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            79999999999997653

>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=84.49  E-value=0.51  Score=39.12  Aligned_cols=19  Identities=32%  Similarity=0.422  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||+..-
T Consensus       238 ~~~vLL~GppGtGKT~lAr  256 (489)
T 3hu3_A          238 PRGILLYGPPGTGKTLIAR  256 (489)
T ss_dssp             CCEEEEECSTTSSHHHHHH
T ss_pred             CCcEEEECcCCCCHHHHHH
Confidence            5789999999999997653

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=84.47  E-value=0.36  Score=35.38  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=13.5

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..|+-+.+.||+|||||...
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~   44 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVA   44 (231)
T ss_dssp             EECCCEEEEECSCC----CHH
T ss_pred             cCCCCEEEEECCCCCCHHHHH
Confidence            345788999999999999765

>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=84.45  E-value=1.4  Score=35.10  Aligned_cols=37  Identities=16%  Similarity=0.114  Sum_probs=23.9

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      .|.-+++.+++|+|||...+-.+.+.. .  .+..++|+.
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~-~--~g~~vlyi~  109 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQ-K--AGGTCAFID  109 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH-H--TTCCEEEEE
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHH-H--CCCeEEEEE
Confidence            357899999999999977654443322 2  233555554

>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=84.24  E-value=0.56  Score=36.59  Aligned_cols=18  Identities=28%  Similarity=0.372  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      ..+++.||+|+|||...-
T Consensus        52 ~~~ll~Gp~G~GKTTLa~   69 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAH   69 (334)
T ss_dssp             CCEEEESSTTSSHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHH
Confidence            689999999999997754

>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=84.17  E-value=0.56  Score=33.82  Aligned_cols=17  Identities=18%  Similarity=0.309  Sum_probs=14.4

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.|++|||||...-
T Consensus         2 ~I~l~G~~GsGKsT~a~   18 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGE   18 (216)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48899999999997653

>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=84.13  E-value=0.63  Score=33.04  Aligned_cols=19  Identities=21%  Similarity=0.391  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .++.+++.|+.|||||...
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            4678999999999999765

>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=84.12  E-value=0.28  Score=38.06  Aligned_cols=19  Identities=26%  Similarity=0.370  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus        45 ~~~vLl~G~~GtGKT~la~   63 (350)
T 1g8p_A           45 IGGVLVFGDRGTGKSTAVR   63 (350)
T ss_dssp             GCCEEEECCGGGCTTHHHH
T ss_pred             CceEEEECCCCccHHHHHH
Confidence            4579999999999997653

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=84.02  E-value=0.99  Score=37.75  Aligned_cols=30  Identities=13%  Similarity=0.004  Sum_probs=20.6

Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChH
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPG  159 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~  159 (178)
                      ++.++.++.........+..++.|||||=.
T Consensus       237 ~~LLVLDdv~~~~~l~~l~~~~~ilvTsR~  266 (591)
T 1z6t_A          237 RSLLILDDVWDSWVLKAFDSQCQILLTTRD  266 (591)
T ss_dssp             TCEEEEEEECCHHHHHTTCSSCEEEEEESC
T ss_pred             CeEEEEeCCCCHHHHHHhcCCCeEEEECCC
Confidence            456666666655566666677899998843

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=84.01  E-value=0.57  Score=34.19  Aligned_cols=19  Identities=16%  Similarity=0.221  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+..+++.|++|||||...
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            3567999999999999765

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=83.96  E-value=1.7  Score=32.37  Aligned_cols=20  Identities=30%  Similarity=0.343  Sum_probs=16.4

Q ss_pred             cEEEEcCCCChHHHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSISI   90 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~i   90 (178)
                      ++++.++.|+|||...+--.
T Consensus         8 ~I~~~~kgGvGKTt~a~~la   27 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAA   27 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHH
Confidence            79999999999998865433

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=83.96  E-value=0.3  Score=35.05  Aligned_cols=24  Identities=17%  Similarity=-0.026  Sum_probs=18.5

Q ss_pred             HHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          64 KPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        64 ~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.+..+.-+.+.|++|||||...-
T Consensus        16 ~~~~~~~~i~i~G~~GsGKSTl~~   39 (207)
T 2qt1_A           16 PRGSKTFIIGISGVTNSGKTTLAK   39 (207)
T ss_dssp             CCSCCCEEEEEEESTTSSHHHHHH
T ss_pred             ccCCCCeEEEEECCCCCCHHHHHH
Confidence            344556778999999999997653

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=83.84  E-value=0.5  Score=33.91  Aligned_cols=19  Identities=21%  Similarity=0.097  Sum_probs=15.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
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            3556889999999999765

>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=83.81  E-value=0.53  Score=38.17  Aligned_cols=17  Identities=18%  Similarity=0.317  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -++|.||||+|||....
T Consensus         4 ~i~i~GptgsGKttla~   20 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSI   20 (409)
T ss_dssp             EEEEEECSSSSHHHHHH
T ss_pred             EEEEECcchhhHHHHHH
Confidence            37899999999997654

>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=83.75  E-value=0.5  Score=35.13  Aligned_cols=20  Identities=30%  Similarity=0.401  Sum_probs=16.7

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        29 ~~Ge~~~i~G~nGsGKSTLl   48 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSSLL   48 (237)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            34788999999999999654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=83.72  E-value=0.61  Score=32.14  Aligned_cols=18  Identities=17%  Similarity=0.322  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +++++.|+.|||||...-
T Consensus         8 ~~i~l~G~~GsGKSTva~   25 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQ   25 (168)
T ss_dssp             CEEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            589999999999997764

>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=83.70  E-value=2  Score=31.63  Aligned_cols=40  Identities=10%  Similarity=0.172  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      |+=.+++++-|+|||...+--+... ..  .+.+++++.|.+.
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~-~~--~g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRT-QF--AKQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHH-HH--TTCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHH-HH--CCCEEEEEEeccC
Confidence            4455688888999997765444333 22  4568888888764

>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=83.58  E-value=0.64  Score=33.67  Aligned_cols=19  Identities=16%  Similarity=0.258  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+++.|++|||||...-
T Consensus         4 ~~~I~l~G~~GsGKsT~a~   22 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAP   22 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5679999999999997653

>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=83.51  E-value=0.56  Score=32.76  Aligned_cols=19  Identities=37%  Similarity=0.455  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|..+++.|+.|||||...
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            4677899999999999764

>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=83.50  E-value=0.69  Score=31.88  Aligned_cols=18  Identities=17%  Similarity=0.200  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +.+++.|++|||||...-
T Consensus         3 ~~I~l~G~~GsGKsT~a~   20 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGR   20 (173)
T ss_dssp             CCEEEESCTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            468999999999997653

>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=83.45  E-value=1.4  Score=34.61  Aligned_cols=43  Identities=14%  Similarity=0.052  Sum_probs=28.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELA  113 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~  113 (178)
                      | -+.+.+|+|+|||...+-.+.+... ...+.+++|+....++-
T Consensus        29 G-iteI~G~pGsGKTtL~Lq~~~~~~~-~g~g~~vlyId~E~s~~   71 (333)
T 3io5_A           29 G-LLILAGPSKSFKSNFGLTMVSSYMR-QYPDAVCLFYDSEFGIT   71 (333)
T ss_dssp             E-EEEEEESSSSSHHHHHHHHHHHHHH-HCTTCEEEEEESSCCCC
T ss_pred             C-eEEEECCCCCCHHHHHHHHHHHHHh-cCCCceEEEEeccchhh
Confidence            5 5899999999999876655544332 21245777777655543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=83.44  E-value=3.3  Score=38.02  Aligned_cols=34  Identities=6%  Similarity=0.057  Sum_probs=26.1

Q ss_pred             CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHH
Q psy9277         128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV  161 (178)
Q Consensus       128 ~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l  161 (178)
                      +-++.++.++....+.+..+..++.|||||=.+.
T Consensus       243 ~KRvLLVLDDVwd~eqLe~f~pGSRILVTTRd~~  276 (1221)
T 1vt4_I          243 YENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQ  276 (1221)
T ss_dssp             TSSCEEEEESCCCHHHHHHHHSSCCEEEECSCSH
T ss_pred             CCCEEEEEeCcChHHHHHhhCCCeEEEEeccChH
Confidence            4567788888777777767778899999996554

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=83.42  E-value=0.93  Score=36.09  Aligned_cols=24  Identities=29%  Similarity=0.553  Sum_probs=18.1

Q ss_pred             HHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      +..++.|.  .++..|+||||||...
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            34456676  4788899999999775

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=83.34  E-value=0.92  Score=37.21  Aligned_cols=19  Identities=26%  Similarity=0.366  Sum_probs=16.4

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus       201 ~~~~LL~G~pG~GKT~la~  219 (468)
T 3pxg_A          201 KNNPVLIGEPGVGKTAIAE  219 (468)
T ss_dssp             SCEEEEESCTTTTTHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHH
Confidence            5699999999999997754

>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=83.33  E-value=1.2  Score=34.55  Aligned_cols=16  Identities=25%  Similarity=0.320  Sum_probs=13.3

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -+++.|+.|||||...
T Consensus         6 v~~i~G~~GaGKTTll   21 (318)
T 1nij_A            6 VTLLTGFLGAGKTTLL   21 (318)
T ss_dssp             EEEEEESSSSSCHHHH
T ss_pred             EEEEEecCCCCHHHHH
Confidence            3689999999999654

>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=83.32  E-value=0.68  Score=32.99  Aligned_cols=19  Identities=21%  Similarity=0.246  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+++.|++|||||...-
T Consensus        20 ~~~I~l~G~~GsGKST~a~   38 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAV   38 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4579999999999997653

>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=83.27  E-value=1  Score=37.34  Aligned_cols=19  Identities=26%  Similarity=0.293  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.++++||+|+|||.+.-
T Consensus        77 ~~~lLL~GppGtGKTtla~   95 (516)
T 1sxj_A           77 FRAAMLYGPPGIGKTTAAH   95 (516)
T ss_dssp             CSEEEEECSTTSSHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            3689999999999997754

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=83.14  E-value=0.6  Score=32.65  Aligned_cols=16  Identities=25%  Similarity=0.345  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      .+++.|++|||||...
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            4789999999999765

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=83.11  E-value=1.1  Score=38.10  Aligned_cols=25  Identities=24%  Similarity=0.267  Sum_probs=20.2

Q ss_pred             HHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          63 IKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        63 i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      -..+..|..+++.||+|+|||..+-
T Consensus        54 ~~~i~~g~~vll~Gp~GtGKTtlar   78 (604)
T 3k1j_A           54 KTAANQKRHVLLIGEPGTGKSMLGQ   78 (604)
T ss_dssp             HHHHHTTCCEEEECCTTSSHHHHHH
T ss_pred             cccccCCCEEEEEeCCCCCHHHHHH
Confidence            3456678999999999999997653

>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=83.11  E-value=0.67  Score=31.80  Aligned_cols=16  Identities=25%  Similarity=0.405  Sum_probs=13.6

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -.++.+|+|+|||...
T Consensus        25 ~~~I~G~NGsGKStil   40 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLL   40 (149)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4689999999999764

>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=83.11  E-value=1.9  Score=39.51  Aligned_cols=58  Identities=19%  Similarity=0.058  Sum_probs=45.5

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.+++|++++++-+..+++.++....  +.++..++|+++..++...+.    ...+|+|+|-
T Consensus       811 ~g~qvlvf~~~v~~~~~l~~~L~~~~p--~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~  872 (1151)
T 2eyq_A          811 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT  872 (1151)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS
T ss_pred             cCCeEEEEECCHHHHHHHHHHHHHhCC--CCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC
Confidence            457899999999999999999887643  577888999988776554432    3579999994

>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=83.10  E-value=1.5  Score=33.34  Aligned_cols=17  Identities=24%  Similarity=0.372  Sum_probs=14.9

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      ++++.||+|+|||...-
T Consensus        48 ~~ll~G~~G~GKT~la~   64 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAAL   64 (327)
T ss_dssp             EEEEESCTTSSHHHHHH
T ss_pred             eEEEECcCCCCHHHHHH
Confidence            69999999999997653

>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=82.99  E-value=0.78  Score=35.66  Aligned_cols=20  Identities=20%  Similarity=0.107  Sum_probs=17.1

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|+-+.+.||+|+|||...
T Consensus       124 ~~Ge~vaIvGpsGsGKSTLl  143 (305)
T 2v9p_A          124 PKKNCLAFIGPPNTGKSMLC  143 (305)
T ss_dssp             TTCSEEEEECSSSSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            34889999999999999664

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=82.99  E-value=0.74  Score=33.40  Aligned_cols=19  Identities=16%  Similarity=0.237  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+++.|++|||||...-
T Consensus         5 ~~~I~l~G~~GsGKsT~~~   23 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCE   23 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            4679999999999997653

>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=82.92  E-value=0.67  Score=35.01  Aligned_cols=27  Identities=19%  Similarity=0.117  Sum_probs=21.5

Q ss_pred             HHHHcCCcEEEEcCCCChHHHHHHHHH
Q psy9277          64 KPIVKGRDVIAQAQSGTGKTATFSISI   90 (178)
Q Consensus        64 ~~i~~g~~v~v~aptGsGKTl~~ll~i   90 (178)
                      .-+..|.-+++.||+|+|||.....-+
T Consensus        25 ggl~~G~i~~i~G~~GsGKTtl~~~l~   51 (279)
T 1nlf_A           25 PNMVAGTVGALVSPGGAGKSMLALQLA   51 (279)
T ss_dssp             TTEETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             CCccCCCEEEEEcCCCCCHHHHHHHHH
Confidence            346678999999999999998765443

>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=82.84  E-value=0.94  Score=45.06  Aligned_cols=21  Identities=29%  Similarity=0.466  Sum_probs=17.9

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      +..+++++++||||+|||...
T Consensus      1264 l~~~~~vLL~GPpGtGKT~la 1284 (2695)
T 4akg_A         1264 LNSKRGIILCGPPGSGKTMIM 1284 (2695)
T ss_dssp             HHHTCEEEEECSTTSSHHHHH
T ss_pred             HHCCCeEEEECCCCCCHHHHH
Confidence            345899999999999999764

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=82.84  E-value=0.78  Score=32.89  Aligned_cols=19  Identities=32%  Similarity=0.501  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |.-+.+.+|+|+|||...-
T Consensus         1 G~~i~i~G~nG~GKTTll~   19 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIH   19 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHH
Confidence            4568899999999997653

>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=82.82  E-value=0.7  Score=33.43  Aligned_cols=19  Identities=21%  Similarity=0.288  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+.+.||+|||||...-
T Consensus         5 ~~~i~i~G~~GsGKSTl~~   23 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCK   23 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            3568999999999997653

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=82.80  E-value=0.62  Score=36.99  Aligned_cols=16  Identities=25%  Similarity=0.576  Sum_probs=13.9

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -++++||+|+|||..+
T Consensus        25 ~~~i~G~NGaGKTTll   40 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSLF   40 (365)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4679999999999776

>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=82.77  E-value=0.64  Score=32.46  Aligned_cols=16  Identities=19%  Similarity=0.146  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -.++.+|+|+|||..+
T Consensus        28 ~~~i~G~NGsGKStll   43 (182)
T 3kta_A           28 FTAIVGANGSGKSNIG   43 (182)
T ss_dssp             EEEEEECTTSSHHHHH
T ss_pred             cEEEECCCCCCHHHHH
Confidence            5689999999999765

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=82.75  E-value=1.1  Score=35.75  Aligned_cols=19  Identities=42%  Similarity=0.545  Sum_probs=15.8

Q ss_pred             cCCc--EEEEcCCCChHHHHH
Q psy9277          68 KGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~--v~v~aptGsGKTl~~   86 (178)
                      .|.+  ++..|+||||||...
T Consensus        82 ~G~n~tifAYGqTGSGKTyTM  102 (360)
T 1ry6_A           82 NGCVCSCFAYGQTGSGKTYTM  102 (360)
T ss_dssp             HCCEEEEEEECCTTSSHHHHH
T ss_pred             CCceeEEEeeCCCCCCCCEEE
Confidence            3766  699999999999765

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=82.66  E-value=0.63  Score=32.71  Aligned_cols=20  Identities=35%  Similarity=0.398  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+++.|+.|||||...-
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~   31 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIAT   31 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHH
Confidence            36679999999999997653

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=82.64  E-value=2.1  Score=36.48  Aligned_cols=60  Identities=18%  Similarity=0.187  Sum_probs=34.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEc--------CccHHHHHHHhc---C--CCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIG--------GTNLSEDLRKLD---Y--GQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g--------~~~~~~~~~~~~---~--~~~IlV~TP  158 (178)
                      .+.++||.++++.-+..+++.+.......++++..++|        +.+..++...+.   .  ..+|||+|-
T Consensus       397 ~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~  469 (696)
T 2ykg_A          397 PETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATS  469 (696)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEE
T ss_pred             CCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEec
Confidence            45689999999999999999998764333366666654        555554443332   2  468999983

>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=82.63  E-value=0.63  Score=34.15  Aligned_cols=20  Identities=35%  Similarity=0.428  Sum_probs=16.9

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|+|||...
T Consensus        33 ~~Ge~~~iiG~NGsGKSTLl   52 (214)
T 1sgw_A           33 EKGNVVNFHGPNGIGKTTLL   52 (214)
T ss_dssp             ETTCCEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35888999999999999654

>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=82.53  E-value=2.6  Score=29.72  Aligned_cols=17  Identities=41%  Similarity=0.358  Sum_probs=13.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      .-+.+.|++|+|||...
T Consensus         7 ~~i~i~G~sGsGKTTl~   23 (174)
T 1np6_A            7 PLLAFAAWSGTGKTTLL   23 (174)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             eEEEEEeCCCCCHHHHH
Confidence            35789999999999653

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=82.53  E-value=1.9  Score=31.23  Aligned_cols=38  Identities=11%  Similarity=0.071  Sum_probs=26.9

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT  109 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt  109 (178)
                      |+=.++.||.|+|||.-.+-.+-+...   .+.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~Ll~~i~n~~~---~~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTELMRRVRRFQI---AQYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHH---TTCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHH---cCCeEEEEccc
Confidence            667899999999999665444433322   34678888877

>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=82.48  E-value=0.64  Score=38.46  Aligned_cols=54  Identities=22%  Similarity=0.314  Sum_probs=31.8

Q ss_pred             ccccccccCCCCHHHHHHHHhCC--CCCCcHHHHHHHHHHH--cCCcEEEEcCCCChHHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYG--FEKPSAIQQRSIKPIV--KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g--~~~~~~~Q~~~i~~i~--~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+|+++.=.++..+.+++.-  +..+.     .+..+-  -.+.+++.||+|+|||+..-
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~~l~~~~-----~~~~~g~~~p~gvLL~GppGtGKT~Lar   67 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVEFLKDPS-----KFNRIGARMPKGILLVGPPGTGKTLLAR   67 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHHHHHCTH-----HHHTTTCCCCSEEEEECCTTSSHHHHHH
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHHHhhChH-----HHhhcCCCCCCeEEEECCCCCCHHHHHH
Confidence            34568888876666655554320  11111     111111  14679999999999997753

>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=82.42  E-value=0.75  Score=34.02  Aligned_cols=18  Identities=17%  Similarity=0.209  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      +..+++.||+|||||...
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            578999999999999765

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=82.32  E-value=0.67  Score=37.92  Aligned_cols=18  Identities=33%  Similarity=0.410  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      .++++.||+|+|||...-
T Consensus        51 ~~vLL~GppGtGKTtlAr   68 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAE   68 (447)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHH
Confidence            479999999999997654

