Psyllid ID: psy11637

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60-------
Protein Sequence
MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVFC
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHccccccEEEEEcccccHHHHHHHHHHHccccEEEEEcccEEEc
Secondary Structure Prediction (SSPRO)
cccccccccEEcHHHHHHHHHHHcccccccEEEEEEccccccEEEEEEEEEEcccEEEEEcccEEEc
Coil and Loop (DISEMBL)
mtidlkpsavlrpyQEKSLRKMFgngrarsgvivlpcgagkslvgvtaCCTVRKRALVLCNSGVVFC
Flexible Loop (DISEMBL)
mtidlkpsavlrpyqEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALvlcnsgvvfc
Low Complexity Region (SEG)
MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVFC
Disordered region (IsUnstruct)
**********************FGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVF*
Disordered Region (DISOPRED)
MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVFC
Disordered Region (DISEMBL)
MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVFC
Disordered Region (DISPRO)
MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVFC
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVFC
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	67	2.2.26 [Sep-21-2011]
Q02870	798	DNA excision repair prote	yes	N/A	0.955	0.080	0.953	2e-31
Q4G005	782	TFIIH basal transcription	yes	N/A	0.955	0.081	0.890	1e-27
Q5RA62	782	TFIIH basal transcription	yes	N/A	0.955	0.081	0.890	1e-27
P49135	783	TFIIH basal transcription	yes	N/A	0.955	0.081	0.890	1e-27
Q60HG1	782	TFIIH basal transcription	N/A	N/A	0.955	0.081	0.890	1e-27
P19447	782	TFIIH basal transcription	yes	N/A	0.955	0.081	0.890	1e-27
Q5ZKK7	788	TFIIH basal transcription	yes	N/A	0.955	0.081	0.890	1e-27
Q1RMT1	782	TFIIH basal transcription	yes	N/A	0.955	0.081	0.890	1e-27
Q7ZVV1	782	TFIIH basal transcription	yes	N/A	0.955	0.081	0.875	3e-27
O00835	800	TFIIH basal transcription	yes	N/A	0.955	0.08	0.75	4e-24

>sp|Q02870|ERCC3_DROME DNA excision repair protein haywire OS=Drosophila melanogaster GN=hay PE=1 SV=2

 Score =  134 bits (336), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 61/64 (95%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 322 INIDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 381

Query: 61  NSGV 64
           NSGV
Sbjct: 382 NSGV 385

Probably an ATP-dependent DNA helicase involved in excision repair of DNA. May have a DNA unwinding function.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp|Q4G005|ERCC3_RAT TFIIH basal transcription factor complex helicase XPB subunit OS=Rattus norvegicus GN=Ercc3 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query: 61  NSGV 64
           NS V
Sbjct: 366 NSAV 369

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q5RA62|ERCC3_PONAB TFIIH basal transcription factor complex helicase XPB subunit OS=Pongo abelii GN=ERCC3 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query: 61  NSGV 64
           NS V
Sbjct: 366 NSAV 369

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P49135|ERCC3_MOUSE TFIIH basal transcription factor complex helicase XPB subunit OS=Mus musculus GN=Ercc3 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 307 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 366

Query: 61  NSGV 64
           NS V
Sbjct: 367 NSAV 370

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q60HG1|ERCC3_MACFA TFIIH basal transcription factor complex helicase XPB subunit OS=Macaca fascicularis GN=ERCC3 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query: 61  NSGV 64
           NS V
Sbjct: 366 NSAV 369

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Macaca fascicularis (taxid: 9541)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|P19447|ERCC3_HUMAN TFIIH basal transcription factor complex helicase XPB subunit OS=Homo sapiens GN=ERCC3 PE=1 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query: 61  NSGV 64
           NS V
Sbjct: 366 NSAV 369

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q5ZKK7|ERCC3_CHICK TFIIH basal transcription factor complex helicase XPB subunit OS=Gallus gallus GN=ERCC3 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 303 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 362

Query: 61  NSGV 64
           NS V
Sbjct: 363 NSAV 366

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q1RMT1|ERCC3_BOVIN TFIIH basal transcription factor complex helicase XPB subunit OS=Bos taurus GN=ERCC3 PE=2 SV=1

 Score =  121 bits (303), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query: 61  NSGV 64
           NS V
Sbjct: 366 NSAV 369

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|Q7ZVV1|ERCC3_DANRE TFIIH basal transcription factor complex helicase XPB subunit OS=Danio rerio GN=ercc3 PE=2 SV=1

 Score =  120 bits (300), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/64 (87%), Positives = 59/64 (92%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + +DLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct: 305 INMDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 364

Query: 61  NSGV 64
           NS V
Sbjct: 365 NSSV 368

ATP-dependent 3'-5' DNA helicase, component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. Acts by opening DNA either around the RNA transcription start site or the DNA damage.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

>sp|O00835|ERCC3_DICDI TFIIH basal transcription factor complex helicase repB subunit OS=Dictyostelium discoideum GN=repB PE=2 SV=1

 Score =  109 bits (273), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 48/64 (75%), Positives = 55/64 (85%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKP+ ++RPYQEKSL KMFGNGRARSG+IVLPCGAGKSL G+TA CTV+K  LVLC
Sbjct: 308 LNIDLKPTTMIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLSGITAACTVKKSILVLC 367

Query: 61  NSGV 64
            S V
Sbjct: 368 TSAV 371

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA by opening DNA around the damage, and in RNA transcription by RNA polymerase II by anchoring the CDK-activating kinase (CAK) complex to the core-TFIIH complex.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 2

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	67
66519335	795	PREDICTED: DNA excision repair protein h	0.955	0.080	0.968	4e-30
383849852	788	PREDICTED: DNA excision repair protein h	0.955	0.081	0.968	4e-30
380015695	800	PREDICTED: DNA excision repair protein h	0.955	0.08	0.968	4e-30
380015693	795	PREDICTED: DNA excision repair protein h	0.955	0.080	0.968	4e-30
350412751	804	PREDICTED: DNA excision repair protein h	0.955	0.079	0.968	4e-30
350412749	795	PREDICTED: DNA excision repair protein h	0.955	0.080	0.968	4e-30
340720531	795	PREDICTED: DNA excision repair protein h	0.955	0.080	0.968	4e-30
332022982	793	DNA excision repair protein haywire [Acr	0.955	0.080	0.968	4e-30
307201000	737	TFIIH basal transcription factor complex	0.955	0.086	0.968	4e-30
307169923	805	DNA excision repair protein haywire [Cam	0.955	0.079	0.968	4e-30

>gi|66519335|ref|XP_624125.1| PREDICTED: DNA excision repair protein haywire [Apis mellifera]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 322 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 381

Query: 61  NSGV 64
           NSGV
Sbjct: 382 NSGV 385

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383849852|ref|XP_003700549.1| PREDICTED: DNA excision repair protein haywire-like [Megachile rotundata]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 321 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 380

Query: 61  NSGV 64
           NSGV
Sbjct: 381 NSGV 384

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380015695|ref|XP_003691833.1| PREDICTED: DNA excision repair protein haywire-like isoform 2 [Apis florea]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 327 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 386

Query: 61  NSGV 64
           NSGV
Sbjct: 387 NSGV 390

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380015693|ref|XP_003691832.1| PREDICTED: DNA excision repair protein haywire-like isoform 1 [Apis florea]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 322 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 381

Query: 61  NSGV 64
           NSGV
Sbjct: 382 NSGV 385

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350412751|ref|XP_003489749.1| PREDICTED: DNA excision repair protein haywire-like isoform 2 [Bombus impatiens]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 331 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 390

Query: 61  NSGV 64
           NSGV
Sbjct: 391 NSGV 394

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350412749|ref|XP_003489748.1| PREDICTED: DNA excision repair protein haywire-like isoform 1 [Bombus impatiens]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 322 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 381

Query: 61  NSGV 64
           NSGV
Sbjct: 382 NSGV 385

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340720531|ref|XP_003398689.1| PREDICTED: DNA excision repair protein haywire-like [Bombus terrestris]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 322 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 381

Query: 61  NSGV 64
           NSGV
Sbjct: 382 NSGV 385

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332022982|gb|EGI63247.1| DNA excision repair protein haywire [Acromyrmex echinatior]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 320 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 379

Query: 61  NSGV 64
           NSGV
Sbjct: 380 NSGV 383

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307201000|gb|EFN80971.1| TFIIH basal transcription factor complex helicase XPB subunit [Harpegnathos saltator]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 264 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 323

Query: 61  NSGV 64
           NSGV
Sbjct: 324 NSGV 327

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307169923|gb|EFN62432.1| DNA excision repair protein haywire [Camponotus floridanus]

 Score =  135 bits (339), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 62/64 (96%), Positives = 63/64 (98%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           + IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct: 332 INIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 391

Query: 61  NSGV 64
           NSGV
Sbjct: 392 NSGV 395

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

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	67
FB|FBgn0001179	798	hay "haywire" [Drosophila mela	0.955	0.080	0.953	2.7e-27
UNIPROTKB|G3V1S1	718	ERCC3 "Excision repair cross-c	0.955	0.089	0.890	4.6e-24
UNIPROTKB|E2RN68	779	ERCC3 "Uncharacterized protein	0.955	0.082	0.890	5.5e-24
UNIPROTKB|F1NDN0	782	ERCC3 "TFIIH basal transcripti	0.955	0.081	0.890	5.5e-24
UNIPROTKB|Q1RMT1	782	ERCC3 "TFIIH basal transcripti	0.955	0.081	0.890	5.5e-24
UNIPROTKB|P19447	782	ERCC3 "TFIIH basal transcripti	0.955	0.081	0.890	5.5e-24
UNIPROTKB|F1RXZ5	782	ERCC3 "Uncharacterized protein	0.955	0.081	0.890	5.5e-24
UNIPROTKB|Q5RA62	782	ERCC3 "TFIIH basal transcripti	0.955	0.081	0.890	5.5e-24
UNIPROTKB|Q60HG1	782	ERCC3 "TFIIH basal transcripti	0.955	0.081	0.890	5.5e-24
RGD|1307139	782	Ercc3 "excision repair cross-c	0.955	0.081	0.890	5.5e-24

FB|FBgn0001179 hay "haywire" [Drosophila melanogaster (taxid:7227)]

 Score = 316 (116.3 bits), Expect = 2.7e-27, P = 2.7e-27
 Identities = 61/64 (95%), Positives = 63/64 (98%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC
Sbjct:   322 INIDLKPAAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 381

Query:    61 NSGV 64
             NSGV
Sbjct:   382 NSGV 385

GO:0008344 "adult locomotory behavior" evidence=IMP

GO:0004386 "helicase activity" evidence=ISS

GO:0009411 "response to UV" evidence=IMP

GO:0006289 "nucleotide-excision repair" evidence=ISS

GO:0001113 "transcriptional open complex formation at RNA polymerase II promoter" evidence=ISS

GO:0043140 "ATP-dependent 3'-5' DNA helicase activity" evidence=ISS

GO:0005675 "holo TFIIH complex" evidence=ISS;IDA

GO:0001111 "promoter clearance from RNA polymerase II promoter" evidence=ISS

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

GO:0004003 "ATP-dependent DNA helicase activity" evidence=NAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IMP

UNIPROTKB|G3V1S1 ERCC3 "Excision repair cross-complementing rodent repair deficiency, complementation group 3 (Xeroderma pigmentosum group B complementing), isoform CRA_b" [Homo sapiens (taxid:9606)]

 Score = 285 (105.4 bits), Expect = 4.6e-24, P = 4.6e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   242 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 301

Query:    61 NSGV 64
             NS V
Sbjct:   302 NSAV 305

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

GO:0001666 "response to hypoxia" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0006468 "protein phosphorylation" evidence=IEA

GO:0009650 "UV protection" evidence=IEA

GO:0032564 "dATP binding" evidence=IEA

GO:0042277 "peptide binding" evidence=IEA

UNIPROTKB|E2RN68 ERCC3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   303 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 362

Query:    61 NSGV 64
             NS V
Sbjct:   363 NSAV 366

GO:0047485 "protein N-terminus binding" evidence=IEA

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

GO:0043138 "3'-5' DNA helicase activity" evidence=IEA

GO:0035315 "hair cell differentiation" evidence=IEA

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=IEA

GO:0009650 "UV protection" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0008104 "protein localization" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=IEA

GO:0000075 "cell cycle checkpoint" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|F1NDN0 ERCC3 "TFIIH basal transcription factor complex helicase XPB subunit" [Gallus gallus (taxid:9031)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   305 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 364

Query:    61 NSGV 64
             NS V
Sbjct:   365 NSAV 368

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

UNIPROTKB|Q1RMT1 ERCC3 "TFIIH basal transcription factor complex helicase XPB subunit" [Bos taurus (taxid:9913)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query:    61 NSGV 64
             NS V
Sbjct:   366 NSAV 369

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=ISS

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=ISS

GO:0000075 "cell cycle checkpoint" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

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

GO:0043138 "3'-5' DNA helicase activity" evidence=ISS

GO:0035315 "hair cell differentiation" evidence=ISS

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0009411 "response to UV" evidence=ISS

GO:0008104 "protein localization" evidence=ISS

GO:0008094 "DNA-dependent ATPase activity" evidence=ISS

GO:0008022 "protein C-terminus binding" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0006917 "induction of apoptosis" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0006289 "nucleotide-excision repair" evidence=ISS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006265 "DNA topological change" evidence=ISS

GO:0005675 "holo TFIIH complex" evidence=ISS

GO:0047485 "protein N-terminus binding" evidence=ISS

GO:0009650 "UV protection" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|P19447 ERCC3 "TFIIH basal transcription factor complex helicase XPB subunit" [Homo sapiens (taxid:9606)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query:    61 NSGV 64
             NS V
Sbjct:   366 NSAV 369

GO:0000439 "core TFIIH complex" evidence=IEA

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

GO:0001666 "response to hypoxia" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005525 "GTP binding" evidence=IEA

GO:0009650 "UV protection" evidence=IEA

GO:0032564 "dATP binding" evidence=IEA

GO:0042277 "peptide binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0047485 "protein N-terminus binding" evidence=IPI

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA;IMP;TAS

GO:0006265 "DNA topological change" evidence=IMP

GO:0005675 "holo TFIIH complex" evidence=IDA;TAS

GO:0006917 "induction of apoptosis" evidence=IDA;IMP

GO:0043138 "3'-5' DNA helicase activity" evidence=IDA;IMP

GO:0005634 "nucleus" evidence=TAS

GO:0003677 "DNA binding" evidence=TAS

GO:0008094 "DNA-dependent ATPase activity" evidence=IDA;IMP

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=IDA;TAS

GO:0004672 "protein kinase activity" evidence=IDA

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=IMP

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

GO:0008022 "protein C-terminus binding" evidence=IPI

GO:0006289 "nucleotide-excision repair" evidence=IMP;TAS

GO:0008104 "protein localization" evidence=IMP

GO:0006281 "DNA repair" evidence=IMP;TAS

GO:0035315 "hair cell differentiation" evidence=IMP

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=IMP

GO:0016887 "ATPase activity" evidence=IDA

GO:0000075 "cell cycle checkpoint" evidence=IMP

GO:0009411 "response to UV" evidence=IMP

GO:0006979 "response to oxidative stress" evidence=IMP

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=IDA

GO:0008134 "transcription factor binding" evidence=IDA

GO:0000718 "nucleotide-excision repair, DNA damage removal" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006360 "transcription from RNA polymerase I promoter" evidence=TAS

GO:0006361 "transcription initiation from RNA polymerase I promoter" evidence=TAS

GO:0006362 "transcription elongation from RNA polymerase I promoter" evidence=TAS

GO:0006363 "termination of RNA polymerase I transcription" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

UNIPROTKB|F1RXZ5 ERCC3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query:    61 NSGV 64
             NS V
Sbjct:   366 NSAV 369

GO:0047485 "protein N-terminus binding" evidence=IEA

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

GO:0043138 "3'-5' DNA helicase activity" evidence=IEA

GO:0035315 "hair cell differentiation" evidence=IEA

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=IEA

GO:0009650 "UV protection" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0008104 "protein localization" evidence=IEA

GO:0008022 "protein C-terminus binding" evidence=IEA

GO:0006979 "response to oxidative stress" evidence=IEA

GO:0006917 "induction of apoptosis" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=IEA

GO:0000075 "cell cycle checkpoint" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB|Q5RA62 ERCC3 "TFIIH basal transcription factor complex helicase XPB subunit" [Pongo abelii (taxid:9601)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query:    61 NSGV 64
             NS V
Sbjct:   366 NSAV 369

GO:0000075 "cell cycle checkpoint" evidence=ISS

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=ISS

GO:0005675 "holo TFIIH complex" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0006265 "DNA topological change" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=ISS

GO:0006289 "nucleotide-excision repair" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0006917 "induction of apoptosis" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0008022 "protein C-terminus binding" evidence=ISS

GO:0008104 "protein localization" evidence=ISS

GO:0009411 "response to UV" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=ISS

GO:0035315 "hair cell differentiation" evidence=ISS

GO:0043138 "3'-5' DNA helicase activity" evidence=ISS

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

GO:0047485 "protein N-terminus binding" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

GO:0008094 "DNA-dependent ATPase activity" evidence=ISS

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=ISS

UNIPROTKB|Q60HG1 ERCC3 "TFIIH basal transcription factor complex helicase XPB subunit" [Macaca fascicularis (taxid:9541)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query:    61 NSGV 64
             NS V
Sbjct:   366 NSAV 369

GO:0000075 "cell cycle checkpoint" evidence=ISS

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=ISS

GO:0005675 "holo TFIIH complex" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0006265 "DNA topological change" evidence=ISS

GO:0006281 "DNA repair" evidence=ISS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=ISS

GO:0006289 "nucleotide-excision repair" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0006917 "induction of apoptosis" evidence=ISS

GO:0006979 "response to oxidative stress" evidence=ISS

GO:0008022 "protein C-terminus binding" evidence=ISS

GO:0008104 "protein localization" evidence=ISS

GO:0009411 "response to UV" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=ISS

GO:0035315 "hair cell differentiation" evidence=ISS

GO:0043138 "3'-5' DNA helicase activity" evidence=ISS

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

GO:0047485 "protein N-terminus binding" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

GO:0008094 "DNA-dependent ATPase activity" evidence=ISS

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=ISS

RGD|1307139 Ercc3 "excision repair cross-complementing rodent repair deficiency, complementation group 3" [Rattus norvegicus (taxid:10116)]

 Score = 285 (105.4 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 57/64 (89%), Positives = 59/64 (92%)

Query:     1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
             + IDLKP+AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA CTVRKR LVL 
Sbjct:   306 INIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLG 365

Query:    61 NSGV 64
             NS V
Sbjct:   366 NSAV 369

GO:0000075 "cell cycle checkpoint" evidence=IEA;ISO

GO:0000439 "core TFIIH complex" evidence=IEA

GO:0000441 "SSL2-core TFIIH complex" evidence=IDA

GO:0000717 "nucleotide-excision repair, DNA duplex unwinding" evidence=IEA;ISO

GO:0001666 "response to hypoxia" evidence=IEP

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IDA

GO:0004672 "protein kinase activity" evidence=ISO;ISS

GO:0005524 "ATP binding" evidence=IDA

GO:0005525 "GTP binding" evidence=IDA

GO:0005675 "holo TFIIH complex" evidence=ISO;ISS

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0006265 "DNA topological change" evidence=IEA;ISO

GO:0006281 "DNA repair" evidence=ISO

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=IEA;ISO

GO:0006289 "nucleotide-excision repair" evidence=ISO

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO;ISS

GO:0006468 "protein phosphorylation" evidence=IDA

GO:0006917 "induction of apoptosis" evidence=IEA;ISO

GO:0006979 "response to oxidative stress" evidence=IEA;ISO

GO:0008022 "protein C-terminus binding" evidence=IEA;ISO

GO:0008094 "DNA-dependent ATPase activity" evidence=ISO;ISS

GO:0008104 "protein localization" evidence=IEA;ISO

GO:0008134 "transcription factor binding" evidence=IEA;ISO

GO:0008353 "RNA polymerase II carboxy-terminal domain kinase activity" evidence=ISO;ISS;IDA

GO:0009411 "response to UV" evidence=ISO

GO:0009650 "UV protection" evidence=IEA;ISO

GO:0016887 "ATPase activity" evidence=ISO;IDA

GO:0032564 "dATP binding" evidence=IDA

GO:0033683 "nucleotide-excision repair, DNA incision" evidence=IEA;ISO

GO:0035315 "hair cell differentiation" evidence=IEA;ISO

GO:0042277 "peptide binding" evidence=IDA

GO:0043138 "3'-5' DNA helicase activity" evidence=IEA;ISO

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

GO:0047485 "protein N-terminus binding" evidence=IEA;ISO

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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)
Q1RMT1	ERCC3_BOVIN	3, ., 6, ., 4, ., 1, 2	0.8906	0.9552	0.0818	yes	N/A
Q8SSK1	RAD25_ENCCU	3, ., 6, ., 4, ., 1, 2	0.6406	0.9552	0.0919	yes	N/A
Q38861	XPB1_ARATH	3, ., 6, ., 4, ., 1, 2	0.6562	0.9552	0.0834	yes	N/A
Q5ZKK7	ERCC3_CHICK	3, ., 6, ., 4, ., 1, 2	0.8906	0.9552	0.0812	yes	N/A
Q7ZVV1	ERCC3_DANRE	3, ., 6, ., 4, ., 1, 2	0.875	0.9552	0.0818	yes	N/A
Q5RA62	ERCC3_PONAB	3, ., 6, ., 4, ., 1, 2	0.8906	0.9552	0.0818	yes	N/A
Q9FUG4	XPB2_ARATH	3, ., 6, ., 4, ., 1, 2	0.6562	0.9552	0.0835	yes	N/A
O13768	ERCC3_SCHPO	3, ., 6, ., 4, ., 1, 2	0.7343	0.9552	0.0796	yes	N/A
O00835	ERCC3_DICDI	3, ., 6, ., 4, ., 1, 2	0.75	0.9552	0.08	yes	N/A
Q02870	ERCC3_DROME	3, ., 6, ., 4, ., 1, 2	0.9531	0.9552	0.0802	yes	N/A
Q4G005	ERCC3_RAT	3, ., 6, ., 4, ., 1, 2	0.8906	0.9552	0.0818	yes	N/A
P49135	ERCC3_MOUSE	3, ., 6, ., 4, ., 1, 2	0.8906	0.9552	0.0817	yes	N/A
Q00578	RAD25_YEAST	3, ., 6, ., 4, ., 1, 2	0.7343	0.9552	0.0759	yes	N/A
P19447	ERCC3_HUMAN	3, ., 6, ., 4, ., 1, 2	0.8906	0.9552	0.0818	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	67
TIGR00603	732	TIGR00603, rad25, DNA repair helicase rad25	3e-44
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	1e-16
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	1e-06
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-05

>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25

 Score =  149 bits (378), Expect = 3e-44
 Identities = 50/62 (80%), Positives = 54/62 (87%)

Query: 3   IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNS 62
           IDLKP+  +RPYQEKSL KMFGNGRARSG+IVLPCGAGKSLVGVTA CTV+K  LVLC S
Sbjct: 248 IDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTS 307

Query: 63  GV 64
            V
Sbjct: 308 AV 309

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 732

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

 Score = 71.3 bits (175), Expect = 1e-16
 Identities = 25/52 (48%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 10 VLRPYQEKSLRKMFGNGRA-RSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           LRPYQE++L  +  N R  R GVIVLP GAGK++V   A   +++  LVL 
Sbjct: 36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLV 87

Length = 442

>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit

 Score = 41.4 bits (98), Expect = 1e-06
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)