>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=82.27  E-value=0.61  Score=34.94  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=16.9

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        33 ~~Ge~~~i~G~nGsGKSTLl   52 (247)
T 2ff7_A           33 KQGEVIGIVGRSGSGKSTLT   52 (247)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            35788999999999999654

>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=82.26  E-value=1  Score=35.68  Aligned_cols=23  Identities=30%  Similarity=0.575  Sum_probs=17.2

Q ss_pred             HHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          64 KPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      ..++.|.|  ++..|+||||||...
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            34456764  688899999999774

>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=82.24  E-value=0.61  Score=34.46  Aligned_cols=20  Identities=25%  Similarity=0.489  Sum_probs=16.8

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|+-+.+.||+|+|||...
T Consensus        32 ~~Ge~~~i~G~nGsGKSTLl   51 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTSLL   51 (229)
T ss_dssp             ETTCEEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            34888999999999999654

>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=82.24  E-value=0.59  Score=35.72  Aligned_cols=19  Identities=26%  Similarity=0.496  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
T Consensus        33 ~Ge~~~iiGpnGsGKSTLl   51 (275)
T 3gfo_A           33 RGEVTAILGGNGVGKSTLF   51 (275)
T ss_dssp             TTSEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999654

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=82.23  E-value=0.76  Score=31.53  Aligned_cols=16  Identities=13%  Similarity=0.038  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      .+++.|+.|||||...
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            5889999999999765

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=82.14  E-value=0.67  Score=32.98  Aligned_cols=20  Identities=25%  Similarity=0.406  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.-+++.|+.|||||...-
T Consensus         3 ~~~~I~i~G~~GsGKsT~~~   22 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQAT   22 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHH
Confidence            35678999999999997653

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=82.11  E-value=0.78  Score=37.60  Aligned_cols=18  Identities=22%  Similarity=0.453  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      .+++++.+|+|+|||...
T Consensus        50 ~~~iLl~GppGtGKT~la   67 (444)
T 1g41_A           50 PKNILMIGPTGVGKTEIA   67 (444)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            468999999999999765

>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=82.11  E-value=0.71  Score=32.27  Aligned_cols=17  Identities=24%  Similarity=0.331  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +.+++.|++|||||...
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            36899999999999765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=82.04  E-value=0.64  Score=35.10  Aligned_cols=20  Identities=20%  Similarity=0.360  Sum_probs=17.0

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        44 ~~Ge~~~i~G~nGsGKSTLl   63 (260)
T 2ghi_A           44 PSGTTCALVGHTGSGKSTIA   63 (260)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35888999999999999664

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=82.03  E-value=0.79  Score=32.71  Aligned_cols=20  Identities=20%  Similarity=0.380  Sum_probs=16.9

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.-++++|+.|||||...-
T Consensus         9 ~~~~I~l~G~~GsGKST~~~   28 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSK   28 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHH
Confidence            46789999999999997653

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=81.89  E-value=0.6  Score=34.37  Aligned_cols=19  Identities=37%  Similarity=0.489  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        29 ~Ge~~~iiG~nGsGKSTLl   47 (224)
T 2pcj_A           29 KGEFVSIIGASGSGKSTLL   47 (224)
T ss_dssp             TTCEEEEEECTTSCHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788899999999999654

>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=81.77  E-value=0.63  Score=35.29  Aligned_cols=19  Identities=26%  Similarity=0.440  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
T Consensus        36 ~Ge~~~liG~nGsGKSTLl   54 (266)
T 4g1u_C           36 SGEMVAIIGPNGAGKSTLL   54 (266)
T ss_dssp             TTCEEEEECCTTSCHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            4788999999999999654

>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=81.76  E-value=0.83  Score=32.61  Aligned_cols=20  Identities=15%  Similarity=0.325  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.-++++|+.|||||...-
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~   27 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSR   27 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            46789999999999997653

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=81.70  E-value=1.3  Score=35.21  Aligned_cols=23  Identities=35%  Similarity=0.577  Sum_probs=17.4

Q ss_pred             HHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          64 KPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ..++.|.  .++..|+||||||...
T Consensus        83 ~~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           83 DAVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhCCCceeEEeecCCCCCCCEEe
Confidence            3445676  5688899999999875

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=81.62  E-value=1.3  Score=35.41  Aligned_cols=23  Identities=30%  Similarity=0.550  Sum_probs=17.5

Q ss_pred             HHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          64 KPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      ..++.|.|  ++..|+||||||...
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            34556764  678999999999774

>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=81.61  E-value=1.3  Score=35.06  Aligned_cols=23  Identities=39%  Similarity=0.602  Sum_probs=17.5

Q ss_pred             HHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          64 KPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      ..++.|.|  ++..|+||||||...
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            44556764  688899999999774

>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=81.54  E-value=0.74  Score=38.59  Aligned_cols=20  Identities=30%  Similarity=0.361  Sum_probs=17.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|..+++.||+|+|||...-
T Consensus       107 ~g~~vll~Gp~GtGKTtlar  126 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAK  126 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHH
Confidence            37789999999999997653

>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=81.50  E-value=0.67  Score=34.87  Aligned_cols=20  Identities=25%  Similarity=0.424  Sum_probs=16.8

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        31 ~~Ge~~~liG~nGsGKSTLl   50 (257)
T 1g6h_A           31 NKGDVTLIIGPNGSGKSTLI   50 (257)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             eCCCEEEEECCCCCCHHHHH
Confidence            34788999999999999654

>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=81.49  E-value=1.2  Score=35.61  Aligned_cols=23  Identities=39%  Similarity=0.631  Sum_probs=17.4

Q ss_pred             HHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          64 KPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ..++.|.  .++..|+||||||...
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            3455676  4678899999999774

>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=81.47  E-value=1.2  Score=36.39  Aligned_cols=54  Identities=7%  Similarity=-0.022  Sum_probs=38.9

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc-CCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP  158 (178)
                      +.++||.+|++.-+..+++.++..    ++.+..+++..... ...... ...+|||+|-
T Consensus       190 ~~~~LVF~~s~~~~~~l~~~L~~~----g~~v~~lh~~~R~~-~~~~f~~g~~~iLVaT~  244 (459)
T 2z83_A          190 AGKTVWFVASVKMGNEIAMCLQRA----GKKVIQLNRKSYDT-EYPKCKNGDWDFVITTD  244 (459)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEEESTTCCCC-CGGGSSSCCCSEEEESS
T ss_pred             CCCEEEEeCChHHHHHHHHHHHhc----CCcEEecCHHHHHH-HHhhccCCCceEEEECC
Confidence            458999999999999999988765    67788887753322 112222 3468999994

>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=81.44  E-value=0.8  Score=33.58  Aligned_cols=19  Identities=21%  Similarity=0.352  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +..+++.|++|||||...-
T Consensus        16 ~~~I~l~G~~GsGKsT~a~   34 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAP   34 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            5689999999999997653

>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=81.39  E-value=0.76  Score=32.71  Aligned_cols=16  Identities=19%  Similarity=0.256  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      .+.+.|++|||||...
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            5789999999999765

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=81.36  E-value=1.2  Score=35.39  Aligned_cols=22  Identities=41%  Similarity=0.620  Sum_probs=17.0

Q ss_pred             HHHcCC--cEEEEcCCCChHHHHH
Q psy9277          65 PIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        65 ~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      .++.|.  .++..|+||||||...
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            445676  4778999999999765

>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=81.26  E-value=0.7  Score=34.40  Aligned_cols=19  Identities=37%  Similarity=0.571  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        31 ~Ge~~~l~G~nGsGKSTLl   49 (240)
T 1ji0_A           31 RGQIVTLIGANGAGKTTTL   49 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999654

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=81.23  E-value=0.83  Score=32.48  Aligned_cols=17  Identities=18%  Similarity=0.298  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +.+++.|+.|||||...
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            46899999999999765

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=81.16  E-value=0.99  Score=35.59  Aligned_cols=22  Identities=18%  Similarity=0.028  Sum_probs=17.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISI   90 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~i   90 (178)
                      |.-+.+.+|+|+|||......+
T Consensus       131 G~i~~I~G~~GsGKTTL~~~l~  152 (349)
T 1pzn_A          131 QAITEVFGEFGSGKTQLAHTLA  152 (349)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            4568999999999998765443

>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=81.14  E-value=1.3  Score=35.26  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=17.8

Q ss_pred             HHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      +..++.|.  .++..|+||||||...
T Consensus        82 v~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           82 LQHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCeeEEEEeCCCCCCCceEe
Confidence            34456676  4678899999999764

>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=81.13  E-value=1.4  Score=35.66  Aligned_cols=23  Identities=39%  Similarity=0.618  Sum_probs=17.6

Q ss_pred             HHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          64 KPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ..++.|.  .++..|+||||||...
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            4456676  4778899999999775

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=81.12  E-value=0.71  Score=34.88  Aligned_cols=19  Identities=26%  Similarity=0.427  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        31 ~Ge~~~liG~nGsGKSTLl   49 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFL   49 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999654

>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=81.12  E-value=0.84  Score=32.60  Aligned_cols=16  Identities=31%  Similarity=0.204  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      .+.+.|+.|||||...
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            4789999999999765

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=81.05  E-value=0.87  Score=33.97  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=16.9

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|..+.+.||+|||||...-
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k   45 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCK   45 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            46789999999999997763

>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=80.98  E-value=1.3  Score=35.09  Aligned_cols=23  Identities=30%  Similarity=0.511  Sum_probs=17.6

Q ss_pred             HHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          64 KPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ..++.|.  .++..|+||||||...
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            4455676  4678999999999775

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=80.95  E-value=1.5  Score=34.78  Aligned_cols=25  Identities=32%  Similarity=0.563  Sum_probs=19.6

Q ss_pred             HHHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.|  ++..|+||||||...
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            5566677875  577899999999775

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=80.94  E-value=1.4  Score=34.63  Aligned_cols=25  Identities=32%  Similarity=0.541  Sum_probs=19.6

Q ss_pred             HHHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.|  ++..|+||||||...
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            4566678875  678999999999765

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=80.93  E-value=1.2  Score=38.75  Aligned_cols=19  Identities=26%  Similarity=0.366  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      ..++++.||+|+|||...-
T Consensus       201 ~~~vLL~G~pGtGKT~la~  219 (758)
T 3pxi_A          201 KNNPVLIGEPGVGKTAIAE  219 (758)
T ss_dssp             SCEEEEESCTTTTTHHHHH
T ss_pred             CCCeEEECCCCCCHHHHHH
Confidence            5699999999999997653

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=80.87  E-value=0.88  Score=32.12  Aligned_cols=16  Identities=19%  Similarity=0.306  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      .+++.|++|||||...
T Consensus         2 ~I~i~G~~GsGKsT~~   17 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTIS   17 (205)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCccCHHHHH
Confidence            4789999999999765

>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=80.86  E-value=0.6  Score=34.80  Aligned_cols=19  Identities=26%  Similarity=0.385  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl   45 (243)
T 1mv5_A           27 PNSIIAFAGPSGGGKSTIF   45 (243)
T ss_dssp             TTEEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4778999999999999664

>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=80.82  E-value=0.73  Score=34.50  Aligned_cols=21  Identities=24%  Similarity=0.230  Sum_probs=17.3

Q ss_pred             HcCCcEEEEcCCCChHHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..|.-+.+.||+|+|||...-
T Consensus        27 ~~Ge~~~l~G~nGsGKSTLlk   47 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTLGK   47 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHH
Confidence            357889999999999997653

>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=80.76  E-value=1.3  Score=35.19  Aligned_cols=24  Identities=38%  Similarity=0.657  Sum_probs=17.9

Q ss_pred             HHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      +..++.|.|  ++..|+||||||...
T Consensus        81 v~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           81 LDEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             HHHHhCCCceEEEEeCCCCCCCceEE
Confidence            344566764  678899999999764

>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=80.73  E-value=0.75  Score=34.86  Aligned_cols=19  Identities=21%  Similarity=0.282  Sum_probs=16.6

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        45 ~Ge~~~l~G~NGsGKSTLl   63 (267)
T 2zu0_C           45 PGEVHAIMGPNGSGKSTLS   63 (267)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999764

>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=80.68  E-value=1.3  Score=35.09  Aligned_cols=25  Identities=28%  Similarity=0.523  Sum_probs=18.7

Q ss_pred             HHHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.|  ++..|+||||||...
T Consensus        84 lv~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           84 ILQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHHhCCceeEEEeeCCCCCCCceEE
Confidence            3445567765  678899999999775

>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=80.65  E-value=0.86  Score=34.16  Aligned_cols=19  Identities=21%  Similarity=0.153  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      +.-++++|++|||||...-
T Consensus         4 ~~lIvl~G~pGSGKSTla~   22 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSK   22 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHH
Confidence            3468999999999997653

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=80.65  E-value=0.92  Score=32.86  Aligned_cols=18  Identities=22%  Similarity=0.403  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      +..+++.|++|||||...
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            467999999999999765

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=80.62  E-value=1.4  Score=35.64  Aligned_cols=25  Identities=32%  Similarity=0.562  Sum_probs=19.6

Q ss_pred             HHHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.|  ++..|+||||||...
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            4566677875  678899999999775

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=80.62  E-value=0.76  Score=34.91  Aligned_cols=20  Identities=20%  Similarity=0.336  Sum_probs=16.8

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        43 ~~Ge~~~i~G~nGsGKSTLl   62 (271)
T 2ixe_A           43 YPGKVTALVGPNGSGKSTVA   62 (271)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            34888999999999999654

>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=80.53  E-value=1.3  Score=35.14  Aligned_cols=23  Identities=35%  Similarity=0.624  Sum_probs=17.3

Q ss_pred             HHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          64 KPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ..++.|.  .++..|+||||||...
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            3445676  4688899999999775

>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=80.46  E-value=1  Score=33.44  Aligned_cols=20  Identities=20%  Similarity=0.175  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+..+++.||+|||||...-
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~   47 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSL   47 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            35679999999999997653

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=80.37  E-value=0.79  Score=34.69  Aligned_cols=19  Identities=21%  Similarity=0.578  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
T Consensus        32 ~Ge~~~liG~nGsGKSTLl   50 (266)
T 2yz2_A           32 EGECLLVAGNTGSGKSTLL   50 (266)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            4788999999999999654

>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=80.37  E-value=0.89  Score=32.77  Aligned_cols=17  Identities=18%  Similarity=0.182  Sum_probs=14.3

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.|++|||||...-
T Consensus         2 ~I~l~G~~GsGKsT~a~   18 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQ   18 (214)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48899999999997653

>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=80.34  E-value=0.77  Score=34.47  Aligned_cols=19  Identities=21%  Similarity=0.365  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        25 ~Ge~~~liG~NGsGKSTLl   43 (249)
T 2qi9_C           25 AGEILHLVGPNGAGKSTLL   43 (249)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHH
Confidence            4788999999999999654

>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=80.25  E-value=1.5  Score=35.32  Aligned_cols=23  Identities=39%  Similarity=0.618  Sum_probs=17.7

Q ss_pred             HHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          64 KPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        64 ~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ..++.|.  .++..|+||||||...
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            4456676  4788899999999775

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=80.23  E-value=1.4  Score=36.29  Aligned_cols=41  Identities=15%  Similarity=-0.013  Sum_probs=27.8

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      +..|.-+++.|++|+|||...+--+.+....  .+..++|++-
T Consensus       239 l~~G~l~li~G~pG~GKT~lal~~a~~~a~~--~g~~vl~~s~  279 (503)
T 1q57_A          239 ARGGEVIMVTSGSGMVMSTFVRQQALQWGTA--MGKKVGLAML  279 (503)
T ss_dssp             CCTTCEEEEEESSCHHHHHHHHHHHHHHTTT--SCCCEEEEES
T ss_pred             cCCCeEEEEeecCCCCchHHHHHHHHHHHHh--cCCcEEEEec
Confidence            4457789999999999997765554443321  1446777764

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=80.21  E-value=0.64  Score=32.37  Aligned_cols=20  Identities=25%  Similarity=0.255  Sum_probs=12.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .+.-+++.|+.|||||...-
T Consensus         4 ~~~~I~l~G~~GsGKST~a~   23 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTAH   23 (183)
T ss_dssp             -CCEEEEECCC----CHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            35679999999999997653

>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=80.18  E-value=1.2  Score=35.52  Aligned_cols=25  Identities=36%  Similarity=0.589  Sum_probs=19.2

Q ss_pred             HHHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.|  ++..|+||||||...
T Consensus        71 lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           71 LVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hhHhhhcCCceEEEEECCCCCCCeEee
Confidence            4556677875  677899999999775

>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=80.18  E-value=0.8  Score=34.52  Aligned_cols=19  Identities=32%  Similarity=0.400  Sum_probs=16.4

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        40 ~Gei~~l~G~NGsGKSTLl   58 (256)
T 1vpl_A           40 EGEIFGLIGPNGAGKTTTL   58 (256)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHH
Confidence            4788999999999999654

>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=80.11  E-value=0.81  Score=34.67  Aligned_cols=19  Identities=32%  Similarity=0.567  Sum_probs=16.3

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        49 ~Gei~~liG~NGsGKSTLl   67 (263)
T 2olj_A           49 EGEVVVVIGPSGSGKSTFL   67 (263)
T ss_dssp             TTCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCcHHHHH
Confidence            4788999999999999654

>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=80.09  E-value=0.74  Score=32.04  Aligned_cols=20  Identities=30%  Similarity=0.243  Sum_probs=16.5

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.+|.|+|||...
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLl   50 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLT   50 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            45778899999999999654

>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=80.08  E-value=2.3  Score=33.00  Aligned_cols=17  Identities=35%  Similarity=0.524  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      ++++.||+|+|||....
T Consensus        48 ~~ll~Gp~G~GKTtla~   64 (340)
T 1sxj_C           48 HLLFYGPPGTGKTSTIV   64 (340)
T ss_dssp             CEEEECSSSSSHHHHHH
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            49999999999997754

---

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	178
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	5e-40
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-29
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-26
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	6e-26
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	7e-25
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-25
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	7e-24
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	6e-23
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	5e-18
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-14
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	9e-14
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-12
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	7e-12
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	1e-04

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  133 bits (334), Expect = 5e-40
 Identities = 123/149 (82%), Positives = 138/149 (92%)

Query: 16  DLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQ 75
           D++ VEFETSE+V+V  TFD MGLREDLLRGIYAYGFEKPSAIQQR+IK I+KGRDVIAQ
Sbjct: 1   DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQ 60

Query: 76  AQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACI 135
           +QSGTGKTATFSIS+LQ LD Q+RETQ L L+PTRELAVQIQK +LALGD+MNVQCHACI
Sbjct: 61  SQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACI 120

Query: 136 GGTNLSEDLRKLDYGQHVVSGTPGRVFDM 164
           GGTN+ ED+RKLDYGQHVV+GTPGRVFDM
Sbjct: 121 GGTNVGEDIRKLDYGQHVVAGTPGRVFDM 149

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  105 bits (263), Expect = 2e-29
 Identities = 94/140 (67%), Positives = 113/140 (80%), Gaps = 1/140 (0%)

Query: 29  EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI 88
           E+V +FD+M L E LLRGIYAYGFEKPSAIQQR+I P +KG DVIAQAQSGTGKTATF+I
Sbjct: 9   EIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAI 68

Query: 89  SILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD 148
           SILQ ++  L+ TQ L L+PTRELA QIQKVV+ALGD+M   CHACIGGTN+  +++KL 
Sbjct: 69  SILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 128