Query: 10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVG---VTACCTVRKRALVLCNS 62
           LRPYQE+++ ++    R   G+IV+  G+GK+L     +      +K+ L +   
Sbjct: 3  ELRPYQEEAIERLLEKKR---GLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPR 55

Length = 100

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

 Score = 40.2 bits (94), Expect = 1e-05
 Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 7/63 (11%)

Query: 3  IDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC-----CTVRKRAL 57
          I+      LRPYQ++++  +    R    ++  P G+GK+L  +             R L
Sbjct: 1  IEKFGFEPLRPYQKEAIEALLSGLR--DVILAAPTGSGKTLAALLPALEALKRGKGGRVL 58

Query: 58 VLC 60
          VL 
Sbjct: 59 VLV 61

Length = 201

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	67
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.67
KOG1123|consensus	776		99.59
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.55
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.5
PHA02558	501	uvsW UvsW helicase; Provisional	99.24
KOG0354|consensus	746		99.24
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.19
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.14
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.06
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.05
COG4096	875	HsdR Type I site-specific restriction-modification	99.04
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	98.98
PRK13766	773	Hef nuclease; Provisional	98.95
PRK01172	674	ski2-like helicase; Provisional	98.95
COG4889	1518	Predicted helicase [General function prediction on	98.94
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.92
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.91
PRK02362	737	ski2-like helicase; Provisional	98.88
PTZ00424	401	helicase 45; Provisional	98.88
COG1204	766	Superfamily II helicase [General function predicti	98.87
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.84
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.82
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	98.81
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	98.79
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.76
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.74
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.73
PRK00254	720	ski2-like helicase; Provisional	98.71
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.71
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.7
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	98.68
PRK13767	876	ATP-dependent helicase; Provisional	98.66
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.65
PRK05580	679	primosome assembly protein PriA; Validated	98.64
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	98.63
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	98.62
KOG1802|consensus	935		98.6
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.58
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.58
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.57
PRK09401	1176	reverse gyrase; Reviewed	98.56
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	98.53
PTZ00110	545	helicase; Provisional	98.52
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.52
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	98.51
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	98.5
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	98.43
PRK14701	1638	reverse gyrase; Provisional	98.43
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.41
KOG0351|consensus	941		98.38
KOG0353|consensus	695		98.35
COG1205	851	Distinct helicase family with a unique C-terminal	98.34
KOG1803|consensus	649		98.32
PRK10689	1147	transcription-repair coupling factor; Provisional	98.32
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	98.32
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	98.31
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	98.26
PF13245	76	AAA_19: Part of AAA domain	98.26
PRK15483	986	type III restriction-modification system StyLTI en	98.19
COG1201	814	Lhr Lhr-like helicases [General function predictio	98.18
KOG0952|consensus	1230		98.14
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.14
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.09
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.08
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.08
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	98.07
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	97.97
KOG0352|consensus	641		97.97
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	97.97
PHA02653	675	RNA helicase NPH-II; Provisional	97.87
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.87
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.86
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	97.86
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.84
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.77
PRK09694	878	helicase Cas3; Provisional	97.76
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	97.66
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	97.64
COG1202	830	Superfamily II helicase, archaea-specific [General	97.64
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	97.59
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.59
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.58
KOG0350|consensus	620		97.57
PRK04914	956	ATP-dependent helicase HepA; Validated	97.54
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.52
TIGR00595	505	priA primosomal protein N'. All proteins in this f	97.47
PRK09200	790	preprotein translocase subunit SecA; Reviewed	97.47
PRK05298	652	excinuclease ABC subunit B; Provisional	97.47
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.45
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.39
COG1198	730	PriA Primosomal protein N' (replication factor Y)	97.39
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	97.35
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.34
smart00382	148	AAA ATPases associated with a variety of cellular	97.34
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.31
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.3
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	97.3
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.28
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.24
KOG0335|consensus	482		97.24
PRK08181	269	transposase; Validated	97.21
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.21
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	97.14
PRK06526	254	transposase; Provisional	97.09
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.09
KOG0348|consensus	708		97.07
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.04
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	97.04
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.02
KOG0947|consensus	1248		96.97
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.96
KOG0390|consensus	776		96.96
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	96.96
KOG1805|consensus	1100		96.95
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.95
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	96.92
PRK10536	262	hypothetical protein; Provisional	96.91
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.91
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.9
KOG1000|consensus	689		96.88
KOG0392|consensus	1549		96.87
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.86
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.84
COG3587	985	Restriction endonuclease [Defense mechanisms]	96.83
KOG0385|consensus	971		96.82
KOG0951|consensus	1674		96.81
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.8
KOG0387|consensus	923		96.8
KOG1807|consensus	1025		96.78
KOG1133|consensus	821		96.76
PRK13851	344	type IV secretion system protein VirB11; Provision	96.76
PRK05642	234	DNA replication initiation factor; Validated	96.74
PRK09183	259	transposase/IS protein; Provisional	96.73
PRK10436	462	hypothetical protein; Provisional	96.72
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	96.71
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	96.71
PRK08084	235	DNA replication initiation factor; Provisional	96.7
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	96.69
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.66
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.66
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.6
KOG0345|consensus	567		96.6
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.59
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.57
KOG0330|consensus	476		96.57
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	96.56
KOG0948|consensus	1041		96.56
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.55
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.54
KOG1806|consensus	1320		96.53
KOG0949|consensus	1330		96.49
KOG0386|consensus	1157		96.48
PRK12402	337	replication factor C small subunit 2; Reviewed	96.41
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.4
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.37
PHA02244	383	ATPase-like protein	96.34
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.34
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	96.34
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	96.33
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	96.32
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.29
KOG1132|consensus	945		96.28
PF00004	132	AAA: ATPase family associated with various cellula	96.25
PRK00440	319	rfc replication factor C small subunit; Reviewed	96.24
PRK11054	684	helD DNA helicase IV; Provisional	96.23
PLN03025	319	replication factor C subunit; Provisional	96.2
PLN02165	334	adenylate isopentenyltransferase	96.19
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.18
PRK08727	233	hypothetical protein; Validated	96.18
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.17
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.17
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	96.16
KOG0340|consensus	442		96.16
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	96.16
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.15
TIGR02237	209	recomb_radB DNA repair and recombination protein R	96.14
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	96.1
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.09
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.09
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.08
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.05
KOG0328|consensus	400		96.05
PF12846	304	AAA_10: AAA-like domain	96.05
KOG0389|consensus	941		96.03
PRK13342	413	recombination factor protein RarA; Reviewed	96.0
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	95.99
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.98
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.94
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	95.93
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	95.93
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.91
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	95.89
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.88
KOG0344|consensus	593		95.83
KOG0342|consensus	543		95.82
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	95.81
KOG0391|consensus	1958		95.81
PRK04328	249	hypothetical protein; Provisional	95.8
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	95.77
PRK06893	229	DNA replication initiation factor; Validated	95.75
PRK04195	482	replication factor C large subunit; Provisional	95.75
COG2256	436	MGS1 ATPase related to the helicase subunit of the	95.74
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	95.73
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	95.73
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.72
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.68
KOG0384|consensus	1373		95.68
PRK13107	908	preprotein translocase subunit SecA; Reviewed	95.67
PRK06835	329	DNA replication protein DnaC; Validated	95.67
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.66
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.66
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.64
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.63
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	95.62
PHA02774	613	E1; Provisional	95.6
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	95.6
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.6
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.59
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.57
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	95.56
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	95.56
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.56
PHA02544	316	44 clamp loader, small subunit; Provisional	95.56
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	95.56
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	95.55
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.55
PRK06067	234	flagellar accessory protein FlaH; Validated	95.53
PRK12377	248	putative replication protein; Provisional	95.52
KOG0334|consensus	997		95.5
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	95.48
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	95.46
COG0606	490	Predicted ATPase with chaperone activity [Posttran	95.44
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	95.43
PRK07952	244	DNA replication protein DnaC; Validated	95.43
PRK12904	830	preprotein translocase subunit SecA; Reviewed	95.42
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.41
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.41
KOG0745|consensus	564		95.41
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	95.41
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	95.4
PRK05973	237	replicative DNA helicase; Provisional	95.4
KOG1002|consensus	791		95.39
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.38
PRK00131	175	aroK shikimate kinase; Reviewed	95.36
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	95.35
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	95.34
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	95.33
PRK08118	167	topology modulation protein; Reviewed	95.33
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.29
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	95.28
PRK07261	171	topology modulation protein; Provisional	95.26
TIGR02236	310	recomb_radA DNA repair and recombination protein R	95.26
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.25
KOG4439|consensus	901		95.24
KOG0989|consensus	346		95.24
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	95.23
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	95.21
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.21
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	95.2
PF13555	62	AAA_29: P-loop containing region of AAA domain	95.19
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	95.16
PRK13764	602	ATPase; Provisional	95.14
PRK08233	182	hypothetical protein; Provisional	95.12
PRK03992	389	proteasome-activating nucleotidase; Provisional	95.1
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.1
PRK14532	188	adenylate kinase; Provisional	95.09
PRK12326	764	preprotein translocase subunit SecA; Reviewed	95.04
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	95.03
KOG4284|consensus	980		94.98
PRK14530	215	adenylate kinase; Provisional	94.97
PRK04296	190	thymidine kinase; Provisional	94.95
TIGR00174	287	miaA tRNA isopentenyltransferase (miaA). Catalyzes	94.95
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	94.95
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	94.94
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	94.9
KOG1131|consensus	755		94.88
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.83
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	94.82
) 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	94.78
PRK13341	725	recombination factor protein RarA/unknown domain f	94.77
KOG0331|consensus	519		94.76
CHL00095	821	clpC Clp protease ATP binding subunit	94.76
PF13479	213	AAA_24: AAA domain	94.76
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.75
PRK08939	306	primosomal protein DnaI; Reviewed	94.74
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.73
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	94.72
PRK13947	171	shikimate kinase; Provisional	94.72
PRK03839	180	putative kinase; Provisional	94.69
KOG2373|consensus	514		94.69
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	94.68
PRK06217	183	hypothetical protein; Validated	94.66
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	94.64
KOG0346|consensus	569		94.62
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.6
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.58
PRK04301	317	radA DNA repair and recombination protein RadA; Va	94.57
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.56
COG3973	747	Superfamily I DNA and RNA helicases [General funct	94.51
TIGR00064	272	ftsY signal recognition particle-docking protein F	94.5
KOG0731|consensus	774		94.49
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	94.46
PHA00729	226	NTP-binding motif containing protein	94.46
KOG0338|consensus	691		94.46
PRK00300	205	gmk guanylate kinase; Provisional	94.44
PRK10416	318	signal recognition particle-docking protein FtsY;	94.44
KOG0922|consensus	674		94.43
PRK06762	166	hypothetical protein; Provisional	94.43
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	94.43
PRK09302	509	circadian clock protein KaiC; Reviewed	94.41
PRK09354	349	recA recombinase A; Provisional	94.38
PLN02748	468	tRNA dimethylallyltransferase	94.38
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	94.37
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.37
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.36
PRK14531	183	adenylate kinase; Provisional	94.31
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	94.31
COG1137	243	YhbG ABC-type (unclassified) transport system, ATP	94.3
cd01368	345	KISc_KIF23_like Kinesin motor domain, KIF23-like s	94.3
PRK14737	186	gmk guanylate kinase; Provisional	94.28
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	94.28
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	94.28
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.27
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	94.26
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	94.26
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	94.2
PRK06921	266	hypothetical protein; Provisional	94.19
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.19
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	94.18
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	94.13
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	94.12
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.12
KOG0388|consensus	1185		94.1
PLN02840	421	tRNA dimethylallyltransferase	94.09
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	94.08
KOG2228|consensus	408		94.07
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	94.06
PRK06696	223	uridine kinase; Validated	94.05
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	94.05
PRK05057	172	aroK shikimate kinase I; Reviewed	94.04
PRK06547	172	hypothetical protein; Provisional	94.03
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	94.02
PRK05480	209	uridine/cytidine kinase; Provisional	93.99
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	93.99
CHL00181	287	cbbX CbbX; Provisional	93.98
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	93.98
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	93.94
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	93.92
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.89
PRK11823	446	DNA repair protein RadA; Provisional	93.88
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	93.88
KOG0090|consensus	238		93.87
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.86
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.84
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	93.83
cd01365	356	KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like p	93.79
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	93.78
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	93.77
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	93.74
cd01373	337	KISc_KLP2_like Kinesin motor domain, KLP2-like sub	93.73
cd01370	338	KISc_KIP3_like Kinesin motor domain, KIP3-like sub	93.73
KOG0341|consensus	610		93.72
PRK10865	857	protein disaggregation chaperone; Provisional	93.72
cd01376	319	KISc_KID_like Kinesin motor domain, KIF22/Kid-like	93.72
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	93.72
TIGR02746	797	TraC-F-type type-IV secretion system protein TraC.	93.7
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	93.7
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	93.68
PRK13873	811	conjugal transfer ATPase TrbE; Provisional	93.67
PRK08116	268	hypothetical protein; Validated	93.65
PRK09302	509	circadian clock protein KaiC; Reviewed	93.65
PHA02624	647	large T antigen; Provisional	93.62
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	93.62
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	93.61
PRK13949	169	shikimate kinase; Provisional	93.6
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	93.6
PF05729	166	NACHT: NACHT domain	93.59
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	93.59
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	93.58
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	93.57
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	93.56
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	93.55
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	93.54
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.51
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	93.51
PRK08699	325	DNA polymerase III subunit delta'; Validated	93.51
PTZ00088	229	adenylate kinase 1; Provisional	93.5
PRK00279	215	adk adenylate kinase; Reviewed	93.5
PRK14528	186	adenylate kinase; Provisional	93.49
cd01367	322	KISc_KIF2_like Kinesin motor domain, KIF2-like gro	93.49
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	93.48
PRK06620	214	hypothetical protein; Validated	93.43
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	93.42
KOG1533|consensus	290		93.34
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	93.34
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	93.34
CHL00195	489	ycf46 Ycf46; Provisional	93.32
PRK14738	206	gmk guanylate kinase; Provisional	93.32
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	93.32
PRK02496	184	adk adenylate kinase; Provisional	93.31
PRK04841	903	transcriptional regulator MalT; Provisional	93.29
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	93.29
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	93.28
PRK04182	180	cytidylate kinase; Provisional	93.27
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	93.26
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	93.24
PRK04220	301	2-phosphoglycerate kinase; Provisional	93.21
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	93.21
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	93.18
PRK01184	184	hypothetical protein; Provisional	93.16
cd01375	334	KISc_KIF9_like Kinesin motor domain, KIF9-like sub	93.15
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	93.14
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	93.13
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	93.11
PRK08356	195	hypothetical protein; Provisional	93.11
KOG0923|consensus	902		93.11
PRK08533	230	flagellar accessory protein FlaH; Reviewed	93.09
PRK00771	437	signal recognition particle protein Srp54; Provisi	93.06
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	93.05
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	93.03
PRK13880	636	conjugal transfer coupling protein TraG; Provision	93.02
PRK10867	433	signal recognition particle protein; Provisional	93.01
cd01128	249	rho_factor Transcription termination factor rho is	92.98
PRK09087	226	hypothetical protein; Validated	92.98
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	92.98
TIGR00929	785	VirB4_CagE type IV secretion/conjugal transfer ATP	92.94
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	92.94
PRK13531	498	regulatory ATPase RavA; Provisional	92.85
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.83
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	92.81
PRK13850	670	type IV secretion system protein VirD4; Provisiona	92.8
COG0714	329	MoxR-like ATPases [General function prediction onl	92.77
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	92.76
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	92.76
PTZ00301	210	uridine kinase; Provisional	92.68
TIGR00618	1042	sbcc exonuclease SbcC. This family is based on the	92.63
TIGR00959	428	ffh signal recognition particle protein. This mode	92.61
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	92.6
cd01369	325	KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy	92.49
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	92.48
TIGR00235	207	udk uridine kinase. Model contains a number of lon	92.48
cd01374	321	KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like	92.48
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	92.47
PF13304	303	AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T	92.46
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	92.42
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	92.42
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	92.4
PRK13946	184	shikimate kinase; Provisional	92.39
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	92.38
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	92.36
CHL00122	870	secA preprotein translocase subunit SecA; Validate	92.35
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.34
PTZ00112	1164	origin recognition complex 1 protein; Provisional	92.34
PRK13948	182	shikimate kinase; Provisional	92.32
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	92.29
TIGR00767	415	rho transcription termination factor Rho. Members	92.29
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	92.29
PRK12608	380	transcription termination factor Rho; Provisional	92.28
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	92.26
PHA02530	300	pseT polynucleotide kinase; Provisional	92.25
PRK03731	171	aroL shikimate kinase II; Reviewed	92.22
PRK00625	173	shikimate kinase; Provisional	92.18
PRK14527	191	adenylate kinase; Provisional	92.16
KOG0951|consensus	1674		92.16
cd00106	328	KISc Kinesin motor domain. This catalytic (head) d	92.16
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	92.15
PRK05541	176	adenylylsulfate kinase; Provisional	92.13
COG0610	962	Type I site-specific restriction-modification syst	92.13
cd01371	333	KISc_KIF3 Kinesin motor domain, kinesins II or KIF	92.07
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	92.04
KOG0343|consensus	758		92.04
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	92.04
PLN02200	234	adenylate kinase family protein	92.03
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	92.02
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	91.97
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	91.97
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	91.94
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	91.93
CHL00176	638	ftsH cell division protein; Validated	91.92
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	91.91
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	91.91
PF13173	128	AAA_14: AAA domain	91.9
cd03279	213	ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complex	91.9
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	91.89
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	91.86
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	91.86
PLN02199	303	shikimate kinase	91.84
PRK13721	844	conjugal transfer ATP-binding protein TraC; Provis	91.83
PF00005	137	ABC_tran: ABC transporter This structure is on hol	91.83
TIGR00665	434	DnaB replicative DNA helicase. This model describe	91.82
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	91.81
PF09439	181	SRPRB: Signal recognition particle receptor beta s	91.81
PRK14974	336	cell division protein FtsY; Provisional	91.79
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	91.78
COG0411	250	LivG ABC-type branched-chain amino acid transport	91.78
PRK06964	342	DNA polymerase III subunit delta'; Validated	91.78
PRK13765	637	ATP-dependent protease Lon; Provisional	91.78
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	91.7
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	91.67
KOG0991|consensus	333		91.63

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.67  E-value=2.8e-18  Score=128.12  Aligned_cols=66  Identities=76%  Similarity=1.248  Sum_probs=58.7

Q ss_pred             CccccccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecceee
Q psy11637          1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVF   66 (67)
Q Consensus         1 ~~~~l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~v   66 (67)
                      ++++|.+.+.|||||++++++|+..+..++|+|++|||+|||++++.+++..++++||+||+..+|
T Consensus       246 ~~i~L~~~~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~~l~k~tLILvps~~Lv  311 (732)
T TIGR00603       246 LNIDLKPTTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAACTVKKSCLVLCTSAVSV  311 (732)
T ss_pred             CCcccccCCCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHHHhCCCEEEEeCcHHHH
Confidence            467788889999999999999997654468999999999999999999999999999999997654

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).

>KOG1123|consensus

Probab=99.59  E-value=2.3e-15  Score=109.98  Aligned_cols=66  Identities=74%  Similarity=1.244  Sum_probs=63.0

Q ss_pred             CccccccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecceee
Q psy11637          1 MTIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVF   66 (67)
Q Consensus         1 ~~~~l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~v   66 (67)
                      |+|+|.+...+||||+..+.+.|.++..++|+|++|+|+|||+++..+++..+++.|++|.+.++|
T Consensus       293 l~idLKPst~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~tikK~clvLcts~VSV  358 (776)
T KOG1123|consen  293 LDIDLKPSTQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACTIKKSCLVLCTSAVSV  358 (776)
T ss_pred             CCcCcCcccccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeeeecccEEEEecCccCH
Confidence            578999999999999999999999888899999999999999999999999999999999999886

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

Probab=99.55  E-value=2.6e-16  Score=111.71  Aligned_cols=60  Identities=42%  Similarity=0.646  Sum_probs=53.2

Q ss_pred             ccceeeccchhhHHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          6 KPSAVLRPYQEKSLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         6 ~~~~~lR~yQ~~av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ...+.|||||++|+++|.+... ++++++++|||+|||++++.++.....++|||||+..+
T Consensus        32 ~~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~~~Lvlv~~~~L   92 (442)
T COG1061          32 AFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRSTLVLVPTKEL   92 (442)
T ss_pred             ccCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcCCEEEEECcHHH
Confidence            4567899999999999998521 48999999999999999999999999999999999754

>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=99.50  E-value=9.8e-16  Score=94.23  Aligned_cols=57  Identities=19%  Similarity=0.469  Sum_probs=46.4

Q ss_pred             ceeeccchhhHHHHHhcC---C-cceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN---G-RARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~---~-~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      +++|||||+++++++.+.   . ..+++++.+|||||||.+++.++.++..+++|++|+..
T Consensus         1 ~~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~~~l~~~p~~~   61 (184)
T PF04851_consen    1 KYKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELARKVLIVAPNIS   61 (184)
T ss_dssp             --EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHCEEEEEESSHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccccceeEecCHHH
Confidence            368999999999998852   1 23789999999999999999888877669999999864

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 ....

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.24  E-value=6.5e-13  Score=95.37  Aligned_cols=55  Identities=20%  Similarity=0.256  Sum_probs=45.4

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE----EEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC----TVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~----~~~~~~lil~p~~~~   65 (67)
                      ...|||||++++..++++   +++++++|||+|||.++..++.    ..+.++||++||..+
T Consensus       112 ~~~~r~~Q~~av~~~l~~---~~~il~apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL  170 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKN---NRRLLNLPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSL  170 (501)
T ss_pred             cCCCCHHHHHHHHHHHhc---CceEEEeCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHH
Confidence            368999999999999986   5789999999999998866543    223499999999754

>KOG0354|consensus

Probab=99.24  E-value=1.1e-12  Score=98.25  Aligned_cols=58  Identities=21%  Similarity=0.419  Sum_probs=50.3

Q ss_pred             cccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecceee
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVVF   66 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~v   66 (67)
                      ....+.||+||++.++..+ .   ++.+|.+|||+|||++|+-++...     +++++|+||+...|
T Consensus        57 ~p~~~~lR~YQ~eivq~AL-g---kNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv  119 (746)
T KOG0354|consen   57 YPTNLELRNYQEELVQPAL-G---KNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLV  119 (746)
T ss_pred             ccCcccccHHHHHHhHHhh-c---CCeEEEeecCCCccchHHHHHHHHHhcCCcceEEEeeCCchHH
Confidence            3456899999999999999 4   699999999999999999888753     68999999997654

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

Probab=99.19  E-value=9.2e-13  Score=102.16  Aligned_cols=59  Identities=20%  Similarity=0.314  Sum_probs=46.3

Q ss_pred             cceeeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~   65 (67)
                      ..+.+||||.+|++++.++  ...++++++||||||||.+++.++.++     .+++||++|++.+
T Consensus       410 ~~~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L  475 (1123)
T PRK11448        410 YGLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSAL  475 (1123)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHH
Confidence            3468999999999887742  112679999999999999987776542     3699999998754

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.14  E-value=3.3e-12  Score=90.88  Aligned_cols=54  Identities=24%  Similarity=0.310  Sum_probs=46.4

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ..+||+|++++..++++   ++.++++|||+|||++++..+....+.++|++|+..+
T Consensus        10 ~~~r~~Q~~ai~~~l~g---~dvlv~apTGsGKTl~y~lp~l~~~~~~lVi~P~~~L   63 (470)
T TIGR00614        10 SSFRPVQLEVINAVLLG---RDCFVVMPTGGGKSLCYQLPALCSDGITLVISPLISL   63 (470)
T ss_pred             CCCCHHHHHHHHHHHcC---CCEEEEcCCCCcHhHHHHHHHHHcCCcEEEEecHHHH
Confidence            37899999999999987   5899999999999998876655567889999998753