Query: 149 YG-QHVVSGTPGRVFDMIRS 167
               H++ GTPGRVFDM+  
Sbjct: 129 MEAPHIIVGTPGRVFDMLNR 148

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 97.2 bits (241), Expect = 3e-26
 Identities = 86/144 (59%), Positives = 111/144 (77%), Gaps = 2/144 (1%)

Query: 23  ETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGK 82
           +T+ D +VV  FD+M L E+LLRG++ YGFE+PSAIQQR+I PI++G DV+AQAQSGTGK
Sbjct: 2   QTNYD-KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGK 60

Query: 83  TATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSE 142
           T TFSI+ LQ +DT ++  Q L L+PTRELA+QIQKVV+AL   M+++ HACIGGT+  E
Sbjct: 61  TGTFSIAALQRIDTSVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVE 120

Query: 143 DLRKLDYGQHVVSGTPGRVFDMIR 166
           D   L     +V GTPGRVFD I+
Sbjct: 121 DAEGLR-DAQIVVGTPGRVFDNIQ 143

>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 = 97.3 bits (241), Expect = 6e-26
 Identities = 47/162 (29%), Positives = 81/162 (50%), Gaps = 12/162 (7%)

Query: 13  IPEDLSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDV 72
           IP  ++  ++       V+  FD + L   +   I    +++P+ IQ+ +I  I++ RD+
Sbjct: 5   IPVSVTGPDYSA---TNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDI 61

Query: 73  IAQAQSGTGKTATFSISILQSL---------DTQLRETQVLCLSPTRELAVQIQKVVLAL 123
           +A AQ+G+GKTA F I I+  L          ++    + L L+PTRELA+QI       
Sbjct: 62  MACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKF 121

Query: 124 GDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI 165
                ++     GG +    +R++  G H++  TPGR+ D I
Sbjct: 122 SLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFI 163

>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 = 93.5 bits (231), Expect = 7e-25
 Identities = 53/134 (39%), Positives = 85/134 (63%), Gaps = 1/134 (0%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           + F++  L+ +LL GI+  G+EKPS IQ+ SI   + GRD++A+A++GTGK+  + I +L
Sbjct: 3   NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLL 62

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVL-ALGDFMNVQCHACIGGTNLSEDLRKLDYG 150
           + LD +    Q + + PTRELA+Q+ ++ +         +  A  GGTNL +D+ +LD  
Sbjct: 63  ERLDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT 122

Query: 151 QHVVSGTPGRVFDM 164
            HVV  TPGR+ D+
Sbjct: 123 VHVVIATPGRILDL 136

>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 = 93.8 bits (232), Expect = 7e-25
 Identities = 52/137 (37%), Positives = 71/137 (51%), Gaps = 2/137 (1%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           S F +  L+ +LLR I   GFE PS +Q   I   + G DV+ QA+SG GKTA F ++ L
Sbjct: 1   SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATL 60

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGG-TNLSEDLRKLD-Y 149
           Q L+    +  VL +  TRELA QI K       +M     A   G  ++ +D   L   
Sbjct: 61  QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKN 120

Query: 150 GQHVVSGTPGRVFDMIR 166
             H+V GTPGR+  + R
Sbjct: 121 CPHIVVGTPGRILALAR 137

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 91.2 bits (225), Expect = 7e-24
 Identities = 60/133 (45%), Positives = 89/133 (66%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           +TF++  L+ +LL GI+  GFEKPS IQ+ +I   + GRD++A+A++GTGKTA F I  L
Sbjct: 1   NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTL 60

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
           + +  +L + Q L + PTRELA+Q  +VV  LG    + C    GGTNL +D+ +L+   
Sbjct: 61  EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETV 120

Query: 152 HVVSGTPGRVFDM 164
           H++ GTPGRV D+
Sbjct: 121 HILVGTPGRVLDL 133

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 88.6 bits (219), Expect = 6e-23
 Identities = 37/136 (27%), Positives = 72/136 (52%), Gaps = 3/136 (2%)

Query: 33  TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISIL 91
            F+ + L +++L  I   GFEKP+ IQ + I   +    +++AQA++G+GKTA+F+I ++
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQ 151
           + ++       ++        A+Q+   + +L    N++     GG  +   ++ L    
Sbjct: 65  ELVNENNGIEAIILTPTREL-AIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NA 122

Query: 152 HVVSGTPGRVFDMIRS 167
           ++V GTPGR+ D I  
Sbjct: 123 NIVVGTPGRILDHINR 138

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 75.9 bits (185), Expect = 5e-18
 Identities = 36/138 (26%), Positives = 64/138 (46%), Gaps = 4/138 (2%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
           + F     +  ++  I    F KP+ IQ+R I   ++G  ++ Q+Q+GTGKT  + + I+
Sbjct: 1   TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM 60

Query: 92  QSLDTQLRE----TQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
           + +  +  E              ++  +  K+         +     IGGT+  + L KL
Sbjct: 61  EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL 120

Query: 148 DYGQHVVSGTPGRVFDMI 165
           +   H+V GTPGR+ D I
Sbjct: 121 NVQPHIVIGTPGRINDFI 138

>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 = 67.2 bits (163), Expect = 1e-14
 Identities = 23/140 (16%), Positives = 43/140 (30%), Gaps = 10/140 (7%)

Query: 32  STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISIL 91
             F    L ++     +     +P AIQ+   K I++     A A +G GKT+      L
Sbjct: 22  CLFPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSL 80

Query: 92  QSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV------QCHACIGGTNLSEDLR 145
                     +   + PT  L +Q  + +    +   V        +         E+  
Sbjct: 81  FLALKG---KRCYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFM 137

Query: 146 KLDYGQHVVSGTPGRVFDMI 165
           +      +V  T   +    
Sbjct: 138 QNLRNFKIVITTTQFLSKHY 157

>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 = 64.3 bits (155), Expect = 9e-14
 Identities = 21/139 (15%), Positives = 44/139 (31%), Gaps = 11/139 (7%)

Query: 31  VSTFDNMGLRE---DLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS 87
           ++  + + L      +L+  +  G+++    Q+  I  ++ GRD +    +G GK+  + 
Sbjct: 1   MAQAEVLNLESGAKQVLQETF--GYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQ 58

Query: 88  ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL 147
           I  L            + +SP   L       + A G               L       
Sbjct: 59  IPALLLNG------LTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCR 112

Query: 148 DYGQHVVSGTPGRVFDMIR 166
                ++   P R+     
Sbjct: 113 TGQIRLLYIAPERLMLDNF 131

>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 = 60.4 bits (145), Expect = 2e-12
 Identities = 12/100 (12%), Positives = 35/100 (35%), Gaps = 3/100 (3%)

Query: 38  GLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ 97
            +    +  +   G E+    Q  +++ +  G++++    +  GKT    +++++     
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 98  LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGG 137
               + L + P R LA +  +              +    
Sbjct: 69  ---GKSLYVVPLRALAGEKYESFKKWEKIGLRIGISTGDY 105

>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 = 59.9 bits (144), Expect = 7e-12
 Identities = 18/100 (18%), Positives = 32/100 (32%), Gaps = 13/100 (13%)

Query: 68  KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFM 127
           K R  I     G GKT  +  +I++      R  + L L+PTR +A ++++ +  L    
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEALRGLPIRY 65

Query: 128 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRS 167
                                  + V           + S
Sbjct: 66  QTPAIRAE-----------HTGREIVDLMCHATFTMRLLS 94

>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 = 39.0 bits (89), Expect = 1e-04
 Identities = 24/116 (20%), Positives = 41/116 (35%), Gaps = 12/116 (10%)

Query: 37  MGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT 96
           M LR DL+         +P   Q+       K  + +    +G GKT    +     L  
Sbjct: 1   MVLRRDLI---------QPRIYQEVIYAKC-KETNCLIVLPTGLGKTLIAMMIAEYRLTK 50

Query: 97  QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQH 152
                +VL L+PT+ L +Q  +    L +    +  A  G  +  E  +     + 
Sbjct: 51  --YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKV 104

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	178
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	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	99.97
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.89
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.87
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.86
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.8
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.67
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.65
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.45
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.42
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.33
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.96
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.84
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.53
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.28
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.23
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.02
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.92
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.88
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.53
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.41
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.79
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.72
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.66
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	96.66
d1okkd2	207	GTPase domain of the signal recognition particle r	96.42
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.28
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.27
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	96.22
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.21
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.17
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.09
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.99
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.89
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	95.79
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	95.39
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	95.33
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	95.26
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	95.16
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.13
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.02
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	94.98
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	94.95
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.82
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	94.75
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	94.51
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	94.43
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.43
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.41
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	94.25
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	94.21
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.09
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	93.99
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	93.85
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.84
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	93.79
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	93.77
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	93.57
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.54
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.48
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	93.46
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	93.26
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	93.22
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	92.99
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	92.8
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.61
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	92.58
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	92.55
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	92.54
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	92.48
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	92.16
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	92.13
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.13
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	91.94
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	91.87
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	91.72
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	91.45
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	91.22
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	90.87
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	90.73
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	90.64
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	90.58
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	90.53
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	90.52
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	90.24
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	90.2
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	90.03
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	89.97
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	89.72
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	89.47
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	89.4
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	89.35
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	89.26
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	89.18
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	89.1
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	88.83
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	88.59
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	88.5
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	88.45
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	88.36
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	88.26
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	88.05
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	87.95
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	87.88
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	87.78
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	87.33
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	87.22
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	87.1
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	86.95
d1vi2a1	182	Putative shikimate dehydrogenase YdiB {Escherichia	86.94
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	86.71
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	86.57
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	86.41
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	86.28
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	86.13
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	86.08
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	86.05
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	86.02
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	85.79
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	85.75
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	85.67
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	85.4
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	85.37
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	85.34
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	85.26
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	85.16
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	85.09
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	84.94
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	84.9
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	84.78
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	84.73
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	84.7
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	84.6
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	84.57
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	84.16
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	84.11
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	83.61
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	83.51
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	83.25
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	82.87
d2awna2	232	Maltose transport protein MalK, N-terminal domain	82.58
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	82.52
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	82.52
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	82.29
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	82.27
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	81.9
d1g2912	240	Maltose transport protein MalK, N-terminal domain	81.7
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	81.42
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	81.4
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	81.17
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	81.12
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	81.04
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	81.02
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	80.95
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	80.8
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	80.72
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	80.67
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	80.58

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=6.7e-39  Score=241.50  Aligned_cols=157  Identities=80%  Similarity=1.198  Sum_probs=146.9

Q ss_pred             CCCcccccccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh
Q psy9277          17 LSNVEFETSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        17 ~~~~~~~~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      +..++.+.+++.+...+|++++|+++++++|+++||.+||++|..+||.+++|+|+++.||||||||++|++|+++.+..
T Consensus         2 ~~~~~~~~~~~~~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~   81 (222)
T d2j0sa1           2 MTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDI   81 (222)
T ss_dssp             SSSCCCCCCTTCCCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCT
T ss_pred             CcccccccCCCCCCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccc
Confidence            44567777788888999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277          97 QLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus        97 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      ....++++|++||++||.|+++.++.+++..++++..++|+....++...+..++||+|+||+||.+++.++..++.
T Consensus        82 ~~~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~  158 (222)
T d2j0sa1          82 QVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTR  158 (222)
T ss_dssp             TSCSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             cccCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccc
Confidence            87889999999999999999999999999999999999999999999888888999999999999999988876543

>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=2.7e-35  Score=219.61  Aligned_cols=141  Identities=38%  Similarity=0.585  Sum_probs=129.0

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      ++|++++|+++++++|.++||++||++|.++||.+++|+|++++||||||||++|++|+++++.....+++++|++||++
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            47999999999999999999999999999999999999999999999999999999999999988778889999999999


Q ss_pred             HHHHHHHHHHHhccCCC-ceEEEEEcCccHHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         112 LAVQIQKVVLALGDFMN-VQCHACIGGTNLSEDLRKL-DYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~-~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      ||.|+++.++.+....+ +++..++|+.....+...+ ..++||+|+||++|.++++++.+++
T Consensus        81 L~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l  143 (207)
T d1t6na_          81 LAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNL  143 (207)
T ss_dssp             HHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCC
T ss_pred             hhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceec
Confidence            99999999999988764 6778888998887776665 4679999999999999999877654

>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=4.5e-35  Score=218.26  Aligned_cols=141  Identities=39%  Similarity=0.716  Sum_probs=131.6

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      ++|++++|+++++++|.++||+.||++|.++||.+++|+|++++||||||||++|++|+++++....++++++|++||++
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            68999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhccCC-CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         112 LAVQIQKVVLALGDFM-NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      |+.|+++.+..+.... ++.+....|+.....+...+..+++|+|+||++|.+++..+....
T Consensus        83 l~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~  144 (206)
T d1veca_          83 LALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKV  144 (206)
T ss_dssp             HHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCC
T ss_pred             hhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccc
Confidence            9999999998887654 577888889999988888888999999999999999999877654

>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=9e-36  Score=223.83  Aligned_cols=148  Identities=64%  Similarity=0.983  Sum_probs=131.7

Q ss_pred             ccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEE
Q psy9277          25 SEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVL  104 (178)
Q Consensus        25 ~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~l  104 (178)
                      +++.+++.+|++++|+++++++|.++||++||++|.++||.++.|+|++++||||||||++|++|+++++..+..+++++
T Consensus         5 ~~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~al   84 (218)
T d2g9na1           5 SNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQAL   84 (218)
T ss_dssp             CCCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEE
T ss_pred             CCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccccCccEE
Confidence            45678899999999999999999999999999999999999999999999999999999999999999998887889999


Q ss_pred             EEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh-cCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         105 CLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL-DYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       105 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      |++||++||.|+++.+..+....+.++..+.++....++.... .++++|+|+||++|.+++.++....
T Consensus        85 il~Pt~eL~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~  153 (218)
T d2g9na1          85 VLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSP  153 (218)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTTTCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCS
T ss_pred             EEcccchhhhhHHHHHhhhccccceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCccc
Confidence            9999999999999999999999999988888776555443333 3578999999999999998776544

>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=1.2e-35  Score=225.88  Aligned_cols=149  Identities=31%  Similarity=0.508  Sum_probs=136.4

Q ss_pred             cccccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc------
Q psy9277          24 TSEDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ------   97 (178)
Q Consensus        24 ~~~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~------   97 (178)
                      ..+.+.++.+|++++|+++++++|.++||++||++|.++||.+++|+|++++||||||||++|++|+++++...      
T Consensus        13 ~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~   92 (238)
T d1wrba1          13 DYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQR   92 (238)
T ss_dssp             SSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----
T ss_pred             CCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccc
Confidence            34556778999999999999999999999999999999999999999999999999999999999999998542      


Q ss_pred             ---CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277          98 ---LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus        98 ---~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                         ..+++++|++||++||.|+++.+..++...++++..+.|+.....+.+....++||+|+||++|.+++..+...+
T Consensus        93 ~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l  170 (238)
T d1wrba1          93 YSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISL  170 (238)
T ss_dssp             --CCBCCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCC
T ss_pred             ccCCCCceEEEeccchhhhcchheeeeecccCCCcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceec
Confidence               235789999999999999999999999999999999999998888888888899999999999999998876654

>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=2.8e-34  Score=214.76  Aligned_cols=147  Identities=58%  Similarity=0.898  Sum_probs=127.9

Q ss_pred             cccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEE
Q psy9277          26 EDVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLC  105 (178)
Q Consensus        26 ~~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~li  105 (178)
                      +-++++.+|++++|+++++++|+++||++||++|.++||.++.|+|+++++|||||||++|++|+++++.....+++++|
T Consensus         4 ~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~li   83 (212)
T d1qdea_           4 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALM   83 (212)
T ss_dssp             SCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEE
T ss_pred             CCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccCCCcceEE
Confidence            44567899999999999999999999999999999999999999999999999999999999999999988888899999


Q ss_pred             EcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCCc
Q psy9277         106 LSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRRT  173 (178)
Q Consensus       106 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~~  173 (178)
                      ++||++|+.|++..+..+.....+++....++....++...++ ++||+|+||+++.++++.+...+.
T Consensus        84 l~pt~el~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~IvI~TP~~l~~~~~~~~~~l~  150 (212)
T d1qdea_          84 LAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTD  150 (212)
T ss_dssp             ECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------CT-TCSEEEECHHHHHHHHHTTSSCCT
T ss_pred             EcccHHHhhhhhhhhcccccccccceeeEeeccchhHHHHHhc-CCcEEEECCCccccccccCceecC
Confidence            9999999999999999999888999999988888777765554 789999999999999998877543

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.1e-32  Score=205.03  Aligned_cols=141  Identities=43%  Similarity=0.741  Sum_probs=134.6

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      .+|++++|++.++++|+++||.+||++|.++||.+++|+|+++.||||||||++|++|+++.+..+..+.++++++|+++
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            47999999999999999999999999999999999999999999999999999999999999988888899999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         112 LAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      ++.+.+..+..+....++++...+|+.....+...+..++||+|+||++|.++++.+.+.+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l  141 (206)
T d1s2ma1          81 LALQTSQVVRTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADL  141 (206)
T ss_dssp             HHHHHHHHHHHHTTTTTCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCC
T ss_pred             hhhhhhhhhhhcccccCeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeec
Confidence            9999999999999999999999999999999988998999999999999999999877654

>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=7.7e-33  Score=206.33  Aligned_cols=139  Identities=31%  Similarity=0.577  Sum_probs=127.6

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      .+|++++|+++++++|.++||.+|+++|.++||.+++|+ |+++++|||+|||++|++|+++.... ..+++++|++||+
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            589999999999999999999999999999999999975 99999999999999999999987654 4668999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      +||.|+++.++.+....+.++..++|+.+..++...+. ++||+||||++|.++++++.+++
T Consensus        83 ~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~  143 (208)
T d1hv8a1          83 ELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNL  143 (208)
T ss_dssp             HHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCT
T ss_pred             ccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCc
Confidence            99999999999999999999999999998888776664 79999999999999999887654

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.97  E-value=4e-30  Score=191.22  Aligned_cols=141  Identities=33%  Similarity=0.554  Sum_probs=125.1

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRE  111 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~  111 (178)
                      ++|++++|+++++++|++.||++||++|.+|||.+++|+|++++||||||||++|++|+++.+.........++++|+..
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            47999999999999999999999999999999999999999999999999999999999999988777889999999999


Q ss_pred             HHHHHHHHHHHhccCC----CceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCCC
Q psy9277         112 LAVQIQKVVLALGDFM----NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGRR  172 (178)
Q Consensus       112 L~~q~~~~~~~~~~~~----~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~~  172 (178)
                      ++.+.+..+.......    ...+..+.++.+...+......+++|+|+||+++.+++.+.....
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~  145 (209)
T d1q0ua_          81 LATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDV  145 (209)
T ss_dssp             HHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCG
T ss_pred             hhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhcccc
Confidence            9999999887765544    356667777777776666677789999999999999998876654

>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=99.89  E-value=8.2e-24  Score=159.61  Aligned_cols=132  Identities=19%  Similarity=0.155  Sum_probs=100.8

Q ss_pred             ccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          31 VSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        31 ~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ...|.+..+.+.+.+ +.+.++.+||++|.++++.++.|+|++++||||+|||++++++++....   ++.+++|++|++
T Consensus        21 ~~~~~~~~~~~~~~~-~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~---~~~rvliv~Pt~   96 (237)
T d1gkub1          21 LCLFPEDFLLKEFVE-FFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLAL---KGKRCYVIFPTS   96 (237)
T ss_dssp             CSCCTTHHHHHHHHH-HHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHT---TSCCEEEEESCH
T ss_pred             cccCccchhHHHHHH-HHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHH---hcCeEEEEeccH
Confidence            344444444455444 4455788999999999999999999999999999999999999887654   456999999999


Q ss_pred             HHHHHHHHHHHHhccCCCce----EEEEEcCccHHHHHHHhc--CCCcEEEeChHHHHHHHH
Q psy9277         111 ELAVQIQKVVLALGDFMNVQ----CHACIGGTNLSEDLRKLD--YGQHVVSGTPGRVFDMIR  166 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~----~~~~~g~~~~~~~~~~~~--~~~~IlV~TP~~l~~~l~  166 (178)
                      +|+.|+++.++++++..++.    +....++.....+...+.  ..++|+|+||++|.+.+.
T Consensus        97 ~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~  158 (237)
T d1gkub1          97 LLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR  158 (237)
T ss_dssp             HHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCST
T ss_pred             HHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhhh
Confidence            99999999999998877644    334444444444433333  457999999999876543

>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=99.87  E-value=1.2e-22  Score=150.08  Aligned_cols=122  Identities=16%  Similarity=0.149  Sum_probs=98.1

Q ss_pred             cccccCCCCHHHHHHHHhC-CCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          32 STFDNMGLREDLLRGIYAY-GFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~-g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ...+.++|++.+.+.|++. ||..++|+|.++++.+++|+|+++++|||||||++|.+|++.      ...++++++|++
T Consensus         2 ~~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~------~~~~~~~v~P~~   75 (206)
T d1oywa2           2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL------LNGLTVVVSPLI   75 (206)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHH------SSSEEEEECSCH
T ss_pred             CchhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhh------ccCceEEeccch
Confidence            3567889999999999876 999999999999999999999999999999999999999876      456899999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHH----HHHHHhcCCCcEEEeChHHHHH
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLS----EDLRKLDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~----~~~~~~~~~~~IlV~TP~~l~~  163 (178)
                      +|+.|+.+.++.+...    .....+.....    ..........+|+++||+++..
T Consensus        76 ~L~~q~~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~  128 (206)
T d1oywa2          76 SLMKDQVDQLQANGVA----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLML  128 (206)
T ss_dssp             HHHHHHHHHHHHTTCC----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTS
T ss_pred             hhhhhHHHHHHhhccc----ccccccccccccchhHHHHHhcCCceEEEEechhhhc
Confidence            9999999999888543    33333332222    2222333568999999998843

>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=99.86  E-value=2.6e-22  Score=147.84  Aligned_cols=125  Identities=13%  Similarity=0.178  Sum_probs=101.6

Q ss_pred             CCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          39 LREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        39 l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      +++++...|++.||++|+|+|.++++.+.+|+|+++++|||+|||.++.++++..+.   ++.++++++|+++|+.|+++
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~---~~~~vl~l~P~~~L~~q~~~   86 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI---KGGKSLYVVPLRALAGEKYE   86 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHH---TTCCEEEEESSHHHHHHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhh---ccCcceeecccHHHHHHHHH
Confidence            678899999999999999999999999999999999999999999999999988765   34689999999999999999


Q ss_pred             HHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCC
Q psy9277         119 VVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQG  170 (178)
Q Consensus       119 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~  170 (178)
                      .++++... ..++....++.....   .....++|+++||..+..++++...
T Consensus        87 ~~~~~~~~-~~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~  134 (202)
T d2p6ra3          87 SFKKWEKI-GLRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRAS  134 (202)
T ss_dssp             HHTTTTTT-TCCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCS
T ss_pred             HHHHHhhc-cccceeeccCccccc---ccccccceeeeccHHHHHHHhccch
Confidence            99887654 345555666554332   2224689999999999988877653

>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=99.80  E-value=6.3e-19  Score=128.83  Aligned_cols=115  Identities=18%  Similarity=0.161  Sum_probs=96.4

Q ss_pred             CCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEE
Q psy9277          53 EKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCH  132 (178)
Q Consensus        53 ~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~  132 (178)
                      .+|+++|.+++..+. ++|+++++|||+|||+++++++...+..  .+.+++|++|+++|+.|.++.++++....+.++.
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~--~~~~il~i~P~~~L~~q~~~~~~~~~~~~~~~v~   84 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK--YGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIV   84 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHH--SCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEE
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHh--cCCcEEEEcCchHHHHHHHHHHHHhhccccccee
Confidence            479999999998875 5689999999999999999888776654  3468999999999999999999999888888888


Q ss_pred             EEEcCccHHHHHHHhcCCCcEEEeChHHHHHHHHcCCCC
Q psy9277         133 ACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRSSQGR  171 (178)
Q Consensus       133 ~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l~~~~~~  171 (178)
                      ...++.........+. .++|+++||+++...+.+....
T Consensus        85 ~~~~~~~~~~~~~~~~-~~~i~i~t~~~~~~~~~~~~~~  122 (200)
T d1wp9a1          85 ALTGEKSPEERSKAWA-RAKVIVATPQTIENDLLAGRIS  122 (200)
T ss_dssp             EECSCSCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSCC
T ss_pred             eeecccchhHHHHhhh-cccccccccchhHHHHhhhhhh
Confidence            8888877776654443 4689999999999988876554

>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=99.67  E-value=6.7e-16  Score=117.35  Aligned_cols=120  Identities=24%  Similarity=0.262  Sum_probs=99.2

Q ss_pred             CHHHHHHH-HhCCCCCCcHHHHHHHHHHHc------CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          40 REDLLRGI-YAYGFEKPSAIQQRSIKPIVK------GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        40 ~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~------g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      +..+.+.+ ..+.| ++|.-|.+|+..+.+      ..+.+++|.+|||||.+|+.+++..+..   +.++++++||..|
T Consensus        69 ~~~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---g~q~~~m~Pt~~L  144 (264)
T d1gm5a3          69 EGKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---GFQTAFMVPTSIL  144 (264)
T ss_dssp             CTHHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---TSCEEEECSCHHH
T ss_pred             ChHHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---ccceeEEeehHhh
Confidence            34444544 67777 599999999999875      3588999999999999999999887763   5699999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeChHHHHH
Q psy9277         113 AVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTPGRVFD  163 (178)
Q Consensus       113 ~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP~~l~~  163 (178)
                      +.|.++.++++....++.+..++|+.+.+++...+.    +.++|+|||-.-+.+
T Consensus       145 a~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~  199 (264)
T d1gm5a3         145 AIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE  199 (264)
T ss_dssp             HHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH
T ss_pred             hHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC
Confidence            999999999999999999999999988776544443    358999999865543

>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=99.65  E-value=4e-15  Score=111.04  Aligned_cols=121  Identities=18%  Similarity=0.124  Sum_probs=99.7

Q ss_pred             CCCHHHHHHH-HhCCCCCCcHHHHHHHHHHHc------CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcH
Q psy9277          38 GLREDLLRGI-YAYGFEKPSAIQQRSIKPIVK------GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTR  110 (178)
Q Consensus        38 ~l~~~i~~~l-~~~g~~~~~~~Q~~~i~~i~~------g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~  110 (178)
                      ..+.+..+.+ ..+.| .+|+-|..++..+.+      ..+.+++|.||||||.+|+.++...+.   .+.++++++||.
T Consensus        39 ~~~~~~~~~~~~~lP~-~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~---~g~qv~~l~Pt~  114 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVD---NHKQVAVLVPTT  114 (233)
T ss_dssp             CCCHHHHHHHHHTCCS-CCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHT---TTCEEEEECSSH
T ss_pred             CCCHHHHHhhhhcccc-ccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHH---cCCceEEEccHH
Confidence            3456666776 45555 699999999988865      348999999999999999999988765   567999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh---c-CCCcEEEeChHHHH
Q psy9277         111 ELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL---D-YGQHVVSGTPGRVF  162 (178)
Q Consensus       111 ~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~-~~~~IlV~TP~~l~  162 (178)
                      .|+.|.++.++++...+++.+..+++..+..++...+   . ...+|+|||-..+.
T Consensus       115 ~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~  170 (233)
T d2eyqa3         115 LLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ  170 (233)
T ss_dssp             HHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH
T ss_pred             HhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc
Confidence            9999999999999999999999999998876654433   3 34799999976654

>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=99.45  E-value=3.2e-14  Score=109.27  Aligned_cols=91  Identities=20%  Similarity=0.146  Sum_probs=65.0

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR  145 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~  145 (178)
                      +.+|+++++.||||||||++|+++++.....  ++.++||++||++||.|+++.++.+..    .+.....+       .
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~--~~~~~lvi~Ptr~La~q~~~~l~~~~~----~~~~~~~~-------~   72 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIK--RGLRTLILAPTRVVAAEMEEALRGLPI----RYQTPAIR-------A   72 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--HTCCEEEEESSHHHHHHHHHHTTTSCC----BCCC------------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHh--cCCEEEEEccHHHHHHHHHHHHhcCCc----ceeeeEEe-------e
Confidence            4568999999999999999998888876654  356899999999999999988765532    21111111       1


Q ss_pred             HhcCCCcEEEeChHHHHHHHHcCC
Q psy9277         146 KLDYGQHVVSGTPGRVFDMIRSSQ  169 (178)
Q Consensus       146 ~~~~~~~IlV~TP~~l~~~l~~~~  169 (178)
                      .......|+++||+.|..++....
T Consensus        73 ~~~~~~~i~~~t~~~l~~~~~~~~   96 (305)
T d2bmfa2          73 EHTGREIVDLMCHATFTMRLLSPI   96 (305)
T ss_dssp             ---CCCSEEEEEHHHHHHHHTSSS
T ss_pred             cccCccccccCCcHHHHHHHhcCc
Confidence            122346799999999977765443

>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=99.42  E-value=3.1e-13  Score=103.63  Aligned_cols=106  Identities=19%  Similarity=0.212  Sum_probs=81.4

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA  133 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  133 (178)
                      .|+++|.+++..+++++..++.+|||+|||+.....+ ..+... ...++|||+|+++|+.|.++.+.+++......+..
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~-~~~~~~-~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~~~~~~~  190 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLA-RYYLEN-YEGKILIIVPTTALTTQMADDFVDYRLFSHAMIKK  190 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHH-HHHHHH-CSSEEEEECSSHHHHHHHHHHHHHHTSCCGGGEEE
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHH-HHhhhc-ccceEEEEEcCchhHHHHHHHHHHhhcccccccee
Confidence            6999999999999999999999999999998865443 333222 34589999999999999999999987665556666


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHHH
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDM  164 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~  164 (178)
                      ..++.....   ......+|+|+|++.+..+
T Consensus       191 ~~~g~~~~~---~~~~~~~i~i~t~qs~~~~  218 (282)
T d1rifa_         191 IGGGASKDD---KYKNDAPVVVGTWQTVVKQ  218 (282)
T ss_dssp             CSTTCSSTT---CCCTTCSEEEECHHHHTTS
T ss_pred             ecceecccc---cccccceEEEEeeehhhhh
Confidence            666654332   1223568999999887543

>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=99.33  E-value=3.2e-12  Score=93.53  Aligned_cols=94  Identities=17%  Similarity=0.129  Sum_probs=71.0

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEE
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHA  133 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~  133 (178)
                      +++++|.+++..+.++.+.++.+|||+|||++++..+..      .+.++||+||+++|+.|..+.+..+...   .+..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~~~------~~~~~Liv~p~~~L~~q~~~~~~~~~~~---~~~~  140 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINE------LSTPTLIVVPTLALAEQWKERLGIFGEE---YVGE  140 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHH------SCSCEEEEESSHHHHHHHHHHHGGGCGG---GEEE
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHHHH------hcCceeEEEcccchHHHHHHHHHhhccc---chhh
Confidence            589999999999999999999999999999887644422      2357999999999999999999877533   2333


Q ss_pred             EEcCccHHHHHHHhcCCCcEEEeChHHHHHHH
Q psy9277         134 CIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMI  165 (178)
Q Consensus       134 ~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~~l  165 (178)
                      ..|+.         .....|+|+|.+.+....
T Consensus       141 ~~~~~---------~~~~~i~i~t~~~~~~~~  163 (206)
T d2fz4a1         141 FSGRI---------KELKPLTVSTYDSAYVNA  163 (206)
T ss_dssp             ESSSC---------BCCCSEEEEEHHHHHHTH
T ss_pred             ccccc---------ccccccccceehhhhhhh
Confidence            33322         224568888888876544

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=98.96  E-value=3.8e-10  Score=76.08  Aligned_cols=54  Identities=28%  Similarity=0.437  Sum_probs=45.2

Q ss_pred             HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      +.+|+++++++|||+|||..++..++.....  .+.++++++|+++++.|.++.+.
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~--~~~~vli~~p~~~l~~q~~~~~~   57 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR--RRLRTLVLAPTRVVLSEMKEAFH   57 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--TTCCEEEEESSHHHHHHHHHHTT
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh--cCceeeeeecchhHHHHHHHHhh
Confidence            3458999999999999999887777776554  45689999999999999988774

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.84  E-value=2.8e-09  Score=72.14  Aligned_cols=51  Identities=16%  Similarity=0.184  Sum_probs=40.6

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+..++.+|||||||+.+...++      ..+.+++|++|+++|++|..+.+.+...
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~------~~~~~vli~~P~~~l~~q~~~~~~~~~~   58 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYA------AQGYKVLVLNPSVAATLGFGAYMSKAHG   58 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHH------TTTCCEEEEESCHHHHHHHHHHHHHHHS
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHH------HcCCcEEEEcChHHHHHHHHHHHHHHhh
Confidence            46789999999999976543332      2456899999999999999999877654

>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=98.53  E-value=9.8e-07  Score=65.76  Aligned_cols=112  Identities=18%  Similarity=0.237  Sum_probs=91.9

Q ss_pred             CCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          50 YGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        50 ~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      +|. +++++|...--.+..|+  +..+.||-|||++..+|+.-...   .+..+-+|+.+--||..=.+++..+.+.+|+
T Consensus        77 lG~-RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al---~g~~vhvvTvNdyLA~RDae~m~~iy~~lGl  150 (273)
T d1tf5a3          77 TGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNAL---TGKGVHVVTVNEYLASRDAEQMGKIFEFLGL  150 (273)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHT---TSSCEEEEESSHHHHHHHHHHHHHHHHHTTC
T ss_pred             hce-EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHh---cCCCceEEecCccccchhhhHHhHHHHHcCC
Confidence            355 68888887776666664  89999999999999888766544   4557899999999999999999999999999


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHH-HHHHHcCC
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRV-FDMIRSSQ  169 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l-~~~l~~~~  169 (178)
                      .+.+...+.+..++....  .|||+.+|...| .|+|+.+-
T Consensus       151 svg~~~~~~~~~~r~~~Y--~~di~Ygt~~e~~fDyLrd~~  189 (273)
T d1tf5a3         151 TVGLNLNSMSKDEKREAY--AADITYSTNNELGFDYLRDNM  189 (273)
T ss_dssp             CEEECCTTSCHHHHHHHH--HSSEEEEEHHHHHHHHHHHTT
T ss_pred             CccccccccCHHHHHHHh--hCCceecchhhhhhhhcchhh
Confidence            999998888887765554  589999999988 67777653

>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=98.23  E-value=2.6e-06  Score=64.04  Aligned_cols=70  Identities=16%  Similarity=0.157  Sum_probs=53.4

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhh-cCCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDT-QLRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      +++|-|.+++..  ....++|.|+.|||||.+.+.-+.+.+.. ..+..+++++++|+++|..+...+.....
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            478999999964  34679999999999998866555444433 22345899999999999999888876654

>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=98.02  E-value=8.3e-06  Score=59.33  Aligned_cols=101  Identities=10%  Similarity=0.057  Sum_probs=66.1

Q ss_pred             CCcHHHHHHHHHHH----cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCc
Q psy9277          54 KPSAIQQRSIKPIV----KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNV  129 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~----~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~  129 (178)
                      .+.++|.+++.-+.    .+.++++.-+.|.|||+..+. ++..+.......+++||+| ..+..|..+.+..+....  
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~-~~~~~~~~~~~~~~LIv~p-~~l~~~W~~e~~~~~~~~--   87 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKENELTPSLVICP-LSVLKNWEEELSKFAPHL--   87 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTCCSSEEEEEC-STTHHHHHHHHHHHCTTS--
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHH-hhhhhhhcccccccceecc-hhhhhHHHHHHHhhcccc--
Confidence            58899999986443    366799999999999998754 4444444444458899999 566777788887776543  


Q ss_pred             eEEEEEcCccHHHHHHHhcCCCcEEEeChHHHHH
Q psy9277         130 QCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFD  163 (178)
Q Consensus       130 ~~~~~~g~~~~~~~~~~~~~~~~IlV~TP~~l~~  163 (178)
                      .+....+.....     .....+|+++|.+.+..
T Consensus        88 ~~~~~~~~~~~~-----~~~~~~vvi~~~~~~~~  116 (230)
T d1z63a1          88 RFAVFHEDRSKI-----KLEDYDIILTTYAVLLR  116 (230)
T ss_dssp             CEEECSSSTTSC-----CGGGSSEEEEEHHHHTT
T ss_pred             cceeeccccchh-----hccCcCEEEeeHHHHHh
Confidence            322222111111     01246899999887743

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.92  E-value=2.2e-05  Score=59.32  Aligned_cols=70  Identities=19%  Similarity=0.251  Sum_probs=53.9

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhc-CCCceEEEEcCcHHHHHHHHHHHHHhcc
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQ-LRETQVLCLSPTRELAVQIQKVVLALGD  125 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~-~~~~~~lil~Pt~~L~~q~~~~~~~~~~  125 (178)
                      .+++-|.+++..  .+..++|.|+.|||||.+.+--+.+.+... ....+++++++++..+..+...+.....
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            478999998874  345699999999999998766555554432 2234899999999999999998866543

>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=97.88  E-value=0.00013  Score=54.90  Aligned_cols=108  Identities=19%  Similarity=0.079  Sum_probs=68.2

Q ss_pred             CCcHHHHHHHHHHH---------cCCcEEEEcCCCChHHHHHHHHHHHHhhhcC-----CCceEEEEcCcHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIV---------KGRDVIAQAQSGTGKTATFSISILQSLDTQL-----RETQVLCLSPTRELAVQIQKV  119 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~---------~g~~v~v~aptGsGKTl~~ll~il~~l~~~~-----~~~~~lil~Pt~~L~~q~~~~  119 (178)
                      .+.|+|.+++.-+.         .+..+++.-..|.|||+..+. ++..+....     ....+|||||.. |+.|-.+.
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia-~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCIT-LIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHH-HHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHH-HHHHHHHhcccccCCCCcEEEEccch-hhHHHHHH
Confidence            58999999986432         356788888999999986543 233332221     123689999975 78888888


Q ss_pred             HHHhccCCCceEEEEEcCccHHHHHH---Hhc-----CCCcEEEeChHHHHHH
Q psy9277         120 VLALGDFMNVQCHACIGGTNLSEDLR---KLD-----YGQHVVSGTPGRVFDM  164 (178)
Q Consensus       120 ~~~~~~~~~~~~~~~~g~~~~~~~~~---~~~-----~~~~IlV~TP~~l~~~  164 (178)
                      +.++... ...++.++++...+....   ...     ...+++|+|.+.+...
T Consensus       133 i~k~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~  184 (298)
T d1z3ix2         133 VGKWLGG-RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLH  184 (298)
T ss_dssp             HHHHHGG-GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHH
T ss_pred             HHhhcCC-ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccc
Confidence            8887654 344445555543332211   111     1347999998877543