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

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.06  E-value=1.3e-11  Score=89.85  Aligned_cols=53  Identities=25%  Similarity=0.374  Sum_probs=46.0

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      .|||+|++++..++++   ++.+++||||+|||++++..+....+.++|++|+.++
T Consensus        13 ~fr~~Q~~~i~~il~g---~dvlv~~PTG~GKTl~y~lpal~~~g~~lVisPl~sL   65 (591)
T TIGR01389        13 DFRPGQEEIISHVLDG---RDVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISL   65 (591)
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEcCCCccHhHHHHHHHHHcCCcEEEEcCCHHH
Confidence            6999999999999986   5899999999999999976655567889999998653

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=99.05  E-value=1.1e-11  Score=90.78  Aligned_cols=53  Identities=25%  Similarity=0.367  Sum_probs=46.0

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      .+||+|++++..+++.   ++.++++|||+|||++++..+....+.++|++|+..+
T Consensus        25 ~~r~~Q~~ai~~il~g---~dvlv~apTGsGKTl~y~lpal~~~g~tlVisPl~sL   77 (607)
T PRK11057         25 QFRPGQQEIIDAVLSG---RDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISL   77 (607)
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEcCCCchHHHHHHHHHHHcCCCEEEEecHHHH
Confidence            6899999999999986   6899999999999999876666667889999998653

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

Probab=99.04  E-value=2.4e-11  Score=91.98  Aligned_cols=60  Identities=20%  Similarity=0.335  Sum_probs=49.2

Q ss_pred             cceeeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecceee
Q psy11637          7 PSAVLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVVF   66 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~v   66 (67)
                      ....+|+||..|+.++.++  ....+.+++|.||+|||.++.+++.++     .+|+||++.++.+|
T Consensus       162 s~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv  228 (875)
T COG4096         162 SAIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALV  228 (875)
T ss_pred             ccccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHH
Confidence            4578999999999886653  122569999999999999999998864     57999999987654

>cd00268 DEADc DEAD-box helicases

Probab=98.98  E-value=3e-11  Score=76.38  Aligned_cols=53  Identities=17%  Similarity=0.224  Sum_probs=42.1

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E-------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T-------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~-------~~~~~lil~p~~~~   65 (67)
                      .++++|+++++.+.++   ++.++.+|||+|||.+++..+. .       .+.+++|++|+..+
T Consensus        21 ~~~~~Q~~~~~~~~~~---~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L   81 (203)
T cd00268          21 KPTPIQARAIPPLLSG---RDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTREL   81 (203)
T ss_pred             CCCHHHHHHHHHHhcC---CcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHH
Confidence            5899999999999985   6899999999999988643322 1       23479999998653

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.

>PRK13766 Hef nuclease; Provisional

Probab=98.95  E-value=4.6e-11  Score=88.79  Aligned_cols=55  Identities=20%  Similarity=0.333  Sum_probs=45.8

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      +.+++|+||++++...++.    ++++++|||+|||.+++.++..    .++++||++|+..+
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~----n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~vLvl~Pt~~L   70 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK----NTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPL   70 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC----CeEEEcCCCccHHHHHHHHHHHHHHhCCCeEEEEeCcHHH
Confidence            4678999999999988874    8999999999999987665543    36899999999654

>PRK01172 ski2-like helicase; Provisional

Probab=98.95  E-value=3.6e-11  Score=88.58  Aligned_cols=55  Identities=15%  Similarity=0.239  Sum_probs=45.5

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .++|+|+|.++++.+.++   ++.++++|||||||+++..++.+   .++++++++|+..+
T Consensus        20 ~~~l~~~Q~~ai~~l~~~---~nvlv~apTGSGKTl~a~lail~~l~~~~k~v~i~P~raL   77 (674)
T PRK01172         20 DFELYDHQRMAIEQLRKG---ENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSL   77 (674)
T ss_pred             CCCCCHHHHHHHHHHhcC---CcEEEECCCCchHHHHHHHHHHHHHHhCCcEEEEechHHH
Confidence            577999999999998665   68999999999999998655443   26789999999754

>COG4889 Predicted helicase [General function prediction only]

Probab=98.94  E-value=1.2e-10  Score=89.63  Aligned_cols=62  Identities=23%  Similarity=0.383  Sum_probs=51.9

Q ss_pred             cccccceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE-eeeeEEEeecce
Q psy11637          3 IDLKPSAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV-RKRALVLCNSGV   64 (67)
Q Consensus         3 ~~l~~~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~-~~~~lil~p~~~   64 (67)
                      +++....++||||++|+++.+++ ..+.+|-+.|.||+|||++++-+...+ ..++|+++|+..
T Consensus       154 l~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLkisEala~~~iL~LvPSIs  217 (1518)
T COG4889         154 LPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLKISEALAAARILFLVPSIS  217 (1518)
T ss_pred             cccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHHHHHHHhhhheEeecchHH
Confidence            45556789999999999998864 224789999999999999999888775 579999999864

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

Probab=98.92  E-value=6.9e-11  Score=85.97  Aligned_cols=56  Identities=21%  Similarity=0.317  Sum_probs=48.4

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecceee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVVF   66 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~v   66 (67)
                      ...+.|.||.....+.+..    +.++++|||-|||+|++.++..    .++++||++||.-+|
T Consensus        12 ~~ie~R~YQ~~i~a~al~~----NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kvlfLAPTKPLV   71 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK----NTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLV   71 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc----CeEEEecCCccHHHHHHHHHHHHHHhcCCeEEEecCCchHH
Confidence            4568999999999998884    8999999999999999988873    356899999998765

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

Probab=98.91  E-value=8.5e-11  Score=91.56  Aligned_cols=54  Identities=20%  Similarity=0.276  Sum_probs=47.2

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ..|||+|++++..++.+   ++.+++||||+|||++++..+....+.+|||+|+..+
T Consensus       459 ~sFRp~Q~eaI~aiL~G---rDVLVimPTGSGKSLcYQLPAL~~~GiTLVISPLiSL  512 (1195)
T PLN03137        459 HSFRPNQREIINATMSG---YDVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSL  512 (1195)
T ss_pred             CCCCHHHHHHHHHHHcC---CCEEEEcCCCccHHHHHHHHHHHcCCcEEEEeCHHHH
Confidence            36899999999999986   6899999999999999977666667889999998754

>PRK02362 ski2-like helicase; Provisional

Probab=98.88  E-value=8.5e-11  Score=87.58  Aligned_cols=55  Identities=20%  Similarity=0.285  Sum_probs=44.4

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .+|+|.|.++++..+..+  ++.++++|||||||+++..++.+   .+++++|++|+..+
T Consensus        22 ~~l~p~Q~~ai~~~~~~g--~nvlv~APTGSGKTlia~lail~~l~~~~kal~i~P~raL   79 (737)
T PRK02362         22 EELYPPQAEAVEAGLLDG--KNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRAL   79 (737)
T ss_pred             CcCCHHHHHHHHHHHhCC--CcEEEECCCcchHHHHHHHHHHHHHhcCCcEEEEeChHHH
Confidence            469999999999844443  69999999999999999655433   36799999999754

>PTZ00424 helicase 45; Provisional

Probab=98.88  E-value=1e-10  Score=80.60  Aligned_cols=53  Identities=17%  Similarity=0.202  Sum_probs=42.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .++|+|++++..++++   ++.++.+|||||||.+++..+..      .+.++||++|+..+
T Consensus        50 ~~~~~Q~~ai~~i~~~---~d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L  108 (401)
T PTZ00424         50 KPSAIQQRGIKPILDG---YDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTREL  108 (401)
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHH
Confidence            5899999999999987   57889999999999887543322      24589999999754

>COG1204 Superfamily II helicase [General function prediction only]

Probab=98.87  E-value=9.6e-11  Score=88.41  Aligned_cols=54  Identities=19%  Similarity=0.236  Sum_probs=46.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      ++.|.|+++++.++..+  +|.+|++|||||||.+++.++..    .++|++++||++++
T Consensus        31 el~~~qq~av~~~~~~~--~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkAL   88 (766)
T COG1204          31 ELFNPQQEAVEKGLLSD--ENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKAL   88 (766)
T ss_pred             HhhHHHHHHhhccccCC--CcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHH
Confidence            78899999999987764  79999999999999999877664    24799999999765

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

Probab=98.84  E-value=1.3e-10  Score=73.50  Aligned_cols=55  Identities=20%  Similarity=0.244  Sum_probs=39.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-----------EEeeeeEEEeecceee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-----------TVRKRALVLCNSGVVF   66 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-----------~~~~~~lil~p~~~~v   66 (67)
                      +|.+.|++|++.+++..  .-.+|.+|+|+|||.+...++.           ..+.++|+++|++.||
T Consensus         1 ~ln~~Q~~Ai~~~~~~~--~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~av   66 (236)
T PF13086_consen    1 KLNESQREAIQSALSSN--GITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAV   66 (236)
T ss_dssp             ---HHHHHHHHHHCTSS--E-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHH
T ss_pred             CCCHHHHHHHHHHHcCC--CCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhH
Confidence            47789999999999874  2488999999999976654432           2367899999998875

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

Probab=98.82  E-value=1.5e-10  Score=70.73  Aligned_cols=50  Identities=20%  Similarity=0.470  Sum_probs=40.4

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E----eeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V----RKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~----~~~~lil~p~~~~   65 (67)
                      |+|+++++.+.++   ++.++.+|||+|||.++...+.. .    ..++++++|+...
T Consensus         2 ~~Q~~~~~~i~~~---~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l   56 (169)
T PF00270_consen    2 PLQQEAIEAIISG---KNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRAL   56 (169)
T ss_dssp             HHHHHHHHHHHTT---SEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHH
T ss_pred             HHHHHHHHHHHcC---CCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeecccc
Confidence            7899999999954   67999999999999999755443 2    2489999998653

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 ....

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=98.81  E-value=2.1e-10  Score=80.40  Aligned_cols=53  Identities=17%  Similarity=0.181  Sum_probs=42.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----------~~~~~lil~p~~~~   65 (67)
                      .++++|++++..++++   ++.++++|||+|||.+++..+..          ...++||++||..+
T Consensus        23 ~p~~iQ~~ai~~~~~g---~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eL   85 (434)
T PRK11192         23 RPTAIQAEAIPPALDG---RDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTREL   85 (434)
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHH
Confidence            5789999999999976   68999999999999987543321          13589999999754

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

Probab=98.79  E-value=6.5e-10  Score=80.25  Aligned_cols=53  Identities=19%  Similarity=0.225  Sum_probs=42.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------------~~~~~lil~p~~~~   65 (67)
                      .++|+|.+++..++++   ++.++++|||||||++++..+..             .+.++||++||..+
T Consensus       143 ~ptpiQ~~aip~il~g---~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreL  208 (518)
T PLN00206        143 FPTPIQMQAIPAALSG---RSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTREL  208 (518)
T ss_pred             CCCHHHHHHHHHHhcC---CCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHH
Confidence            6889999999999976   68999999999999988643211             24579999999754

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

Probab=98.76  E-value=2.2e-09  Score=79.32  Aligned_cols=53  Identities=25%  Similarity=0.371  Sum_probs=47.1

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      -.+||-|+++|+..++.   ++.+++||||+|||+++.-.+.-..+.||||.|-.+
T Consensus        16 ~~FR~gQ~evI~~~l~g---~d~lvvmPTGgGKSlCyQiPAll~~G~TLVVSPLiS   68 (590)
T COG0514          16 ASFRPGQQEIIDALLSG---KDTLVVMPTGGGKSLCYQIPALLLEGLTLVVSPLIS   68 (590)
T ss_pred             cccCCCHHHHHHHHHcC---CcEEEEccCCCCcchHhhhHHHhcCCCEEEECchHH
Confidence            37899999999999998   699999999999999998777777889999999654

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

Probab=98.74  E-value=6.3e-10  Score=82.65  Aligned_cols=58  Identities=19%  Similarity=0.289  Sum_probs=45.3

Q ss_pred             ceeeccchhhHHHHHhcC--C-----cceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGN--G-----RARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~--~-----~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~   65 (67)
                      +.-.|+||.+|+++++++  .     ..++++|.+|||||||.+++.++..+     ..++||++|+..+
T Consensus       236 k~~~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L  305 (667)
T TIGR00348       236 KPYQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDRREL  305 (667)
T ss_pred             eeehHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHH
Confidence            456799999999987643  1     23689999999999999998776542     4689999998643

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

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.73  E-value=1.1e-09  Score=66.66  Aligned_cols=56  Identities=29%  Similarity=0.485  Sum_probs=44.4

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecce
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGV   64 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~   64 (67)
                      ....+||+|+++++.+....  .+.++.+|||+|||.+++..+.+.     .+++++++|+..
T Consensus         5 ~~~~~~~~Q~~~~~~~~~~~--~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~   65 (201)
T smart00487        5 GFEPLRPYQKEAIEALLSGL--RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRE   65 (201)
T ss_pred             CCCCCCHHHHHHHHHHHcCC--CcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHH
Confidence            35689999999999988753  488999999999999776554432     367999999754

>PRK00254 ski2-like helicase; Provisional

Probab=98.71  E-value=6.5e-10  Score=82.74  Aligned_cols=55  Identities=24%  Similarity=0.320  Sum_probs=43.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE----EEeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC----TVRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~----~~~~~~lil~p~~~~   65 (67)
                      ..|+|.|.+++..++..+  ++.++.+|||||||.++...+.    ..++++++++|+.++
T Consensus        22 ~~l~~~Q~~ai~~~~~~g--~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aL   80 (720)
T PRK00254         22 EELYPPQAEALKSGVLEG--KNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKAL   80 (720)
T ss_pred             CCCCHHHHHHHHHHHhCC--CcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHH
Confidence            368999999999855444  6899999999999999954432    236799999999754

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.71  E-value=8.3e-10  Score=78.36  Aligned_cols=54  Identities=19%  Similarity=0.209  Sum_probs=42.5

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----------eeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----------RKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----------~~~~lil~p~~~~   65 (67)
                      ..+.|+|++++..+++.   ++.++++|||||||.+++..+.. +           ..++||++||..+
T Consensus        22 ~~pt~iQ~~ai~~il~g---~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreL   87 (456)
T PRK10590         22 REPTPIQQQAIPAVLEG---RDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTREL   87 (456)
T ss_pred             CCCCHHHHHHHHHHhCC---CCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHH
Confidence            36889999999999986   68999999999999987543321 1           1269999999754

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.70  E-value=1e-09  Score=81.60  Aligned_cols=58  Identities=14%  Similarity=0.239  Sum_probs=46.5

Q ss_pred             ceeeccchhhHHHHHhcCC---cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNG---RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~---~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .++|+++|++++.++.+..   ...+.++.+|||||||.+++..+..   .+.+++|++||..+
T Consensus       259 ~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~g~q~lilaPT~~L  322 (681)
T PRK10917        259 PFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEIL  322 (681)
T ss_pred             CCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEeccHHH
Confidence            5689999999999988742   2357899999999999998765543   35689999999754

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.68  E-value=1e-09  Score=78.07  Aligned_cols=53  Identities=17%  Similarity=0.242  Sum_probs=42.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E------------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V------------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~------------~~~~lil~p~~~~   65 (67)
                      .++|+|.+++..++++   ++.++.+|||||||++++..+.. +            ..++||++||..+
T Consensus       109 ~~~~iQ~~ai~~~~~G---~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreL  174 (475)
T PRK01297        109 YCTPIQAQVLGYTLAG---HDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTREL  174 (475)
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHH
Confidence            5789999999999886   68999999999999887543321 1            3579999999764

>PRK13767 ATP-dependent helicase; Provisional

Probab=98.66  E-value=2.1e-09  Score=81.84  Aligned_cols=54  Identities=19%  Similarity=0.266  Sum_probs=42.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------------~~~~~lil~p~~~~   65 (67)
                      ..|+|.|++++..++++   ++.++++|||||||.++...+..            .+.++||++|+.++
T Consensus        31 ~~~tpiQ~~Ai~~il~g---~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         31 GTFTPPQRYAIPLIHEG---KNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             CCCCHHHHHHHHHHHcC---CCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            35999999999998876   69999999999999987643321            12369999998754

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.65  E-value=1.2e-09  Score=80.43  Aligned_cols=58  Identities=14%  Similarity=0.244  Sum_probs=45.5

Q ss_pred             ceeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .++|.++|+++++++++.   ....+.++.+|||||||.+++..+..   .+.+++|++||..+
T Consensus       233 pf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~g~qvlilaPT~~L  296 (630)
T TIGR00643       233 PFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEIL  296 (630)
T ss_pred             CCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEECCHHHH
Confidence            468999999999998864   22346799999999999998654432   36689999999754

>PRK05580 primosome assembly protein PriA; Validated

Probab=98.64  E-value=1.8e-09  Score=80.43  Aligned_cols=58  Identities=22%  Similarity=0.195  Sum_probs=46.3

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ...|+++|+++++++.+.......++.+|||||||.+++.++..   .++++||++|+..+
T Consensus       142 ~~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g~~vLvLvPt~~L  202 (679)
T PRK05580        142 PPTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIAL  202 (679)
T ss_pred             CCCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcCCeEEEEeCcHHH
Confidence            45799999999999987411256899999999999999766543   36789999999754

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.63  E-value=2.2e-09  Score=75.27  Aligned_cols=53  Identities=23%  Similarity=0.248  Sum_probs=41.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------------~~~~~lil~p~~~~   65 (67)
                      .+.|.|++++..++++   ++.++.+|||||||++++..+..             .+.++||++||..+
T Consensus        30 ~pt~iQ~~aip~il~g---~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreL   95 (423)
T PRK04837         30 NCTPIQALALPLTLAG---RDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTREL   95 (423)
T ss_pred             CCCHHHHHHHHHHhCC---CcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHH
Confidence            5678999999999986   68999999999999987543321             12479999999754

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=98.62  E-value=2e-09  Score=76.09  Aligned_cols=53  Identities=25%  Similarity=0.361  Sum_probs=41.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----~~~~lil~p~~~~   65 (67)
                      .+.|.|++++..++++   ++.++.+|||||||.+++..+.. +     ..++||++||..+
T Consensus        26 ~~t~iQ~~ai~~~l~g---~dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreL   84 (460)
T PRK11776         26 EMTPIQAQSLPAILAG---KDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTREL   84 (460)
T ss_pred             CCCHHHHHHHHHHhcC---CCEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHH
Confidence            5789999999999986   68999999999999876443322 1     2368999999753

>KOG1802|consensus

Probab=98.60  E-value=7e-09  Score=78.15  Aligned_cols=57  Identities=19%  Similarity=0.244  Sum_probs=50.1

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecceee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVVF   66 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~v   66 (67)
                      ...+|...|..|++.++.+   --.+|.+|+|+|||+++..++..    ..+++|+++|+++||
T Consensus       407 ~lpkLN~SQ~~AV~~VL~r---plsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VLvcApSNiAV  467 (935)
T KOG1802|consen  407 NLPKLNASQSNAVKHVLQR---PLSLIQGPPGTGKTVTSATIVYHLARQHAGPVLVCAPSNIAV  467 (935)
T ss_pred             CchhhchHHHHHHHHHHcC---CceeeecCCCCCceehhHHHHHHHHHhcCCceEEEcccchhH
Confidence            3467888999999999997   47899999999999999887765    578999999999987

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.58  E-value=4.5e-09  Score=71.48  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=42.0

Q ss_pred             cccceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEE----EEee-----eeEEEeecc
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACC----TVRK-----RALVLCNSG   63 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~----~~~~-----~~lil~p~~   63 (67)
                      +.+.+++||.|.+.++.+.+. ..++++++.+|||+|||+.++..+.    ..+.     +++|.++|.
T Consensus         3 ~~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~   71 (289)
T smart00488        3 FYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTV   71 (289)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccH
Confidence            345666799999988775542 1236899999999999988875542    1222     788887764

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.58  E-value=4.5e-09  Score=71.48  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=42.0

Q ss_pred             cccceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEE----EEee-----eeEEEeecc
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACC----TVRK-----RALVLCNSG   63 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~----~~~~-----~~lil~p~~   63 (67)
                      +.+.+++||.|.+.++.+.+. ..++++++.+|||+|||+.++..+.    ..+.     +++|.++|.
T Consensus         3 ~~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~~~~kvi~~t~T~   71 (289)
T smart00489        3 FYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERIQKIKLIYLSRTV   71 (289)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccccccceeEEeccH
Confidence            345666799999988775542 1236899999999999988875542    1222     788887764

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=98.57  E-value=4.8e-09  Score=72.79  Aligned_cols=51  Identities=20%  Similarity=0.207  Sum_probs=41.5

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ||.++++.+.+.+ .++.++.+|||||||.+++..+.....++++++|+.++
T Consensus         1 hQ~~~~~~~~~~~-~~~~~i~apTGsGKT~~~~~~~l~~~~~~~~~~P~~aL   51 (357)
T TIGR03158         1 HQVATFEALQSKD-ADIIFNTAPTGAGKTLAWLTPLLHGENDTIALYPTNAL   51 (357)
T ss_pred             CHHHHHHHHHcCC-CCEEEEECCCCCCHHHHHHHHHHHcCCCEEEEeChHHH
Confidence            7999999999864 13578899999999999877665666789999998754

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.

>PRK09401 reverse gyrase; Reviewed

Probab=98.56  E-value=4.4e-09  Score=82.33  Aligned_cols=55  Identities=16%  Similarity=0.289  Sum_probs=43.5

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      .+.++|+|++++..++++   ++.++++|||+|||..++.++.   ..+.+++|++||..+
T Consensus        78 G~~pt~iQ~~~i~~il~g---~dv~i~ApTGsGKT~f~l~~~~~l~~~g~~alIL~PTreL  135 (1176)
T PRK09401         78 GSKPWSLQRTWAKRLLLG---ESFAIIAPTGVGKTTFGLVMSLYLAKKGKKSYIIFPTRLL  135 (1176)
T ss_pred             CCCCcHHHHHHHHHHHCC---CcEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEeccHHH
Confidence            357899999999999986   6899999999999965443222   235789999999764

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

Probab=98.53  E-value=5.8e-09  Score=78.40  Aligned_cols=53  Identities=21%  Similarity=0.156  Sum_probs=43.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      .|+++|++++..++++   ++.++..|||||||.+++..+..     .+.++||++||..+
T Consensus        36 ~p~~~Q~~ai~~il~G---~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraL   93 (742)
T TIGR03817        36 RPWQHQARAAELAHAG---RHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKAL   93 (742)
T ss_pred             cCCHHHHHHHHHHHCC---CCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHH
Confidence            6889999999999876   68999999999999998654332     24589999999754

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.