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.41  E-value=0.00033  Score=54.25  Aligned_cols=67  Identities=18%  Similarity=0.194  Sum_probs=51.4

Q ss_pred             CCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHHH--HHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHH
Q psy9277          54 KPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFSI--SILQSLDTQLRETQVLCLSPTRELAVQIQKVVL  121 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~ll--~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~  121 (178)
                      .....|..|+..++.++-+++.||+|+|||....-  ..+.... ...+.++++.+||..-|..+.+...
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~~~l~~l~~~~-~~~~~~I~l~ApTgkAA~~L~e~~~  216 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMA-DGERCRIRLAAPTGKAAARLTESLG  216 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTC-SSCCCCEEEEBSSHHHHHHHHHHHT
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehHHHHHHHHHHHH-hccCCeEEEecCcHHHHHHHHHHHH
Confidence            45778999999999999999999999999977432  2222221 2345689999999998888877663

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=96.79  E-value=0.0012  Score=52.01  Aligned_cols=67  Identities=24%  Similarity=0.341  Sum_probs=48.4

Q ss_pred             CCcHHHHHHHHHHHc----C-CcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          54 KPSAIQQRSIKPIVK----G-RDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~~----g-~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      .|+--|=++|..+.+    | ++.++.|-||||||++.. .++..     .+..+|||+|+..+|.|+++.++.+...
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA-~l~~~-----~~rp~LVVt~n~~~A~qL~~dL~~~l~~   82 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTIS-NVIAQ-----VNKPTLVIAHNKTLAGQLYSELKEFFPH   82 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHH-HHHHH-----HTCCEEEECSSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHH-HHHHH-----hCCCEEEEeCCHHHHHHHHHHHHHHcCC
Confidence            355566666665554    4 578999999999995542 22221     1235899999999999999999988754

>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=96.72  E-value=0.0026  Score=45.24  Aligned_cols=87  Identities=18%  Similarity=0.224  Sum_probs=49.0

Q ss_pred             CCc-EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHH--
Q psy9277          69 GRD-VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSED--  143 (178)
Q Consensus        69 g~~-v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~--  143 (178)
                      .++ +++.+|||+|||....--+.. +..  ++.++.+++.  .|.=|.++.+.+.+   .+++.+.......+...-  
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~-~~~--~g~kV~lit~Dt~R~gA~eQL~~~a~---~l~v~~~~~~~~~~~~~~~~   82 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALY-YKG--KGRRPLLVAADTQRPAAREQLRLLGE---KVGVPVLEVMDGESPESIRR   82 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH-HHH--TTCCEEEEECCSSCHHHHHHHHHHHH---HHTCCEEECCTTCCHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH-HHH--CCCcEEEEecccccchHHHHHHHHHH---hcCCccccccccchhhHHHH
Confidence            345 466999999999876543322 222  2345555553  36666666555533   336666665555544322  


Q ss_pred             ----HHHhcCCCcEEEeChHHH
Q psy9277         144 ----LRKLDYGQHVVSGTPGRV  161 (178)
Q Consensus       144 ----~~~~~~~~~IlV~TP~~l  161 (178)
                          .....+.--|+|=||||.
T Consensus        83 ~~~~~~~~~~~d~vlIDTaGr~  104 (207)
T d1ls1a2          83 RVEEKARLEARDLILVDTAGRL  104 (207)
T ss_dssp             HHHHHHHHHTCCEEEEECCCCS
T ss_pred             HHHHHHhhccCcceeecccccc
Confidence                112222234778899864

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.66  E-value=0.0028  Score=45.17  Aligned_cols=84  Identities=21%  Similarity=0.264  Sum_probs=48.2

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc-Cc-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHh--
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS-PT-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKL--  147 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~-Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--  147 (178)
                      ++++||||+|||.+..--+. ++..  .+.++.+++ -| |.=|.++.+.+   ++..++.+.....+..........  
T Consensus        12 i~lvGptGvGKTTTiAKLA~-~~~~--~g~kV~lit~Dt~R~gA~eQL~~~---a~~l~v~~~~~~~~~d~~~~l~~~~~   85 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLAR-QFEQ--QGKSVMLAAGDTFRAAAVEQLQVW---GQRNNIPVIAQHTGADSASVIFDAIQ   85 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHH-HHHT--TTCCEEEECCCTTCHHHHHHHHHH---HHHTTCCEECCSTTCCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHH--CCCcEEEEecccccccchhhhhhh---hhhcCCcccccccCCCHHHHHHHHHH
Confidence            56799999999988764432 2332  233455554 33 55555554444   444577776666555544332211  


Q ss_pred             ---cCCC-cEEEeChHHH
Q psy9277         148 ---DYGQ-HVVSGTPGRV  161 (178)
Q Consensus       148 ---~~~~-~IlV~TP~~l  161 (178)
                         .+++ -|+|=||||.
T Consensus        86 ~a~~~~~d~ilIDTaGr~  103 (211)
T d2qy9a2          86 AAKARNIDVLIADTAGRL  103 (211)
T ss_dssp             HHHHTTCSEEEECCCCCG
T ss_pred             HHHHcCCCEEEeccCCCc
Confidence               2344 4778999864

>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=96.66  E-value=0.005  Score=42.50  Aligned_cols=56  Identities=9%  Similarity=0.053  Sum_probs=47.0

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.|+++..+..+.+.+.+.    |+++..++|+++..++...+.    ...+|||+|-
T Consensus        30 ~g~r~lvfc~t~~~~~~l~~~L~~~----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~   89 (174)
T d1c4oa2          30 RGERTLVTVLTVRMAEELTSFLVEH----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN   89 (174)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC
T ss_pred             cCCcEEEEEcchhHHHHHHHHHHhc----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee
Confidence            4669999999999999999988765    899999999999887766554    3579999983

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.42  E-value=0.0074  Score=42.79  Aligned_cols=87  Identities=18%  Similarity=0.090  Sum_probs=49.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC--cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHH-
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP--TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLR-  145 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P--t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~-  145 (178)
                      ++-++++||||+|||.+..--+. ++..  .+.++.+++-  -|.=+.++.+.+-+.   +++.+.....+.+...... 
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~-~~~~--~g~kV~lit~Dt~R~gA~eQL~~~a~~---l~i~~~~~~~~~d~~~~~~~   79 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGR-YYQN--LGKKVMFCAGDTFRAAGGTQLSEWGKR---LSIPVIQGPEGTDPAALAYD   79 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHH-HHHT--TTCCEEEECCCCSSTTHHHHHHHHHHH---HTCCEECCCTTCCHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-HHHH--CCCcEEEEEeccccccchhhHhhcccc---cCceEEeccCCccHHHHHHH
Confidence            45578899999999988654332 2332  2345555552  266666666555333   3566554444444433221 


Q ss_pred             -----HhcCCCcEEEeChHHH
Q psy9277         146 -----KLDYGQHVVSGTPGRV  161 (178)
Q Consensus       146 -----~~~~~~~IlV~TP~~l  161 (178)
                           ...+.-.|+|=|||+.
T Consensus        80 ~~~~~~~~~~d~ilIDTaGr~  100 (207)
T d1okkd2          80 AVQAMKARGYDLLFVDTAGRL  100 (207)
T ss_dssp             HHHHHHHHTCSEEEECCCCCC
T ss_pred             HHHHHHHCCCCEEEcCccccc
Confidence                 1122335788999973

>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=96.28  E-value=0.015  Score=39.59  Aligned_cols=55  Identities=15%  Similarity=0.257  Sum_probs=44.5

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ...++||.|+++.-+..+++.+...    ++.+..++|+.+..++...+.    ..+.|+|+|
T Consensus        26 ~~~k~iIF~~~~~~~~~l~~~L~~~----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T   84 (168)
T d1t5ia_          26 EFNQVVIFVKSVQRCIALAQLLVEQ----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVAT   84 (168)
T ss_dssp             CCSSEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEES
T ss_pred             CCCeEEEEEeeeecchhhhhhhccc----cccccccccccchhhhhhhhhhhccccceeeecc
Confidence            4568999999999999888877654    788899999998887765553    357899999

>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=96.27  E-value=0.017  Score=39.26  Aligned_cols=57  Identities=11%  Similarity=0.092  Sum_probs=46.1

Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          98 LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        98 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ....++||.|+++.-+..++..+...    ++.+..++|+.+..++...+.    ...+|+|+|.
T Consensus        30 ~~~~k~iVF~~~~~~~~~l~~~L~~~----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td   90 (171)
T d1s2ma2          30 LQINQAIIFCNSTNRVELLAKKITDL----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD   90 (171)
T ss_dssp             SCCSEEEEECSSHHHHHHHHHHHHHH----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS
T ss_pred             CCCCceEEEEeeeehhhHhHHhhhcc----cccccccccccchhhhhhhhhhcccCccccccchh
Confidence            35569999999999999999888766    788888999998876655553    3578999995

>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=96.22  E-value=0.014  Score=39.53  Aligned_cols=59  Identities=12%  Similarity=0.064  Sum_probs=46.9

Q ss_pred             hcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          96 TQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        96 ~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ......++||.|.++.-+.++++.+...    ++.+..++|+.+..++...+.    ....|+|+|-
T Consensus        23 ~~~~~~k~iIF~~s~~~~~~l~~~L~~~----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td   85 (162)
T d1fuka_          23 DSISVTQAVIFCNTRRKVEELTTKLRND----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD   85 (162)
T ss_dssp             HHTTCSCEEEEESSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG
T ss_pred             HhCCCCcEEEEEEEEchHHHHHHHHhhc----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc
Confidence            3334568999999999999998887655    788899999998887766553    3578999994

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.21  E-value=0.0051  Score=43.78  Aligned_cols=83  Identities=18%  Similarity=0.215  Sum_probs=40.6

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC-c-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH---
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP-T-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK---  146 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P-t-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---  146 (178)
                      +++.||||+|||.+..=-+. ++..  ++.++.+++- | |.=+.++.+.+   ++..++.+...............   
T Consensus        15 i~lvGptGvGKTTTiAKLA~-~~~~--~g~kV~lit~Dt~R~ga~eQL~~~---a~~l~v~~~~~~~~~~~~~~~~~a~~   88 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAY-FYKK--KGFKVGLVGADVYRPAALEQLQQL---GQQIGVPVYGEPGEKDVVGIAKRGVE   88 (211)
T ss_dssp             EEEECSCCC----HHHHHHH-HHHH--TTCCEEEEECCCSSHHHHHHHHHH---HHHHTCCEECCTTCCCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-HHHH--CCCceEEEEeeccccchhHHHHHh---ccccCcceeecccchhhhHHHHHHHH
Confidence            66789999999988654332 3332  2334444443 2 55555554444   33346665554444443222111   


Q ss_pred             --hcCCC-cEEEeChHH
Q psy9277         147 --LDYGQ-HVVSGTPGR  160 (178)
Q Consensus       147 --~~~~~-~IlV~TP~~  160 (178)
                        ...+. -|+|=|||+
T Consensus        89 ~~~~~~~d~IlIDTaGr  105 (211)
T d1j8yf2          89 KFLSEKMEIIIVDTAGR  105 (211)
T ss_dssp             HHHHTTCSEEEEECCCS
T ss_pred             HhhccCCceEEEecCCc
Confidence              12334 577889986

>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=96.17  E-value=0.011  Score=40.92  Aligned_cols=55  Identities=13%  Similarity=0.157  Sum_probs=46.1

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeC
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGT  157 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~T  157 (178)
                      ++.+++|.++++.-+..++..+...    |+.+..++|+.+..++...+.    ...+|||+|
T Consensus        30 ~~~~~iif~~~~~~~~~~~~~l~~~----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaT   88 (181)
T d1t5la2          30 RNERTLVTTLTKKMAEDLTDYLKEA----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI   88 (181)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHTT----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEES
T ss_pred             cCCeEEEEeehhhhhHHHHHHHHhC----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEeh
Confidence            4568999999999999888887654    899999999999887766654    357999999

>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=96.09  E-value=0.0061  Score=46.17  Aligned_cols=65  Identities=26%  Similarity=0.379  Sum_probs=37.8

Q ss_pred             HHHHHhCCCCC---CcHHHHHHHHH-HHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHH
Q psy9277          44 LRGIYAYGFEK---PSAIQQRSIKP-IVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTREL  112 (178)
Q Consensus        44 ~~~l~~~g~~~---~~~~Q~~~i~~-i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L  112 (178)
                      +..+.+.|+..   ..+-+...+.. +..++|++|+|+||||||.. +-+++..+.   ...+.+.+--+.||
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~---~~~rivtiEd~~El  205 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIP---KEERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSC---TTCCEEEEESSCCC
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhcc---cccceeeccchhhh
Confidence            34444555433   23444555544 44589999999999999965 344444332   23355555555554

>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=95.99  E-value=0.0038  Score=42.07  Aligned_cols=26  Identities=27%  Similarity=0.385  Sum_probs=19.6

Q ss_pred             CcEEEEcCCCChHHHHHHHHHHHHhhh
Q psy9277          70 RDVIAQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      +++++.||+|+|||... -.++..+..
T Consensus         2 k~v~ItG~~GtGKTtl~-~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLI-HKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHHH-HHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHH-HHHHHHHHH
Confidence            68999999999999843 345555544

>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=95.89  E-value=0.029  Score=39.72  Aligned_cols=85  Identities=21%  Similarity=0.259  Sum_probs=46.4

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCc-HHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHH-----
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPT-RELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDL-----  144 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt-~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-----  144 (178)
                      -++++||||+|||....--+. ++... +..-++|=+-| |.=|.++.+.+   ++.+++.+.....+.......     
T Consensus        13 vi~lvGptGvGKTTTiAKLAa-~~~~~-~~kV~lit~Dt~R~gA~eQL~~~---a~~l~i~~~~~~~~~d~~~~~~~~~~   87 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAK-MFVDE-GKSVVLAAADTFRAAAIEQLKIW---GERVGATVISHSEGADPAAVAFDAVA   87 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH-HHHHT-TCCEEEEEECTTCHHHHHHHHHH---HHHHTCEEECCSTTCCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHC-CCceEEEeecccccchhHHHHHH---hhhcCccccccCCCCcHHHHHHHHHH
Confidence            367899999999988654332 33332 23334444443 66666555544   333467666555444432211     


Q ss_pred             HHhcCCC-cEEEeChHH
Q psy9277         145 RKLDYGQ-HVVSGTPGR  160 (178)
Q Consensus       145 ~~~~~~~-~IlV~TP~~  160 (178)
                      ....+++ -|+|=||||
T Consensus        88 ~~~~~~~d~ilIDTaGr  104 (213)
T d1vmaa2          88 HALARNKDVVIIDTAGR  104 (213)
T ss_dssp             HHHHTTCSEEEEEECCC
T ss_pred             HHHHcCCCEEEEecccc
Confidence            1112344 478999984

>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=95.79  E-value=0.031  Score=39.13  Aligned_cols=57  Identities=11%  Similarity=0.040  Sum_probs=45.2

Q ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          98 LRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        98 ~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ..+.++||.++|+.-+..++..+...    ++.+..++|+.+..++...+.    ...+|+|+|-
T Consensus        28 ~~~~~~IIF~~t~~~~~~l~~~l~~~----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd   88 (200)
T d1oywa3          28 QRGKSGIIYCNSRAKVEDTAARLQSK----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV   88 (200)
T ss_dssp             TTTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT
T ss_pred             cCCCCEEEEEeeehhhHHhhhhhccC----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc
Confidence            34568999999999999998887655    788899999998776655543    3578999994

>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=95.33  E-value=0.057  Score=35.83  Aligned_cols=56  Identities=13%  Similarity=0.141  Sum_probs=44.5

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      .+.++||.|++++-+.+++..++..    ++.+..++++.+..++...+.    ....|+|+|-
T Consensus        27 ~~~k~IIF~~s~~~~~~l~~~L~~~----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~   86 (155)
T d1hv8a2          27 KEFYGLVFCKTKRDTKELASMLRDI----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD   86 (155)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHHHT----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT
T ss_pred             CCCCEEEEECchHHHHHHHhhhccc----ccccccccccchhhhhhhhhhhhhcccceeeeehh
Confidence            3458999999999999988888765    788889999988777655543    3468999994

>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=95.26  E-value=0.028  Score=39.34  Aligned_cols=35  Identities=23%  Similarity=0.265  Sum_probs=25.4

Q ss_pred             CcHHHHHHHHHHHc----CC---cEEEEcCCCChHHHHHHHH
Q psy9277          55 PSAIQQRSIKPIVK----GR---DVIAQAQSGTGKTATFSIS   89 (178)
Q Consensus        55 ~~~~Q~~~i~~i~~----g~---~v~v~aptGsGKTl~~ll~   89 (178)
                      ++|||..++..+.+    ++   .+++.||.|+|||.....-
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~   44 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYAL   44 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHH
Confidence            34777777766543    33   4999999999999876543

>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=95.16  E-value=0.0044  Score=49.00  Aligned_cols=18  Identities=22%  Similarity=0.453  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      ..|+++.||||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            469999999999999765

>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=95.13  E-value=0.0068  Score=45.44  Aligned_cols=19  Identities=21%  Similarity=0.426  Sum_probs=16.9

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .++++++||||+|||..+-
T Consensus        49 ~~~iLl~GPpG~GKT~lAk   67 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIAR   67 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            5799999999999998764

>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=95.02  E-value=0.025  Score=39.98  Aligned_cols=58  Identities=19%  Similarity=0.058  Sum_probs=47.5

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ++.++.+|||..+-+...+..+.++..  ++++..++|.++.++....+.    ...+|+|+|.
T Consensus        30 rGgQvy~V~p~I~~~e~~~~~l~~~~p--~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt   91 (211)
T d2eyqa5          30 RGGQVYYLYNDVENIQKAAERLAELVP--EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT   91 (211)
T ss_dssp             TTCEEEEECCCSSCHHHHHHHHHHHCT--TSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS
T ss_pred             cCCeEEEEEcCccchhhHHHHHHHhCC--ceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh
Confidence            677999999999999999998888754  578889999998877655543    3579999995

>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=94.98  E-value=0.0043  Score=45.16  Aligned_cols=55  Identities=15%  Similarity=0.130  Sum_probs=33.1

Q ss_pred             ccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHH--HcCCcEEEEcCCCChHHHHH
Q psy9277          29 EVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPI--VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        29 ~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i--~~g~~v~v~aptGsGKTl~~   86 (178)
                      .|..+|++++-.+.+.+.|++. + .+ ..+.+.+..+  ...+.+++.||+|+|||...
T Consensus         3 ~p~~~~~di~G~~~~k~~l~~~-i-~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           3 APKVTFKDVAGAEEAKEELKEI-V-EF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHH-H-HH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCCCcHHHHccHHHHHHHHHHH-H-HH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            3557899997777766666432 1 11 0111122221  11367999999999999765

>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=94.95  E-value=0.066  Score=36.19  Aligned_cols=56  Identities=14%  Similarity=0.077  Sum_probs=45.0