>PTZ00110 helicase; Provisional

Probab=98.52  E-value=5.3e-09  Score=76.12  Aligned_cols=53  Identities=19%  Similarity=0.173  Sum_probs=41.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E----------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T----------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~----------~~~~~lil~p~~~~   65 (67)
                      ++.|.|.+++..+++.   ++.++++|||||||++++..+. .          .+..+||++||..+
T Consensus       152 ~pt~iQ~~aip~~l~G---~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreL  215 (545)
T PTZ00110        152 EPTPIQVQGWPIALSG---RDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTREL  215 (545)
T ss_pred             CCCHHHHHHHHHHhcC---CCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHH
Confidence            5788999999999986   6899999999999998753221 1          13468999999754

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.52  E-value=5.4e-09  Score=80.32  Aligned_cols=59  Identities=20%  Similarity=0.206  Sum_probs=46.3

Q ss_pred             cceeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ..+++.|.|+++++.+++.   +...+.++++|||||||.+++.++..   .+.+++|++||..+
T Consensus       448 ~~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g~qvlvLvPT~~L  512 (926)
T TIGR00580       448 FPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLL  512 (926)
T ss_pred             CCCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhCCeEEEEeCcHHH
Confidence            3567899999999999874   22357899999999999988755432   36789999999754

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.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=98.51  E-value=7.1e-09  Score=76.84  Aligned_cols=53  Identities=17%  Similarity=0.197  Sum_probs=41.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~-----~~~~~lil~p~~~~   65 (67)
                      ++.|+|++++..+++.   ++.++.+|||+|||.++...+. .     ...++||++||..+
T Consensus        28 ~ptpiQ~~ai~~ll~g---~dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreL   86 (629)
T PRK11634         28 KPSPIQAECIPHLLNG---RDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTREL   86 (629)
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHH
Confidence            6789999999999976   6899999999999988743321 1     13478999999754

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

Probab=98.50  E-value=1.7e-08  Score=74.55  Aligned_cols=64  Identities=14%  Similarity=0.228  Sum_probs=53.0

Q ss_pred             ccccccceeeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          2 TIDLKPSAVLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         2 ~~~l~~~~~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      +|.|...+.+-.-|-+|++++.++  +..+..++.+.||||||++++.+|.+.++|+||++|++++
T Consensus         4 ~F~l~s~f~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~AnVI~~~~rPtLV~AhNKTL   69 (663)
T COG0556           4 PFKLHSPFKPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMANVIAKVQRPTLVLAHNKTL   69 (663)
T ss_pred             ceEeccCCCCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHHHHHHHhCCCeEEEecchhH
Confidence            355666666666799999997764  2236789999999999999999999999999999998764

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.43  E-value=1.4e-08  Score=74.47  Aligned_cols=53  Identities=23%  Similarity=0.202  Sum_probs=42.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------------~~~~~lil~p~~~~   65 (67)
                      .+.|.|++++..+++.   ++.++.+|||||||.+++..+..             ...++||++||..+
T Consensus        31 ~ptpiQ~~~ip~~l~G---~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreL   96 (572)
T PRK04537         31 RCTPIQALTLPVALPG---GDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTREL   96 (572)
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHH
Confidence            5778899999999986   68999999999999988654321             02589999999754

>PRK14701 reverse gyrase; Provisional

Probab=98.43  E-value=1.6e-08  Score=81.15  Aligned_cols=54  Identities=20%  Similarity=0.280  Sum_probs=42.8

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      +.+++.|++++..++++   ++.++++|||+|||.+++.++..   .+.+++|++||..+
T Consensus        78 ~~pt~iQ~~~i~~il~G---~d~li~APTGsGKTl~~~~~al~~~~~g~~aLVl~PTreL  134 (1638)
T PRK14701         78 FEFWSIQKTWAKRILRG---KSFSIVAPTGMGKSTFGAFIALFLALKGKKCYIILPTTLL  134 (1638)
T ss_pred             CCCCHHHHHHHHHHHcC---CCEEEEEcCCCCHHHHHHHHHHHHHhcCCeEEEEECHHHH
Confidence            47899999999999997   68899999999999854322221   24589999999754

>TIGR00376 DNA helicase, putative

Probab=98.41  E-value=1.8e-08  Score=74.85  Aligned_cols=56  Identities=21%  Similarity=0.147  Sum_probs=46.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecceee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVVF   66 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~v   66 (67)
                      ..|-+.|.+|++.++...  +..+|.+|+|+|||.++..++..   .+.++|+++||+.||
T Consensus       156 ~~ln~~Q~~Av~~~l~~~--~~~lI~GpPGTGKT~t~~~ii~~~~~~g~~VLv~a~sn~Av  214 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSK--DLFLIHGPPGTGKTRTLVELIRQLVKRGLRVLVTAPSNIAV  214 (637)
T ss_pred             CCCCHHHHHHHHHHhcCC--CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEcCcHHHH
Confidence            356778999999988753  57889999999999998877765   367999999999875

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.

>KOG0351|consensus

Probab=98.38  E-value=4e-07  Score=70.39  Aligned_cols=53  Identities=19%  Similarity=0.282  Sum_probs=46.5

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      -.+||.|.++|..++.+   +..++.||||+||++|+...+....+=++||.|-.+
T Consensus       263 ~~FR~~Q~eaI~~~l~G---kd~fvlmpTG~GKSLCYQlPA~l~~gitvVISPL~S  315 (941)
T KOG0351|consen  263 KGFRPNQLEAINATLSG---KDCFVLMPTGGGKSLCYQLPALLLGGVTVVISPLIS  315 (941)
T ss_pred             ccCChhHHHHHHHHHcC---CceEEEeecCCceeeEeeccccccCCceEEeccHHH
Confidence            47899999999998887   689999999999999998888778888899988643

>KOG0353|consensus

Probab=98.35  E-value=1.1e-07  Score=68.87  Aligned_cols=53  Identities=26%  Similarity=0.406  Sum_probs=47.1

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ++||.|.+++......   ...++++|||.|||+++...+...++.+|+++|-..+
T Consensus        94 kfrplq~~ain~~ma~---ed~~lil~tgggkslcyqlpal~adg~alvi~plisl  146 (695)
T KOG0353|consen   94 KFRPLQLAAINATMAG---EDAFLILPTGGGKSLCYQLPALCADGFALVICPLISL  146 (695)
T ss_pred             hcChhHHHHhhhhhcc---CceEEEEeCCCccchhhhhhHHhcCCceEeechhHHH
Confidence            6799999999998886   5889999999999999988888889999999997543

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

Probab=98.34  E-value=4.9e-08  Score=74.63  Aligned_cols=53  Identities=25%  Similarity=0.233  Sum_probs=45.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      .|+.||.+|++.+.+.   ++.+|.-|||||||.+++..+..     ...++|+|.|++++
T Consensus        70 ~lY~HQ~~A~~~~~~G---~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnAL  127 (851)
T COG1205          70 RLYSHQVDALRLIREG---RNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNAL  127 (851)
T ss_pred             cccHHHHHHHHHHHCC---CCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhh
Confidence            4899999999999887   79999999999999999866543     35578999999875

>KOG1803|consensus

Probab=98.32  E-value=8.9e-08  Score=71.17  Aligned_cols=57  Identities=26%  Similarity=0.236  Sum_probs=47.3

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecceee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVVF   66 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~v   66 (67)
                      +..|-+.|++|+....+..  .-.+|++|+|+|||.+...++..   .++++|+.+||+.||
T Consensus       183 ~~~ln~SQk~Av~~~~~~k--~l~~I~GPPGTGKT~TlvEiI~qlvk~~k~VLVcaPSn~AV  242 (649)
T KOG1803|consen  183 NKNLNSSQKAAVSFAINNK--DLLIIHGPPGTGKTRTLVEIISQLVKQKKRVLVCAPSNVAV  242 (649)
T ss_pred             CccccHHHHHHHHHHhccC--CceEeeCCCCCCceeeHHHHHHHHHHcCCeEEEEcCchHHH
Confidence            3456678999988877653  56888999999999999888876   478999999999886

>PRK10689 transcription-repair coupling factor; Provisional

Probab=98.32  E-value=3.6e-08  Score=77.19  Aligned_cols=59  Identities=19%  Similarity=0.220  Sum_probs=45.7

Q ss_pred             cceeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      ..+.+.+.|++++..+++.   ....+.++++|||+|||.+++.++.   ..+.+++|++||+.+
T Consensus       597 ~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~qvlvLvPT~eL  661 (1147)
T PRK10689        597 FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLL  661 (1147)
T ss_pred             CCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHcCCeEEEEeCcHHH
Confidence            4567889999999998874   2235789999999999988754332   236789999999754

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

Probab=98.32  E-value=5.8e-08  Score=73.70  Aligned_cols=58  Identities=22%  Similarity=0.256  Sum_probs=42.2

Q ss_pred             cceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          7 PSAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..++.||.|.++++.+.+. .+++..++.+|||+|||..++..+..   .+++++|.+||..
T Consensus       242 ~~~~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~~~~vvi~t~t~~  303 (850)
T TIGR01407       242 LGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAITEKPVVISTNTKV  303 (850)
T ss_pred             cCCccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcCCCeEEEEeCcHH
Confidence            3578999999877654432 11267888999999999888654322   3679999999864

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.

>TIGR01054 rgy reverse gyrase

Probab=98.31  E-value=4.1e-08  Score=76.99  Aligned_cols=55  Identities=18%  Similarity=0.296  Sum_probs=43.1

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      ...+.|.|+.++..++.+   ++.++.+|||+|||..++.++.   ..+.+++|++||..+
T Consensus        76 g~~p~~iQ~~~i~~il~G---~d~vi~ApTGsGKT~f~l~~~~~l~~~g~~vLIL~PTreL  133 (1171)
T TIGR01054        76 GSEPWSIQKMWAKRVLRG---DSFAIIAPTGVGKTTFGLAMSLFLAKKGKRCYIILPTTLL  133 (1171)
T ss_pred             CCCCcHHHHHHHHHHhCC---CeEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeCHHHH
Confidence            357889999999999987   6889999999999975443322   235789999999754

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=98.26  E-value=2.2e-08  Score=57.75  Aligned_cols=36  Identities=22%  Similarity=0.392  Sum_probs=29.6

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeeccee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVV   65 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~   65 (67)
                      +.++.+|||+|||.+++.++...     .++++|++|+..+
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l   42 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTREL   42 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHH
Confidence            57899999999999998776653     3799999998753

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

>PF13245 AAA_19: Part of AAA domain

Probab=98.26  E-value=3.1e-08  Score=55.89  Aligned_cols=48  Identities=23%  Similarity=0.294  Sum_probs=33.9

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-------eeeeEEEeecceee
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-------RKRALVLCNSGVVF   66 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-------~~~~lil~p~~~~v   66 (67)
                      ++++..+..  ++..+|.+|+|||||.+++..+.+.       ++++++++|++.++
T Consensus         1 ~av~~al~~--~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa   55 (76)
T PF13245_consen    1 EAVRRALAG--SPLFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAA   55 (76)
T ss_pred             CHHHHHHhh--CCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHH
Confidence            355554552  1456679999999998776665542       67899999998653

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

Probab=98.19  E-value=2e-07  Score=72.21  Aligned_cols=35  Identities=14%  Similarity=0.155  Sum_probs=29.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecce
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGV   64 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~   64 (67)
                      +..+.|+||+|||.+++..+.++     ..++||+||+.+
T Consensus        61 n~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~~a  100 (986)
T PRK15483         61 NIDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPTPA  100 (986)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCCHH
Confidence            67889999999999998887764     357999999964

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

Probab=98.18  E-value=4.4e-07  Score=69.30  Aligned_cols=53  Identities=19%  Similarity=0.288  Sum_probs=41.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E-------eeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V-------RKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~-------~~~~lil~p~~~   64 (67)
                      ..|+|.|++|+..+.++   .+.+|++|||||||..|...+..    .       +-.+|+|.|-++
T Consensus        21 ~~~t~~Q~~a~~~i~~G---~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkA   84 (814)
T COG1201          21 TSLTPPQRYAIPEIHSG---ENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKA   84 (814)
T ss_pred             CCCCHHHHHHHHHHhCC---CceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHH
Confidence            47899999999999976   79999999999999988543221    1       135889888654

>KOG0952|consensus

Probab=98.14  E-value=2e-07  Score=72.72  Aligned_cols=51  Identities=12%  Similarity=0.201  Sum_probs=40.5

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------------EeeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------------VRKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------------~~~~~lil~p~~~~   65 (67)
                      .-|.++..-+++.+  .+.+|++|||||||.+++..|.+             -+.++++|+|++++
T Consensus       113 ~iQS~vFp~aY~Sn--eNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKAL  176 (1230)
T KOG0952|consen  113 RIQSEVFPVAYKSN--ENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKAL  176 (1230)
T ss_pred             HHHHHhhhhhhcCC--CCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHH
Confidence            34888887777765  79999999999999999765543             14589999999865

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

Probab=98.14  E-value=1e-06  Score=67.63  Aligned_cols=56  Identities=20%  Similarity=0.205  Sum_probs=38.3

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEee---eeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGV---TACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~---~~~~~---~~~~~lil~p~~~~   65 (67)
                      .+++.|||++++..++++.  ...++.+|||||||.+++   .....   ...+.++++|+...
T Consensus        13 G~~PtpiQ~~~i~~il~G~--~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReL   74 (844)
T TIGR02621        13 GYSPFPWQLSLAERFVAGQ--PPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTV   74 (844)
T ss_pred             CCCCCHHHHHHHHHHHcCC--CcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHH
Confidence            4568999999999999752  246667999999997432   11111   12356667798754

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.