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhc----CCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLD----YGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~----~~~~IlV~TP  158 (178)
                      ...++||.|.++.-+..++..++..    ++.+..++|+.+.+++...+.    ...+|+|+|-
T Consensus        33 ~~~k~iiF~~~~~~~~~~~~~l~~~----~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td   92 (168)
T d2j0sa2          33 TITQAVIFCNTKRKVDWLTEKMREA----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD   92 (168)
T ss_dssp             TSSEEEEECSSHHHHHHHHHHHHHT----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG
T ss_pred             CCCceEEEeeeHHHHHHHHHHhhhc----ccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc
Confidence            4568999999999999998888765    677888999998887765553    3568999993

>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=94.82  E-value=0.017  Score=44.67  Aligned_cols=48  Identities=15%  Similarity=0.264  Sum_probs=33.1

Q ss_pred             HHHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHH
Q psy9277          64 KPIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAV  114 (178)
Q Consensus        64 ~~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~  114 (178)
                      |.-...++++|.|+||||||... ..++..+..  .+..++|+=|..++..
T Consensus        45 ~~~~~~~H~~I~G~tGsGKT~~l-~~li~~~~~--~g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          45 PRDAEPRHLLVNGATGTGKSVLL-RELAYTGLL--RGDRMVIVDPNGDMLS   92 (433)
T ss_dssp             CGGGGGGCEEEEECTTSSHHHHH-HHHHHHHHH--TTCEEEEEEETTHHHH
T ss_pred             CCCcccceEEEEeCCCCcHHHHH-HHHHHHHHh--CCCCEEEEeCChhHHH
Confidence            33345689999999999999764 334444433  3557888888877643

>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=94.75  E-value=0.02  Score=40.64  Aligned_cols=45  Identities=20%  Similarity=0.253  Sum_probs=29.3

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~ll   88 (178)
                      ++|+++--.+.+.+.|+..            +.....    -.++++.||+|+|||.++-.
T Consensus         6 ~~~ddivGq~~~~~~L~~~------------i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~   54 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKLRVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLAHV   54 (239)
T ss_dssp             CSGGGSCSCHHHHHHHHHH------------HHHHTTSSSCCCCEEEECCTTSCHHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHH------------HHHHHhcCCCCCeEEEECCCCCCHHHHHHH
Confidence            4688876666666665432            111111    25899999999999977643

>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=94.51  E-value=0.048  Score=42.34  Aligned_cols=67  Identities=30%  Similarity=0.349  Sum_probs=46.0

Q ss_pred             CCcHHHHHHHHHHH----cCC-cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccC
Q psy9277          54 KPSAIQQRSIKPIV----KGR-DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDF  126 (178)
Q Consensus        54 ~~~~~Q~~~i~~i~----~g~-~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~  126 (178)
                      .|+--|-++|..+.    .|. .+.+.|-+||+|+++.  +.+..   ..+ .-+|||+|+...|.++++.+..+...
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~--A~l~~---~~~-rp~LvVt~~~~~A~~l~~dL~~~l~~   79 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTM--AKVIE---ALG-RPALVLAPNKILAAQLAAEFRELFPE   79 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH--HHHHH---HHT-CCEEEEESSHHHHHHHHHHHHHHCTT
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHH--HHHHH---HhC-CCEEEEeCCHHHHHHHHHHHHHhcCc
Confidence            34445555666544    354 4789999999999543  22221   112 25789999999999999999988653

>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=94.43  E-value=0.0064  Score=43.59  Aligned_cols=54  Identities=13%  Similarity=0.089  Sum_probs=33.0

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHH-HHHHH-----HcCCcEEEEcCCCChHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQR-SIKPI-----VKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~-~i~~i-----~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ++|+++-.++...+.|++.  -.-+..... .++..     .....+++.||+|+|||.+.-
T Consensus        11 ~~~~dlig~~~~~~~L~~~--l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          11 TNLQQVCGNKGSVMKLKNW--LANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SSGGGCCSCHHHHHHHHHH--HHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH--HHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHH
Confidence            4799999999888887642  111111111 11111     112579999999999997654

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=94.43  E-value=0.011  Score=38.69  Aligned_cols=19  Identities=21%  Similarity=0.338  Sum_probs=16.5

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      .+++++.||+|||||...-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4789999999999997764

>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=94.41  E-value=0.031  Score=43.32  Aligned_cols=39  Identities=23%  Similarity=0.442  Sum_probs=26.7

Q ss_pred             cHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHHHHHHHhh
Q psy9277          56 SAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSISILQSLD   95 (178)
Q Consensus        56 ~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll~il~~l~   95 (178)
                      .+.|.+.|..+...  -=++++||||||||... ..++..+.
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            45666666666653  35899999999999774 34555553

>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=94.25  E-value=0.0032  Score=46.20  Aligned_cols=57  Identities=19%  Similarity=0.229  Sum_probs=33.4

Q ss_pred             cccccccccCCCCHHHHHHHHhC-C-CCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          28 VEVVSTFDNMGLREDLLRGIYAY-G-FEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        28 ~~~~~~f~~~~l~~~i~~~l~~~-g-~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ..+..+|+|.+-.+.+.+.+.+. . +..+..+|..   .+...+.+++.||+|+|||+..-
T Consensus         5 ~~~~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~---g~~~~~~iLL~GppGtGKT~la~   63 (256)
T d1lv7a_           5 DQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKL---GGKIPKGVLMVGPPGTGKTLLAK   63 (256)
T ss_dssp             CSSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHHH
T ss_pred             CCCCCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHc---CCCCCCeEEeeCCCCCCccHHHH
Confidence            35667899988777777666432 0 0111111110   01124789999999999997753

>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=94.21  E-value=0.038  Score=36.32  Aligned_cols=53  Identities=19%  Similarity=0.228  Sum_probs=42.3

Q ss_pred             CCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeCh
Q psy9277          99 RETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP  158 (178)
Q Consensus        99 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP  158 (178)
                      ++.++||.|+|+.-|.++++.+...    |+.+..++++....+.   .....+|+|+|-
T Consensus        34 ~~~k~IVFc~t~~~ae~la~~L~~~----G~~~~~~H~~~~~~~~---~~~~~~vlvaTd   86 (138)
T d1jr6a_          34 KGGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVSVI---PTNGDVVVVATD   86 (138)
T ss_dssp             TTSCEEEECSCHHHHHHHHHHHHHH----TCEEEEECTTCCSCCC---TTSSCEEEEESS
T ss_pred             CCCCEEEEeCcHHHHHHHHHHHhcc----ccchhhhhccchhhhh---hhhhcceeehhH
Confidence            4458999999999999999998776    7889999998875532   234578999993

>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=94.09  E-value=0.077  Score=37.55  Aligned_cols=17  Identities=35%  Similarity=0.470  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      .++++.||+|+|||.+.
T Consensus        44 ~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            68999999999999665

>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=93.99  E-value=0.05  Score=38.53  Aligned_cols=44  Identities=16%  Similarity=0.296  Sum_probs=31.5

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      ++|+++--++.+.+.|+..- ...           ....++++.||+|+|||....
T Consensus         8 ~~~~diig~~~~~~~L~~~~-~~~-----------~~~~~lll~Gp~G~GKTt~~~   51 (252)
T d1sxje2           8 KSLNALSHNEELTNFLKSLS-DQP-----------RDLPHLLLYGPNGTGKKTRCM   51 (252)
T ss_dssp             CSGGGCCSCHHHHHHHHTTT-TCT-----------TCCCCEEEECSTTSSHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHHH-HcC-----------CCCCeEEEECCCCCCHHHHHH
Confidence            36888888999988887531 100           112369999999999997764

>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=93.85  E-value=0.015  Score=41.29  Aligned_cols=46  Identities=17%  Similarity=0.251  Sum_probs=30.0

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc---CCcEEEEcCCCChHHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK---GRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~---g~~v~v~aptGsGKTl~~ll   88 (178)
                      ++|+++--.+.+.+.|+..       ++.    ....   ..++++.||+|+|||.++-+
T Consensus         6 ~~~~divGqe~~~~~l~~~-------i~~----~~~~~~~~~~~L~~GPpGtGKT~lA~~   54 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLA-------LEA----AKMRGEVLDHVLLAGPPGLGKTTLAHI   54 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHH-------HHH----HHHHTCCCCCEEEESSTTSSHHHHHHH
T ss_pred             CcHHHcCChHHHHHHHHHH-------HHH----HHhcCCCCCeEEEECCCCCcHHHHHHH
Confidence            4788887777777666421       000    0111   25899999999999987643

>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=93.84  E-value=0.016  Score=38.68  Aligned_cols=18  Identities=33%  Similarity=0.593  Sum_probs=16.0

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      +.++++.||+|||||...
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            568999999999999765

>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=93.79  E-value=0.17  Score=34.96  Aligned_cols=77  Identities=13%  Similarity=0.084  Sum_probs=43.9

Q ss_pred             HHHHHHHHHc---CCcEEEEcCCCChHHHHHHHHHHHHhh-hcCCCceEEEEcCcHH--HHHHHHHHHHHhccC---CCc
Q psy9277          59 QQRSIKPIVK---GRDVIAQAQSGTGKTATFSISILQSLD-TQLRETQVLCLSPTRE--LAVQIQKVVLALGDF---MNV  129 (178)
Q Consensus        59 Q~~~i~~i~~---g~~v~v~aptGsGKTl~~ll~il~~l~-~~~~~~~~lil~Pt~~--L~~q~~~~~~~~~~~---~~~  129 (178)
                      |.+.+..+.+   +.++++.||.|+|||..+.... ..+. .....+-.+++.|...  -+.|+.+..+.+...   .+.
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~   80 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTR   80 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSS
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCC
Confidence            5556666554   4689999999999998875433 2222 2223456788888532  244444433333221   245


Q ss_pred             eEEEEEc
Q psy9277         130 QCHACIG  136 (178)
Q Consensus       130 ~~~~~~g  136 (178)
                      +++.+..
T Consensus        81 KviIId~   87 (198)
T d2gnoa2          81 KYVIVHD   87 (198)
T ss_dssp             EEEEETT
T ss_pred             EEEEEeC
Confidence            6655543

>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=93.77  E-value=0.054  Score=37.88  Aligned_cols=42  Identities=21%  Similarity=0.405  Sum_probs=29.2

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll   88 (178)
                      ++|+++-.++.+.+.|++.               +.++  .++++.||+|+|||...-.
T Consensus        11 ~~~~divg~~~~~~~L~~~---------------i~~~~~~~lLl~Gp~G~GKttl~~~   54 (227)
T d1sxjc2          11 ETLDEVYGQNEVITTVRKF---------------VDEGKLPHLLFYGPPGTGKTSTIVA   54 (227)
T ss_dssp             SSGGGCCSCHHHHHHHHHH---------------HHTTCCCCEEEECSSSSSHHHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH---------------HHcCCCCeEEEECCCCCChhHHHHH
Confidence            5778877777777776432               1122  2699999999999966543

>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=93.57  E-value=0.082  Score=37.04  Aligned_cols=42  Identities=17%  Similarity=0.310  Sum_probs=29.3

Q ss_pred             ccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcCCcEEEEcCCCChHHHHHH
Q psy9277          33 TFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        33 ~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +|+|+-.++.+.+.|...       ++.      -.-.++++.||+|+|||.+.-
T Consensus        22 ~~~diig~~~~~~~l~~~-------i~~------~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          22 RLDDIVGQEHIVKRLKHY-------VKT------GSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             STTTCCSCHHHHHHHHHH-------HHH------TCCCEEEEESCTTSSHHHHHH
T ss_pred             CHHHccCcHHHHHHHHHH-------HHc------CCCCeEEEECCCCCcHHHHHH
Confidence            788887788777776542       000      012479999999999997754

>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=93.54  E-value=0.024  Score=43.44  Aligned_cols=17  Identities=24%  Similarity=0.450  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      .|++++||||+|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            58999999999999776

>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=93.48  E-value=0.02  Score=38.01  Aligned_cols=19  Identities=21%  Similarity=0.275  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      -.+++++||+|||||...-
T Consensus         4 ~~~I~i~G~pGsGKTTia~   22 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGK   22 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHH
Confidence            3579999999999997653

>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=93.46  E-value=0.056  Score=40.19  Aligned_cols=55  Identities=9%  Similarity=-0.092  Sum_probs=39.7

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP  158 (178)
                      +.++++++|+..-+.+++..+++.    |.+++.++|.....+.........+|||+|.
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~----g~~V~~l~~~~~~~e~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKA----GKSVVVLNRKTFEREYPTIKQKKPDFILATD   90 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHT----TCCEEECCSSSCC--------CCCSEEEESS
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhc----CCeEEEEcCcCcHhHHhhhhcCCcCEEEEec
Confidence            458999999999999999988765    6778888988877766554445578999995

>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=93.26  E-value=0.02  Score=37.35  Aligned_cols=15  Identities=20%  Similarity=0.386  Sum_probs=13.1

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      ++++|++|||||...
T Consensus         5 Iii~G~pGsGKTTla   19 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999999764

>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=93.22  E-value=0.064  Score=37.54  Aligned_cols=42  Identities=14%  Similarity=0.260  Sum_probs=27.4

Q ss_pred             cccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHcC--CcEEEEcCCCChHHHHHHH
Q psy9277          32 STFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVKG--RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        32 ~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~g--~~v~v~aptGsGKTl~~ll   88 (178)
                      ++|+++=-++.+++.|+..               +.++  .++++.||+|+|||.++-+
T Consensus        12 ~~~~d~ig~~~~~~~L~~~---------------~~~~~~~~~ll~Gp~G~GKTt~a~~   55 (224)
T d1sxjb2          12 QVLSDIVGNKETIDRLQQI---------------AKDGNMPHMIISGMPGIGKTTSVHC   55 (224)
T ss_dssp             SSGGGCCSCTHHHHHHHHH---------------HHSCCCCCEEEECSTTSSHHHHHHH
T ss_pred             CCHHHhcCCHHHHHHHHHH---------------HHcCCCCeEEEECCCCCCchhhHHH
Confidence            4566665566666555431               1222  3699999999999987643

>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=92.99  E-value=0.019  Score=38.35  Aligned_cols=19  Identities=16%  Similarity=0.284  Sum_probs=16.1

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      -+.+++.||+|+|||...-
T Consensus         7 ~K~I~i~G~~GsGKTTla~   25 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVN   25 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHH
Confidence            4689999999999997653

>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=92.80  E-value=0.026  Score=37.26  Aligned_cols=16  Identities=31%  Similarity=0.412  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -+++.||+|||||..+
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999775

>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=92.61  E-value=0.18  Score=38.68  Aligned_cols=54  Identities=20%  Similarity=0.215  Sum_probs=39.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcC---------CCceEEEEcCcHHHHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQL---------RETQVLCLSPTRELAVQIQKVVLA  122 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~---------~~~~~lil~Pt~~L~~q~~~~~~~  122 (178)
                      ...++|.|.-|||||.+.+-=++..+....         ..-.+|+|+=|+.=|.++.+++..
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~   78 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRS   78 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHH
Confidence            456899999999999887766666654321         113588999998888887776533

>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=92.58  E-value=0.022  Score=37.99  Aligned_cols=19  Identities=21%  Similarity=0.436  Sum_probs=16.1

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|+-+++.||+|||||...
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            4677899999999999764

>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=92.55  E-value=0.021  Score=38.05  Aligned_cols=21  Identities=19%  Similarity=0.249  Sum_probs=17.6

Q ss_pred             HHcCCcEEEEcCCCChHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~   86 (178)
                      -.+|.-++++|++|||||...
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            345778999999999999876

>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=92.54  E-value=0.023  Score=41.01  Aligned_cols=18  Identities=28%  Similarity=0.338  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +++++.||+|+|||...-
T Consensus        41 ~~vLL~GppGtGKT~la~   58 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAA   58 (246)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHH
Confidence            479999999999997753

>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=92.48  E-value=0.021  Score=40.90  Aligned_cols=17  Identities=29%  Similarity=0.409  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +.+++.||+|+|||..+
T Consensus        33 ~~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          33 TAFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEEECCTTSCTHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            46999999999999765

>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=92.16  E-value=0.039  Score=36.85  Aligned_cols=18  Identities=17%  Similarity=0.364  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      +|++++|++|+|||...-
T Consensus         1 k~I~liG~~GsGKsTi~k   18 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLAR   18 (161)
T ss_dssp             CCEEEECCTTSCHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHH
Confidence            579999999999997753

>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=92.13  E-value=0.095  Score=36.78  Aligned_cols=37  Identities=19%  Similarity=0.243  Sum_probs=26.1

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      |.-+++.|++|+|||...+--+.+...   .+..+++++-
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            678999999999999877655544322   4446666663

>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=92.13  E-value=0.18  Score=36.21  Aligned_cols=42  Identities=19%  Similarity=0.089  Sum_probs=28.3

Q ss_pred             HHHcCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          65 PIVKGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        65 ~i~~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      -+..|.=+++.|+||+|||...+-.+.+....  .+..++|++.
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~--~g~~v~~~s~   72 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAML   72 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHT--SCCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhh--cccceeEeee
Confidence            35567889999999999996655444443222  3456777763

>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=91.94  E-value=0.005  Score=45.22  Aligned_cols=18  Identities=28%  Similarity=0.366  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      .+.+++.||+|+|||...
T Consensus        41 ~~giLL~Gp~GtGKT~l~   58 (265)
T d1r7ra3          41 SKGVLFYGPPGCGKTLLA   58 (265)
T ss_dssp             CCEEEEBCCTTSSHHHHH
T ss_pred             CCeEEEECCCCCcchhHH
Confidence            578999999999999664

>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=91.87  E-value=0.12  Score=33.82  Aligned_cols=33  Identities=27%  Similarity=0.294  Sum_probs=20.1

Q ss_pred             EEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEc
Q psy9277          72 VIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLS  107 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~  107 (178)
                      +.++|+.|||||... -.++..+..  ++.++.++.
T Consensus         5 i~itG~~GSGKTTL~-~~L~~~l~~--~g~~v~v~~   37 (170)
T d1np6a_           5 LAFAAWSGTGKTTLL-KKLIPALCA--RGIRPGLIK   37 (170)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHHH--TTCCEEEEE
T ss_pred             EEEEcCCCCCHHHHH-HHHHHHHHH--CCCeEEEec
Confidence            678999999999653 344444443  333444443

>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=91.72  E-value=0.015  Score=42.32  Aligned_cols=18  Identities=33%  Similarity=0.449  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      .+.+++.||+|+|||+..
T Consensus        38 ~~giLL~GppGtGKT~l~   55 (258)
T d1e32a2          38 PRGILLYGPPGTGKTLIA   55 (258)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CceeEEecCCCCCchHHH
Confidence            478999999999999754

>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=91.45  E-value=0.11  Score=35.86  Aligned_cols=39  Identities=21%  Similarity=0.202  Sum_probs=25.5

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP  108 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P  108 (178)
                      .|.-+++.|++|+|||...+--+.+....  .+..++|+..
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            46889999999999997765434333332  2235666654

>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=91.22  E-value=0.052  Score=35.88  Aligned_cols=20  Identities=25%  Similarity=0.353  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.+=++++|++|||||...-
T Consensus         2 ~~kiI~l~G~~GsGKsTva~   21 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIVR   21 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            34568899999999997653

>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=90.87  E-value=0.094  Score=35.70  Aligned_cols=17  Identities=35%  Similarity=0.663  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +-++++||+|+|||...
T Consensus         2 rpIvl~GpsG~GK~tl~   18 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLL   18 (186)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46899999999999643

>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=90.73  E-value=0.24  Score=34.88  Aligned_cols=46  Identities=17%  Similarity=0.205  Sum_probs=32.4

Q ss_pred             ccccccccccCCCCHHHHHHHHhCCCCCCcHHHHHHHHHHHc---CCcEEEEcCCCChHHHHHHH
Q psy9277          27 DVEVVSTFDNMGLREDLLRGIYAYGFEKPSAIQQRSIKPIVK---GRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        27 ~~~~~~~f~~~~l~~~i~~~l~~~g~~~~~~~Q~~~i~~i~~---g~~v~v~aptGsGKTl~~ll   88 (178)
                      +.+| ++|+++-.++.+.+.|+..               +.+   ...+++.||+|+|||.++..
T Consensus         5 KyrP-~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~~   53 (239)
T d1njfa_           5 KWRP-QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIARL   53 (239)
T ss_dssp             HTCC-SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHHH
T ss_pred             hhCC-CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHHH
Confidence            3445 5888888888888877532               112   23589999999999987653

>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=90.64  E-value=0.062  Score=35.49  Aligned_cols=18  Identities=33%  Similarity=0.302  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll   88 (178)
                      =+++.|++|||||...-.
T Consensus         8 iivl~G~~GsGKsT~a~~   25 (171)
T d1knqa_           8 IYVLMGVSGSGKSAVASE   25 (171)
T ss_dssp             EEEEECSTTSCHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            377899999999977643

>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=90.58  E-value=0.063  Score=36.33  Aligned_cols=17  Identities=29%  Similarity=0.415  Sum_probs=14.0

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      .=++++|++|||||..+
T Consensus        15 ~liil~G~pGsGKST~a   31 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFI   31 (172)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            35789999999999654

>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=90.53  E-value=0.034  Score=37.67  Aligned_cols=19  Identities=37%  Similarity=0.384  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |.-++++|++|||||..+-
T Consensus        19 g~vI~L~G~pGSGKTTiAk   37 (195)
T d1x6va3          19 GCTVWLTGLSGAGKTTVSM   37 (195)
T ss_dssp             CEEEEEESSCHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHH
Confidence            5578899999999998764

>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=90.52  E-value=0.082  Score=35.83  Aligned_cols=25  Identities=20%  Similarity=0.088  Sum_probs=19.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      .|+-+++.||+|+|||...+--+.+
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHH
Confidence            3678999999999999776544443

>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=90.24  E-value=0.072  Score=35.46  Aligned_cols=23  Identities=30%  Similarity=0.537  Sum_probs=16.5

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .+++.||+|+|||... -.++..+
T Consensus         2 ki~I~G~~G~GKSTLl-~~i~~~l   24 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLV-KKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHH
T ss_pred             EEEEECCCCcHHHHHH-HHHHhcC
Confidence            4899999999999753 3344433

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

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: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=90.20  E-value=0.94  Score=32.55  Aligned_cols=87  Identities=13%  Similarity=0.072  Sum_probs=45.9

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhh-cCCCc--eEEEEc----CcHHHHHHHHHHHHHhccC-----------------
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDT-QLRET--QVLCLS----PTRELAVQIQKVVLALGDF-----------------  126 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~-~~~~~--~~lil~----Pt~~L~~q~~~~~~~~~~~-----------------  126 (178)
                      -+.+.|.-|.|||..+... ++.... ....+  .+++-+    +...+...+...+......                 
T Consensus        46 ~v~I~GmgGiGKTtLA~~v-~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (277)
T d2a5yb3          46 FLFLHGRAGSGKSVIASQA-LSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLK  124 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHH-HHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHH
Confidence            4779999999999765332 232111 11111  233322    3344555544444332110                 


Q ss_pred             --------CCceEEEEEcCccHHHHHHHhc-CCCcEEEeCh
Q psy9277         127 --------MNVQCHACIGGTNLSEDLRKLD-YGQHVVSGTP  158 (178)
Q Consensus       127 --------~~~~~~~~~g~~~~~~~~~~~~-~~~~IlV~TP  158 (178)
                              .+-++..+.++....++...+. .++.|||||=
T Consensus       125 ~~~~~~~L~~kr~LlVLDDv~~~~~~~~~~~~~srilvTTR  165 (277)
T d2a5yb3         125 RMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTR  165 (277)
T ss_dssp             HHHHHHHTTSTTEEEEEEEECCHHHHHHHHHTTCEEEEEES
T ss_pred             HHHHHHHhccCCeeEecchhhHHhhhhhhcccCceEEEEee
Confidence                    1235667777766555555443 5788998884

>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=90.03  E-value=0.18  Score=35.30  Aligned_cols=24  Identities=17%  Similarity=0.037  Sum_probs=19.4

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      |+-+++.||+|+|||...+-.+.+
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            578999999999999877655444

>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=89.97  E-value=0.1  Score=36.44  Aligned_cols=19  Identities=32%  Similarity=0.417  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll   88 (178)
                      .++++.||+|+|||...-.
T Consensus        34 ~~lll~Gp~G~GKTtl~~~   52 (237)
T d1sxjd2          34 PHMLFYGPPGTGKTSTILA   52 (237)
T ss_dssp             CCEEEECSTTSSHHHHHHH
T ss_pred             CeEEEECCCCCChHHHHHH
Confidence            3699999999999976543

>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=89.72  E-value=0.47  Score=32.97  Aligned_cols=44  Identities=18%  Similarity=0.241  Sum_probs=27.0

Q ss_pred             cEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcCcHHHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSPTRELAVQIQK  118 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~Pt~~L~~q~~~  118 (178)
                      .+++.||+|+|||... .++.+.+..  .+..++++ +...+..+...
T Consensus        38 ~l~l~G~~G~GKTHLl-~A~~~~~~~--~~~~~~~~-~~~~~~~~~~~   81 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLL-QAAGNEAKK--RGYRVIYS-SADDFAQAMVE   81 (213)
T ss_dssp             SEEEECSSSSSHHHHH-HHHHHHHHH--TTCCEEEE-EHHHHHHHHHH
T ss_pred             cEEEECCCCCcHHHHH-HHHHHHhcc--CccceEEe-chHHHHHHHHH
Confidence            4899999999999553 355555443  23344444 55555555444

>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=89.47  E-value=0.099  Score=35.44  Aligned_cols=19  Identities=21%  Similarity=0.352  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCChHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~l   87 (178)
                      |..+++.||+|||||...-
T Consensus         3 ~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHH
Confidence            5678899999999998764

>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=89.40  E-value=0.092  Score=35.12  Aligned_cols=17  Identities=18%  Similarity=0.366  Sum_probs=14.8

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      ++++.||+|||||...-
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58999999999998764

>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=89.35  E-value=0.21  Score=37.98  Aligned_cols=37  Identities=19%  Similarity=0.125  Sum_probs=25.1

Q ss_pred             CCCCCcHHHHHHHHHHHc----CCcEEEEcCCCChHHHHHH
Q psy9277          51 GFEKPSAIQQRSIKPIVK----GRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        51 g~~~~~~~Q~~~i~~i~~----g~~v~v~aptGsGKTl~~l   87 (178)
                      ++......-..++..++.    ++.+++.||+|+|||....
T Consensus       132 ~~~~~~~~i~~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~  172 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAA  172 (362)
T ss_dssp             TSTTHHHHHHHHHHHHHHCCTTCCEEEEECSTTSSHHHHHH
T ss_pred             cccchHHHHHHHHHHHHhCCCCcCeEEEECCCCCCHHHHHH
Confidence            455544444455555444    4689999999999997654

>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=89.26  E-value=0.1  Score=34.78  Aligned_cols=19  Identities=16%  Similarity=0.142  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll   88 (178)
                      +.+++.|++|||||...-.
T Consensus         3 ~~Iil~G~~GsGKSTia~~   21 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRE   21 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHH
Confidence            5789999999999977643

>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=89.18  E-value=0.052  Score=38.75  Aligned_cols=16  Identities=25%  Similarity=0.210  Sum_probs=13.0

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      +++.||+|+|||.+.-
T Consensus        49 l~l~GppGtGKT~l~~   64 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLAK   64 (287)
T ss_dssp             EECTTCCSSSHHHHHH
T ss_pred             EEeECCCCCCHHHHHH
Confidence            4567999999998753

>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=89.10  E-value=0.13  Score=34.95  Aligned_cols=18  Identities=11%  Similarity=0.278  Sum_probs=14.9

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      .+-++++||+|+||+...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~   20 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIK   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            356899999999999664

>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=88.83  E-value=0.11  Score=34.97  Aligned_cols=18  Identities=33%  Similarity=0.536  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      |+=++++||+|+||+...
T Consensus         2 G~iivl~GpsG~GK~tl~   19 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVV   19 (182)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567899999999999764

>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=88.59  E-value=0.11  Score=34.85  Aligned_cols=18  Identities=22%  Similarity=0.278  Sum_probs=15.2

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll   88 (178)
                      ++++.||+|||||...-.
T Consensus         2 ~I~i~G~pGsGKsT~a~~   19 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVK   19 (181)
T ss_dssp             EEEEECCTTSSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            689999999999987643

>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=88.50  E-value=0.12  Score=35.05  Aligned_cols=18  Identities=17%  Similarity=0.279  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      ..+++.||+|||||...-
T Consensus         4 m~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CCEEEEESTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            468999999999987654

>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=88.45  E-value=0.12  Score=35.86  Aligned_cols=23  Identities=17%  Similarity=0.037  Sum_probs=18.3

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISI   90 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~i   90 (178)
                      .|+-+++.||+|+|||...+--+
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~   55 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLA   55 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHH
Confidence            36789999999999997665433

>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=88.36  E-value=0.076  Score=39.61  Aligned_cols=19  Identities=26%  Similarity=0.354  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .+.++++.||+|+|||..+
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            4578999999999999775

>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=88.26  E-value=0.12  Score=34.71  Aligned_cols=17  Identities=18%  Similarity=0.182  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.||+|||||...-
T Consensus         2 ~I~i~G~pGSGKsT~~~   18 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQ   18 (179)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            57899999999998763

>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=88.05  E-value=0.14  Score=35.65  Aligned_cols=19  Identities=37%  Similarity=0.541  Sum_probs=15.8

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      +|+=++++||+|+||+...
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            3667899999999999654

>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=87.95  E-value=0.13  Score=34.55  Aligned_cols=17  Identities=18%  Similarity=0.397  Sum_probs=14.6

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .+++.||+|||||...-
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQAD   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58899999999998764

>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=87.88  E-value=0.14  Score=34.92  Aligned_cols=16  Identities=31%  Similarity=0.565  Sum_probs=13.8

Q ss_pred             cEEEEcCCCChHHHHH
Q psy9277          71 DVIAQAQSGTGKTATF   86 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~   86 (178)
                      -+++.||+|+|||...
T Consensus         2 pIvl~GPsGsGK~tl~   17 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLL   17 (190)
T ss_dssp             CEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4899999999999754

>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=87.78  E-value=0.13  Score=34.98  Aligned_cols=17  Identities=24%  Similarity=0.347  Sum_probs=14.2

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -+++.||+|||||...-
T Consensus         8 iI~i~G~pGSGKsT~a~   24 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCA   24 (194)
T ss_dssp             EEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999997653

>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=87.33  E-value=0.15  Score=34.73  Aligned_cols=17  Identities=18%  Similarity=0.306  Sum_probs=14.0

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      -+++.||+|||||...-
T Consensus        10 iI~i~GppGSGKsT~a~   26 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCE   26 (196)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999986654

>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=87.22  E-value=0.14  Score=34.36  Aligned_cols=18  Identities=33%  Similarity=0.291  Sum_probs=13.7

Q ss_pred             CCc-EEEEcCCCChHHHHH
Q psy9277          69 GRD-VIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~-v~v~aptGsGKTl~~   86 (178)
                      |+- +-|.|++|||||...
T Consensus        21 ~~~iIgI~G~~GSGKSTla   39 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTLA   39 (198)
T ss_dssp             SSEEEEEEECTTSSHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            443 449999999999764

>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=87.10  E-value=0.17  Score=33.48  Aligned_cols=17  Identities=24%  Similarity=0.411  Sum_probs=14.3

Q ss_pred             CcEEEEcCCCChHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATF   86 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~   86 (178)
                      +-+++.|++|||||...
T Consensus         2 kiI~i~G~~GsGKsT~~   18 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSS   18 (190)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45889999999999654

>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=86.95  E-value=0.48  Score=34.02  Aligned_cols=55  Identities=13%  Similarity=0.019  Sum_probs=41.8

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHHhcCCCcEEEeCh
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRKLDYGQHVVSGTP  158 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~IlV~TP  158 (178)
                      +.++++.++++.-+..+++.+++.    +..+..++|+..............+++|+|.
T Consensus       178 ~~~~lvf~~~~~~~~~l~~~L~~~----~~~~~~l~~~~~~~~~~~~~~~~~~~lvaT~  232 (305)
T d2bmfa2         178 KGKTVWFVPSIKAGNDIAACLRKN----GKKVIQLSRKTFDSEYIKTRTNDWDFVVTTD  232 (305)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH----TCCCEECCTTCHHHHGGGGGTSCCSEEEECG
T ss_pred             CCCEEEEeccHHHHHHHHHHHHhC----CCCEEEeCCcChHHHHhhhhccchhhhhhhH
Confidence            457999999999999999998776    5566777887765544333344578999996

>d1vi2a1 c.2.1.7 (A:107-288) Putative shikimate dehydrogenase YdiB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Aminoacid dehydrogenase-like, C-terminal domain
domain: Putative shikimate dehydrogenase YdiB
species: Escherichia coli [TaxId: 562]

Probab=86.94  E-value=1.4  Score=29.39  Aligned_cols=81  Identities=11%  Similarity=0.103  Sum_probs=44.6

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHhhhcCCCceEEEEcC-cHHHHHHHHHHHHHhccCCCceEEEEEcCccHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSLDTQLRETQVLCLSP-TRELAVQIQKVVLALGDFMNVQCHACIGGTNLSEDLRK  146 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l~~~~~~~~~lil~P-t~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~  146 (178)
                      ++++++|.+--|+||+.++.+.-        .+.+.++++. +.+-+......++++....+..+. ...-.........
T Consensus        17 ~~k~vlIlGaGGaarai~~al~~--------~g~~~i~i~nR~~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~   87 (182)
T d1vi2a1          17 KGKTMVLLGAGGASTAIGAQGAI--------EGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVT-VTDLADQQAFAEA   87 (182)
T ss_dssp             TTCEEEEECCSHHHHHHHHHHHH--------TTCSEEEEEECSSTTHHHHHHHHHHHHHHSSCEEE-EEETTCHHHHHHH
T ss_pred             CCCEEEEECCcHHHHHHHHHHhh--------cCCceEeeeccchHHHHHHHHHHHHHHhhcCcceE-eeecccccchhhh
Confidence            57899999999999986654322        2344555554 334444444555555444444332 3323333322222


Q ss_pred             hcCCCcEEE-eCh
Q psy9277         147 LDYGQHVVS-GTP  158 (178)
Q Consensus       147 ~~~~~~IlV-~TP  158 (178)
                      + ..+||+| +||
T Consensus        88 ~-~~~diiIN~Tp   99 (182)
T d1vi2a1          88 L-ASADILTNGTK   99 (182)
T ss_dssp             H-HTCSEEEECSS
T ss_pred             h-cccceeccccC
Confidence            2 3578887 777

>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=86.71  E-value=0.22  Score=33.78  Aligned_cols=22  Identities=18%  Similarity=0.350  Sum_probs=17.7

Q ss_pred             HHcCCcEEEEcCCCChHHHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~~l   87 (178)
                      +.+++-+++.||+||||+...-
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a~   26 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQCE   26 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHH
Confidence            4456779999999999997653

>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=86.57  E-value=0.18  Score=33.30  Aligned_cols=19  Identities=16%  Similarity=0.195  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCChHHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~ll   88 (178)
                      .++++.|++|+|||...-.
T Consensus         2 p~IvliG~~G~GKSTig~~   20 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRR   20 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHH
Confidence            3588899999999987643

>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=86.41  E-value=0.55  Score=30.73  Aligned_cols=23  Identities=13%  Similarity=0.044  Sum_probs=15.1

Q ss_pred             EEEcCCCChHHHHHHHHHHHHhhh
Q psy9277          73 IAQAQSGTGKTATFSISILQSLDT   96 (178)
Q Consensus        73 ~v~aptGsGKTl~~ll~il~~l~~   96 (178)
                      -|+|+.|||||... --++..+..
T Consensus         5 ~I~G~~gSGKTTli-~~l~~~L~~   27 (165)
T d1xjca_           5 QVVGYKHSGKTTLM-EKWVAAAVR   27 (165)
T ss_dssp             EEECCTTSSHHHHH-HHHHHHHHH
T ss_pred             EEEeCCCCCHHHHH-HHHHHHHHh
Confidence            48999999999653 233343433

>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=86.28  E-value=1.8  Score=29.43  Aligned_cols=59  Identities=19%  Similarity=0.033  Sum_probs=37.7

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCC--------------------------CceEEEEEcCccHHHHHHHh---c-C
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFM--------------------------NVQCHACIGGTNLSEDLRKL---D-Y  149 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~--------------------------~~~~~~~~g~~~~~~~~~~~---~-~  149 (178)
                      +..+||.+|+|..+...+..+.......                          ...++..+++.+..++....   + .
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g  119 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRG  119 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCC
Confidence            4578999999888877777665432211                          01256678888776554332   2 3


Q ss_pred             CCcEEEeCh
Q psy9277         150 GQHVVSGTP  158 (178)
Q Consensus       150 ~~~IlV~TP  158 (178)
                      ..+|+|+|.
T Consensus       120 ~i~vlvaT~  128 (201)
T d2p6ra4         120 NIKVVVATP  128 (201)
T ss_dssp             SCCEEEECS
T ss_pred             CceEEEech
Confidence            468999885

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=86.13  E-value=0.29  Score=36.87  Aligned_cols=24  Identities=38%  Similarity=0.649  Sum_probs=18.2

Q ss_pred             HHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      +..++.|.|  ++..|+||||||...
T Consensus        72 v~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          72 VDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHhhccCceeEEecccCCCCcceee
Confidence            345566765  778899999999774

>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=86.08  E-value=0.17  Score=37.60  Aligned_cols=18  Identities=22%  Similarity=0.307  Sum_probs=15.3

Q ss_pred             cEEEEcCCCChHHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~ll   88 (178)
                      +++++||||+|||..+-.
T Consensus        54 ~~lf~Gp~GvGKT~lak~   71 (315)
T d1r6bx3          54 SFLFAGPTGVGKTEVTVQ   71 (315)
T ss_dssp             EEEEECSTTSSHHHHHHH
T ss_pred             EEEEECCCcchhHHHHHH
Confidence            689999999999977643

>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=86.05  E-value=0.64  Score=32.88  Aligned_cols=29  Identities=17%  Similarity=0.127  Sum_probs=22.0

Q ss_pred             HHHHHcCCcEEEEcCCCChHHHHHHHHHH
Q psy9277          63 IKPIVKGRDVIAQAQSGTGKTATFSISIL   91 (178)
Q Consensus        63 i~~i~~g~~v~v~aptGsGKTl~~ll~il   91 (178)
                      ++-+..|.-+++.|++|+|||...+-.++
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHHHHH
Confidence            44555688899999999999977655444

>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=86.02  E-value=0.18  Score=36.07  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=16.9

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|..+.++||+|||||...
T Consensus        27 ~~Ge~vaIvG~sGsGKSTLl   46 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKSTLT   46 (241)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHH
Confidence            34889999999999999543

>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=85.79  E-value=0.22  Score=33.86  Aligned_cols=20  Identities=20%  Similarity=0.097  Sum_probs=16.3

Q ss_pred             CCcEEEEcCCCChHHHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATFSI   88 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll   88 (178)
                      ...+++.||+|||||...-.
T Consensus         6 ~mrIiliG~PGSGKtT~a~~   25 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSR   25 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHH
T ss_pred             ceeEEEECCCCCCHHHHHHH
Confidence            45789999999999977643

>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=85.75  E-value=2.1  Score=30.49  Aligned_cols=66  Identities=14%  Similarity=0.200  Sum_probs=42.3

Q ss_pred             HHHHHHhhhcCCCceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHH--------HHHH---Hhc-CCCcEEE
Q psy9277          88 ISILQSLDTQLRETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS--------EDLR---KLD-YGQHVVS  155 (178)
Q Consensus        88 l~il~~l~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~--------~~~~---~~~-~~~~IlV  155 (178)
                      .-++..+.....+.++||.+.+++-+..+++.+.+-    ++++..+.|.....        ++..   ... ..++|+|
T Consensus       149 ~~~l~~~~~~~~~~k~iiF~~~~~~~~~~~~~L~~~----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv  224 (286)
T d1wp9a2         149 KEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKD----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLV  224 (286)
T ss_dssp             HHHHHHHHHHCTTCCEEEECSCHHHHHHHHHHHHHT----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEE
T ss_pred             HHHHHHHHHhCCCCcEEEEeCcHHhHHHHHHHHHHc----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEE
Confidence            344444444445679999999999999998887654    66666666643221        1212   222 3578999


Q ss_pred             eC
Q psy9277         156 GT  157 (178)
Q Consensus       156 ~T  157 (178)
                      +|
T Consensus       225 ~T  226 (286)
T d1wp9a2         225 AT  226 (286)
T ss_dssp             EC
T ss_pred             Ec
Confidence            98

>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=85.67  E-value=0.22  Score=34.73  Aligned_cols=25  Identities=20%  Similarity=-0.050  Sum_probs=19.7

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQ   92 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~   92 (178)
                      .|.-+++.|++|+|||...+--+.+
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            3678999999999999887654443

>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=85.40  E-value=0.36  Score=35.78  Aligned_cols=24  Identities=33%  Similarity=0.605  Sum_probs=18.7

Q ss_pred             HHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ++.+++|.  .++..|+||||||...
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            44556676  5788999999999775

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.37  E-value=0.21  Score=33.46  Aligned_cols=18  Identities=17%  Similarity=0.265  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCChHHHHHH
Q psy9277          70 RDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        70 ~~v~v~aptGsGKTl~~l   87 (178)
                      ..+++.||+|||||...-
T Consensus         3 mrIvl~G~pGSGKtT~a~   20 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQAP   20 (180)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            458899999999997764

>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=85.34  E-value=0.21  Score=35.93  Aligned_cols=20  Identities=20%  Similarity=0.283  Sum_probs=17.2

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.++||+|||||...
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl   57 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVA   57 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            34889999999999999654

>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=85.26  E-value=0.21  Score=33.67  Aligned_cols=16  Identities=25%  Similarity=0.410  Sum_probs=13.8

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      +++.||+|||||...-
T Consensus         4 I~i~GppGSGKsT~a~   19 (194)
T d1teva_           4 VFVLGGPGAGKGTQCA   19 (194)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7899999999997763

>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=85.16  E-value=0.2  Score=34.69  Aligned_cols=19  Identities=37%  Similarity=0.483  Sum_probs=16.5

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||..+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl   44 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLL   44 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCChHHHHH
Confidence            4788999999999999664

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=85.09  E-value=0.71  Score=33.93  Aligned_cols=38  Identities=16%  Similarity=0.256  Sum_probs=32.1

Q ss_pred             CceEEEEcCcHHHHHHHHHHHHHhccCCCceEEEEEcCccHH
Q psy9277         100 ETQVLCLSPTRELAVQIQKVVLALGDFMNVQCHACIGGTNLS  141 (178)
Q Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~  141 (178)
                      +.++||.+++++.++++...+++.    |+++..++++.+.+
T Consensus        36 ggk~LVFcnSR~~aE~La~~L~~~----Gi~a~~~Hgglsq~   73 (299)
T d1a1va2          36 GGRHLIFCHSKKKCDELAAKLVAL----GINAVAYYRGLDVS   73 (299)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHT----TCCEEEECTTSCGG
T ss_pred             CCCEEEECCcHHHHHHHHHHHHHC----CCCEEEEeCCchHH
Confidence            458999999999999999998765    78888888886654

>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=84.94  E-value=0.22  Score=33.73  Aligned_cols=16  Identities=19%  Similarity=0.219  Sum_probs=13.8

Q ss_pred             EEEEcCCCChHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFS   87 (178)
Q Consensus        72 v~v~aptGsGKTl~~l   87 (178)
                      ++++|.+|||||..+-
T Consensus         5 i~l~GlpgsGKSTla~   20 (213)
T d1bifa1           5 IVMVGLPARGKTYISK   20 (213)
T ss_dssp             EEEECCTTSSHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6889999999998764

>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=84.90  E-value=0.54  Score=31.85  Aligned_cols=34  Identities=12%  Similarity=0.125  Sum_probs=20.5

Q ss_pred             CcEEEEcC-CCChHHHHHHHHHHHHhhhcCCCceEEEE
Q psy9277          70 RDVIAQAQ-SGTGKTATFSISILQSLDTQLRETQVLCL  106 (178)
Q Consensus        70 ~~v~v~ap-tGsGKTl~~ll~il~~l~~~~~~~~~lil  106 (178)
                      +.++|++- ||.|||.+.+.-+ ..+..  .+.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La-~aLa~--~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALL-QAAKA--AGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHH-HHHHH--TTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHH-HHHHH--CCCeEEEE
Confidence            45778887 6999998765322 22322  34455554

>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=84.78  E-value=0.29  Score=33.77  Aligned_cols=27  Identities=19%  Similarity=0.076  Sum_probs=21.4

Q ss_pred             cCCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          68 KGRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      .|.-+++.|++|+|||...+-.+.+.+
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            467899999999999988766665543

>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=84.73  E-value=0.2  Score=36.15  Aligned_cols=20  Identities=35%  Similarity=0.433  Sum_probs=17.0

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.++||+|||||...
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl   61 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLI   61 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCCcHHHHH
Confidence            45889999999999999653

>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=84.70  E-value=0.22  Score=35.87  Aligned_cols=20  Identities=30%  Similarity=0.473  Sum_probs=17.2

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|..+.+++|+|||||...
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl   58 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIA   58 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            35889999999999999654

>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=84.60  E-value=0.48  Score=33.71  Aligned_cols=20  Identities=25%  Similarity=0.331  Sum_probs=16.8

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..+..+++.|++|+||+.++
T Consensus        21 ~~~~pvlI~Ge~GtGK~~~A   40 (247)
T d1ny5a2          21 CAECPVLITGESGVGKEVVA   40 (247)
T ss_dssp             TCCSCEEEECSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCcCHHHHH
Confidence            34789999999999999654

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=84.57  E-value=0.73  Score=33.15  Aligned_cols=26  Identities=27%  Similarity=0.189  Sum_probs=20.7

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      |+=+.+.+|+|+|||...+..+.+..
T Consensus        54 g~itei~G~~gsGKTtl~l~~~~~~q   79 (263)
T d1u94a1          54 GRIVEIYGPESSGKTTLTLQVIAAAQ   79 (263)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHHHH
Confidence            46789999999999988766655543

>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=84.16  E-value=0.26  Score=33.88  Aligned_cols=15  Identities=13%  Similarity=0.302  Sum_probs=12.2

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      +-+.|++|||||...
T Consensus         5 IgI~G~~gSGKSTla   19 (213)
T d1uj2a_           5 IGVSGGTASGKSSVC   19 (213)
T ss_dssp             EEEECSTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            457899999999665

>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=84.11  E-value=0.23  Score=35.33  Aligned_cols=19  Identities=32%  Similarity=0.417  Sum_probs=16.5

Q ss_pred             HcCCcEEEEcCCCChHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTAT   85 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~   85 (178)
                      ..|.-+.+.||+|||||..
T Consensus        29 ~~Ge~~~iiG~sGsGKSTL   47 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKSTM   47 (230)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCcchh
Confidence            4588999999999999955

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=83.61  E-value=0.26  Score=32.59  Aligned_cols=15  Identities=27%  Similarity=0.452  Sum_probs=12.7

Q ss_pred             EEEEcCCCChHHHHH
Q psy9277          72 VIAQAQSGTGKTATF   86 (178)
Q Consensus        72 v~v~aptGsGKTl~~   86 (178)
                      +++.|++|+|||...
T Consensus         4 ivi~G~~GsGKTT~~   18 (194)
T d1nksa_           4 GIVTGIPGVGKSTVL   18 (194)
T ss_dssp             EEEEECTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            578999999999665

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.51  E-value=0.56  Score=32.72  Aligned_cols=13  Identities=31%  Similarity=0.450  Sum_probs=11.6

Q ss_pred             EEEEcCCCChHHH
Q psy9277          72 VIAQAQSGTGKTA   84 (178)
Q Consensus        72 v~v~aptGsGKTl   84 (178)
                      +++.|.-|||||.
T Consensus         6 ~iitGFLGaGKTT   18 (222)
T d1nija1           6 TLLTGFLGAGKTT   18 (222)
T ss_dssp             EEEEESSSSSCHH
T ss_pred             EEEeeCCCCCHHH
Confidence            5789999999996

>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=83.25  E-value=0.51  Score=35.62  Aligned_cols=24  Identities=38%  Similarity=0.642  Sum_probs=17.8

Q ss_pred             HHHHHcCCc--EEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGRD--VIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~~--v~v~aptGsGKTl~~   86 (178)
                      +..++.|.|  ++..|+||||||...
T Consensus       106 v~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         106 VQTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCceEEeeccCCCCCceee
Confidence            345566764  667799999999775

>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=82.87  E-value=0.26  Score=35.28  Aligned_cols=20  Identities=25%  Similarity=0.303  Sum_probs=16.8

Q ss_pred             HHcCCcEEEEcCCCChHHHH
Q psy9277          66 IVKGRDVIAQAQSGTGKTAT   85 (178)
Q Consensus        66 i~~g~~v~v~aptGsGKTl~   85 (178)
                      +.+|.-+.+.||+|||||..
T Consensus        28 i~~Ge~~~iiG~sGsGKSTL   47 (240)
T d3dhwc1          28 VPAGQIYGVIGASGAGKSTL   47 (240)
T ss_dssp             ECSSCEEEEEESTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34588999999999999954

>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=82.58  E-value=0.28  Score=34.87  Aligned_cols=20  Identities=30%  Similarity=0.428  Sum_probs=16.7

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.+|+|||||...
T Consensus        24 ~~Gei~~liGpsGsGKSTLl   43 (232)
T d2awna2          24 HEGEFVVFVGPSGCGKSTLL   43 (232)
T ss_dssp             CTTCEEEEECCTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            35888999999999999553

>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=82.52  E-value=0.26  Score=35.20  Aligned_cols=19  Identities=26%  Similarity=0.385  Sum_probs=16.2

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|||||...
T Consensus        27 ~Ge~vaivG~sGsGKSTLl   45 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIF   45 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999644

>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=82.52  E-value=0.37  Score=32.78  Aligned_cols=20  Identities=30%  Similarity=0.385  Sum_probs=17.1

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|+.+++++++|+|||...+
T Consensus        14 ~g~gvli~G~sG~GKS~lal   33 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECAL   33 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHH
Confidence            47889999999999986654

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

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: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=82.29  E-value=0.3  Score=36.44  Aligned_cols=19  Identities=21%  Similarity=0.380  Sum_probs=14.2

Q ss_pred             CCcE-EEEcCCCChHHHHHH
Q psy9277          69 GRDV-IAQAQSGTGKTATFS   87 (178)
Q Consensus        69 g~~v-~v~aptGsGKTl~~l   87 (178)
                      .+++ ++.||+|+|||+..-
T Consensus       122 ~~g~~l~~G~pG~GKT~la~  141 (321)
T d1w44a_         122 ASGMVIVTGKGNSGKTPLVH  141 (321)
T ss_dssp             ESEEEEEECSSSSCHHHHHH
T ss_pred             CCceEEEECCCCccHHHHHH
Confidence            3454 558999999997764

>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=82.27  E-value=0.4  Score=32.52  Aligned_cols=20  Identities=35%  Similarity=0.458  Sum_probs=17.1

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|+.++++|++|+|||.+.+
T Consensus        13 ~g~gvl~~G~sG~GKStlal   32 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETAL   32 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHH
Confidence            47889999999999987654

>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=81.90  E-value=0.34  Score=33.95  Aligned_cols=18  Identities=17%  Similarity=0.189  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCChHHHHH
Q psy9277          69 GRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~   86 (178)
                      ++.+++.||.|+|||...
T Consensus        29 ~~~i~i~G~~G~GKTsLl   46 (283)
T d2fnaa2          29 APITLVLGLRRTGKSSII   46 (283)
T ss_dssp             SSEEEEEESTTSSHHHHH
T ss_pred             CCEEEEEcCCCCcHHHHH
Confidence            567999999999999654

>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=81.70  E-value=0.31  Score=34.81  Aligned_cols=20  Identities=40%  Similarity=0.503  Sum_probs=16.8

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|||||...
T Consensus        27 ~~Ge~~~liG~sGaGKSTll   46 (240)
T d1g2912          27 KDGEFMILLGPSGCGKTTTL   46 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHHH
T ss_pred             cCCCEEEEECCCCChHHHHH
Confidence            35888999999999999653

>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=81.42  E-value=0.52  Score=35.55  Aligned_cols=25  Identities=36%  Similarity=0.517  Sum_probs=19.3

Q ss_pred             HHHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.  .++..|+||||||...
T Consensus        66 lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          66 LVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCceeeeccccCCCCccccc
Confidence            355667776  4678899999999774

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=81.40  E-value=0.57  Score=34.97  Aligned_cols=25  Identities=36%  Similarity=0.578  Sum_probs=18.9

Q ss_pred             HHHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.  .++..|+||||||...
T Consensus        72 lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          72 ILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhccCCceEEeeeeccccceEEe
Confidence            345566776  4678999999999764

>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=81.17  E-value=0.42  Score=34.86  Aligned_cols=19  Identities=32%  Similarity=0.559  Sum_probs=16.0

Q ss_pred             cCCcEEEEcCCCChHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~   86 (178)
                      .|.-+.+.||+|+|||...
T Consensus        61 ~Ge~vaivG~nGsGKSTLl   79 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLL   79 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHH
T ss_pred             CCCEEEEECCCCChHHHHH
Confidence            3788999999999999643

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

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: Staphylococcus xylosus [TaxId: 1288]

Probab=81.12  E-value=0.45  Score=32.01  Aligned_cols=20  Identities=35%  Similarity=0.451  Sum_probs=16.9

Q ss_pred             cCCcEEEEcCCCChHHHHHH
Q psy9277          68 KGRDVIAQAQSGTGKTATFS   87 (178)
Q Consensus        68 ~g~~v~v~aptGsGKTl~~l   87 (178)
                      .|+.+++++++|+|||...+
T Consensus        14 ~g~gvli~G~sg~GKS~la~   33 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETAL   33 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHH
Confidence            47889999999999986553

>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=81.04  E-value=0.55  Score=35.48  Aligned_cols=25  Identities=36%  Similarity=0.517  Sum_probs=19.5

Q ss_pred             HHHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          62 SIKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        62 ~i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      .+..++.|.  .++..|+||||||...
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            455667776  5788899999999774

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

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: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=81.02  E-value=0.35  Score=34.54  Aligned_cols=20  Identities=35%  Similarity=0.491  Sum_probs=16.9

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|+|||...
T Consensus        30 ~~Ge~~~liGpsGaGKSTLl   49 (239)
T d1v43a3          30 KDGEFLVLLGPSGCGKTTTL   49 (239)
T ss_dssp             CTTCEEEEECCTTSSHHHHH
T ss_pred             CCCCEEEEECCCCChHHHHH
Confidence            35788999999999999654

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=80.95  E-value=0.66  Score=33.57  Aligned_cols=25  Identities=24%  Similarity=0.330  Sum_probs=18.3

Q ss_pred             CCcEEEEcCCCChHHHHHHHHHHHHh
Q psy9277          69 GRDVIAQAQSGTGKTATFSISILQSL   94 (178)
Q Consensus        69 g~~v~v~aptGsGKTl~~ll~il~~l   94 (178)
                      ..|+++.|++|.|||...- .+.+++
T Consensus        39 k~n~lLVG~~GvGKTalv~-~la~ri   63 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIAE-GLAWRI   63 (268)
T ss_dssp             SCEEEEECCTTSSHHHHHH-HHHHHH
T ss_pred             cCCcEEECCCCCcHHHHHH-HHHHHH
Confidence            4689999999999996543 344444

>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=80.80  E-value=1.1  Score=30.83  Aligned_cols=21  Identities=24%  Similarity=0.278  Sum_probs=14.9

Q ss_pred             EEEEcCCCChHHHHHHHHHHHH
Q psy9277          72 VIAQAQSGTGKTATFSISILQS   93 (178)
Q Consensus        72 v~v~aptGsGKTl~~ll~il~~   93 (178)
                      +++.|+.|||||.. +-.+++.
T Consensus         3 i~v~G~~GsGKTTL-l~~ll~~   23 (244)
T d1yrba1           3 VVFVGTAGSGKTTL-TGEFGRY   23 (244)
T ss_dssp             EEEECSTTSSHHHH-HHHHHHH
T ss_pred             EEEEcCCCCcHHHH-HHHHHHH
Confidence            68899999999954 3334443

>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=80.72  E-value=0.71  Score=34.51  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=18.4

Q ss_pred             HHHHHcCC--cEEEEcCCCChHHHHH
Q psy9277          63 IKPIVKGR--DVIAQAQSGTGKTATF   86 (178)
Q Consensus        63 i~~i~~g~--~v~v~aptGsGKTl~~   86 (178)
                      ++.+++|.  .++..|+||||||...
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            34456775  5788899999999775

>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=80.67  E-value=0.29  Score=34.75  Aligned_cols=20  Identities=25%  Similarity=0.386  Sum_probs=16.8

Q ss_pred             HcCCcEEEEcCCCChHHHHH
Q psy9277          67 VKGRDVIAQAQSGTGKTATF   86 (178)
Q Consensus        67 ~~g~~v~v~aptGsGKTl~~   86 (178)
                      ..|.-+.+.||+|+|||...
T Consensus        24 ~~Ge~~~liGpsGaGKSTll   43 (229)
T d3d31a2          24 ESGEYFVILGPTGAGKTLFL   43 (229)
T ss_dssp             CTTCEEEEECCCTHHHHHHH
T ss_pred             CCCCEEEEECCCCCcHHHHH
Confidence            45788999999999999654

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=80.58  E-value=0.33  Score=36.00  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=14.7

Q ss_pred             cEEEEcCCCChHHHHHH
Q psy9277          71 DVIAQAQSGTGKTATFS   87 (178)
Q Consensus        71 ~v~v~aptGsGKTl~~l   87 (178)
                      .++++||||+|||..+-
T Consensus        55 ~~lf~Gp~G~GKt~lak   71 (315)
T d1qvra3          55 SFLFLGPTGVGKTELAK   71 (315)
T ss_dssp             EEEEBSCSSSSHHHHHH
T ss_pred             EEEEECCCcchHHHHHH
Confidence            57899999999998764