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

Probab=98.09  E-value=1.6e-07  Score=60.53  Aligned_cols=54  Identities=24%  Similarity=0.351  Sum_probs=39.3

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      |-+.|++|++.++..+. +..+|.+|.|+|||++...+...   .+.++++++||..|
T Consensus         2 L~~~Q~~a~~~~l~~~~-~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~A   58 (196)
T PF13604_consen    2 LNEEQREAVRAILTSGD-RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKA   58 (196)
T ss_dssp             S-HHHHHHHHHHHHCTC-SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHH
T ss_pred             CCHHHHHHHHHHHhcCC-eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHH
Confidence            56789999999986531 46778899999999877555433   35799999999754

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

Probab=98.08  E-value=3.3e-07  Score=71.33  Aligned_cols=56  Identities=18%  Similarity=0.245  Sum_probs=46.9

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ..+.|=|+|++|+..+-..   ++.++++|||||||+++..++..   .+.++++..|.+++
T Consensus       116 ~~F~LD~fQ~~a~~~Ler~---esVlV~ApTssGKTvVaeyAi~~al~~~qrviYTsPIKAL  174 (1041)
T COG4581         116 YPFELDPFQQEAIAILERG---ESVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKAL  174 (1041)
T ss_pred             CCCCcCHHHHHHHHHHhCC---CcEEEEccCCCCcchHHHHHHHHHHHcCCceEeccchhhh
Confidence            4578889999999988776   69999999999999999766654   46789999998765

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.08  E-value=2.1e-07  Score=72.46  Aligned_cols=56  Identities=18%  Similarity=0.263  Sum_probs=43.4

Q ss_pred             eeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~   64 (67)
                      .+|||||.+++...+.. ..+.++++...+|.|||+.+++++..      ..+|+|||||.++
T Consensus       168 ~~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~Sl  230 (1033)
T PLN03142        168 GKMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKST  230 (1033)
T ss_pred             cchHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeChHH
Confidence            58999999999765431 12267999999999999988777643      2468999999864

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=98.07  E-value=4.2e-07  Score=69.06  Aligned_cols=53  Identities=17%  Similarity=0.270  Sum_probs=42.3

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..+||||.+++-.+..+.   ..++.|+||+|||++++..+..   .+..++|++|+..
T Consensus        67 lglrpydVQlig~l~l~~---G~Iaem~TGeGKTLta~Lpa~l~aL~g~~V~VVTpn~y  122 (762)
T TIGR03714        67 LGMFPYDVQVLGAIVLHQ---GNIAEMKTGEGKTLTATMPLYLNALTGKGAMLVTTNDY  122 (762)
T ss_pred             cCCCccHHHHHHHHHhcC---CceeEecCCcchHHHHHHHHHHHhhcCCceEEeCCCHH
Confidence            468999999999988653   3688999999999999765432   3567999999874

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.

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

Probab=97.97  E-value=4.6e-07  Score=66.59  Aligned_cols=57  Identities=19%  Similarity=0.253  Sum_probs=42.4

Q ss_pred             cceeeccchhhHHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEeecc
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLCNSG   63 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~p~~   63 (67)
                      +.+.+||.|.++++.+..... ++..++-+|||+|||+-++..+...    +.+++|.++|.
T Consensus        12 ~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~viist~t~   73 (654)
T COG1199          12 PGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRTK   73 (654)
T ss_pred             CCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcEEEECCCH
Confidence            457899999999988665322 2458899999999999887665543    36777776664

>KOG0352|consensus

Probab=97.97  E-value=2.6e-06  Score=62.31  Aligned_cols=50  Identities=20%  Similarity=0.190  Sum_probs=42.1

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      |-|+.|+..+.+..  ....++||||+|||+++.......++=++|+.|-.+
T Consensus        23 ~LQE~A~~c~VK~k--~DVyVsMPTGaGKSLCyQLPaL~~~gITIV~SPLiA   72 (641)
T KOG0352|consen   23 RLQEQAINCIVKRK--CDVYVSMPTGAGKSLCYQLPALVHGGITIVISPLIA   72 (641)
T ss_pred             hHHHHHHHHHHhcc--CcEEEeccCCCchhhhhhchHHHhCCeEEEehHHHH
Confidence            56999999999875  678899999999999998777777778888887643

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=97.97  E-value=4.5e-07  Score=61.91  Aligned_cols=35  Identities=20%  Similarity=0.211  Sum_probs=28.1

Q ss_pred             eeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      .++.+|||||||.+++..+.+     ...++++++|+..+
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L   41 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRAT   41 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHH
Confidence            478899999999998776652     35789999998754

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=97.87  E-value=3.3e-06  Score=63.46  Aligned_cols=54  Identities=13%  Similarity=0.083  Sum_probs=36.3

Q ss_pred             eeeccc----hhhHHHHHhcCCcceeeeEEEeCCCCceeEe-------------eeeEEE-----EeeeeEEEeeccee
Q psy11637          9 AVLRPY----QEKSLRKMFGNGRARSGVIVLPCGAGKSLVG-------------VTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~y----Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~-------------~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      ..|++.    |+++++.++++   +..++.++||||||...             +.....     ...++++++||..+
T Consensus       159 ~~l~~~~~~iQ~qil~~i~~g---kdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~~~~~~~ilvt~PrreL  234 (675)
T PHA02653        159 IPLASLQPDVQLKIFEAWISR---KPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDPNFIERPIVLSLPRVAL  234 (675)
T ss_pred             ccCCchhHHHHHHHHHHHHhC---CCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcccccCCcEEEEECcHHHH
Confidence            466665    55555666655   68899999999999862             111111     23589999999654

>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=97.87  E-value=6.7e-07  Score=58.74  Aligned_cols=50  Identities=22%  Similarity=0.397  Sum_probs=33.2

Q ss_pred             chhhHHHHHhcC----------CcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeecc
Q psy11637         14 YQEKSLRKMFGN----------GRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSG   63 (67)
Q Consensus        14 yQ~~av~~~~~~----------~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~   63 (67)
                      ||.++++..++.          ...+.+++...+|+|||.++++++..+        ..++||+||+.
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~~   68 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPSS   68 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-TT
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeeccc
Confidence            799999875532          235678888999999999998887632        12599999984

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.

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.86  E-value=2.1e-06  Score=66.51  Aligned_cols=54  Identities=17%  Similarity=0.201  Sum_probs=42.1

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .|.+||||.+++-.+..+   +..+..|+||+|||++++..+..   .+.+++|++||..
T Consensus        90 p~~~tp~qvQ~I~~i~l~---~gvIAeaqTGeGKTLAf~LP~l~~aL~g~~v~IVTpTrE  146 (970)
T PRK12899         90 QWDMVPYDVQILGAIAMH---KGFITEMQTGEGKTLTAVMPLYLNALTGKPVHLVTVNDY  146 (970)
T ss_pred             CCCCChHHHHHhhhhhcC---CCeEEEeCCCCChHHHHHHHHHHHHhhcCCeEEEeCCHH
Confidence            355899999999888876   45777899999999999765442   2346899999864

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=97.86  E-value=3e-06  Score=63.39  Aligned_cols=57  Identities=14%  Similarity=0.244  Sum_probs=39.9

Q ss_pred             cceee-ccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE----Ee--eeeEEEeecc
Q psy11637          7 PSAVL-RPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT----VR--KRALVLCNSG   63 (67)
Q Consensus         7 ~~~~l-R~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~----~~--~~~lil~p~~   63 (67)
                      +.+.. ||.|++.++.+.+. ..++++++.+|||+|||+..+..+..    .+  .++++.+.|.
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~~~kIiy~sRTh   70 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIYASRTH   70 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccccccEEEEcccc
Confidence            34444 99999999987754 23478999999999999877654432    12  4566666553

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).

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

Probab=97.84  E-value=2.2e-06  Score=65.38  Aligned_cols=57  Identities=16%  Similarity=0.131  Sum_probs=42.1

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE--EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT--VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~--~~~~~lil~p~~~   64 (67)
                      .++.||-|.+..+++.+. .++...++.++||+|||+.++..+..  .+.+++|.+||..
T Consensus       243 ~~e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~~~~~vvI~t~T~~  302 (820)
T PRK07246        243 GLEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQSDQRQIIVSVPTKI  302 (820)
T ss_pred             CCccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhcCCCcEEEEeCcHH
Confidence            578999999966654432 11256788899999999988755332  3678999999864

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

Probab=97.77  E-value=2.9e-06  Score=65.29  Aligned_cols=57  Identities=14%  Similarity=0.166  Sum_probs=42.0

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEE----EEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACC----TVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~----~~~~~~lil~p~~~   64 (67)
                      .++.||-|.+..+.+.+. .++...++-+|||+|||+-++..+.    ..+++++|-++|..
T Consensus       255 ~~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~~vvIsT~T~~  316 (928)
T PRK08074        255 KYEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPVVISTYTIQ  316 (928)
T ss_pred             CCcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccCCeEEEEcCCHH
Confidence            578999999977665542 1226778889999999998875433    24678888888864

>PRK09694 helicase Cas3; Provisional

Probab=97.76  E-value=2.3e-06  Score=65.88  Aligned_cols=54  Identities=13%  Similarity=0.054  Sum_probs=39.4

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~   64 (67)
                      .+.+||+|+.+.+. ...  .+..+|.+|||+|||..++.++..+     ..+++|..||.+
T Consensus       284 ~~~p~p~Q~~~~~~-~~~--pgl~ileApTGsGKTEAAL~~A~~l~~~~~~~gi~~aLPT~A  342 (878)
T PRK09694        284 GYQPRQLQTLVDAL-PLQ--PGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQA  342 (878)
T ss_pred             CCCChHHHHHHHhh-ccC--CCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCCeEEEECcHHH
Confidence            46789999977433 222  2678889999999999988765532     357888888754

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

Probab=97.66  E-value=4.5e-06  Score=65.27  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=43.3

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecceee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVVF   66 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~v   66 (67)
                      +.++..|+--..+++++   ++.-+++|||.|||+.++....   ..++|..+++||+.+|
T Consensus        81 ~~~ws~QR~WakR~~rg---~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv  138 (1187)
T COG1110          81 FRPWSAQRVWAKRLVRG---KSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLV  138 (1187)
T ss_pred             CCchHHHHHHHHHHHcC---CceEEEcCCCCchhHHHHHHHHHHHhcCCeEEEEecCHHHH
Confidence            35566688888888876   6888999999999988765443   3468999999998764

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=97.64  E-value=5.4e-06  Score=62.10  Aligned_cols=62  Identities=16%  Similarity=0.219  Sum_probs=51.2

Q ss_pred             cccccceeeccchhhHHHHHhcCCc--ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          3 IDLKPSAVLRPYQEKSLRKMFGNGR--ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         3 ~~l~~~~~lR~yQ~~av~~~~~~~~--~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      |+|..++.+.-.|.++++++.+.-.  .+..++.+.||||||++++.++...++++|||+|+..
T Consensus         2 f~~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~~~~~~~~p~Lvi~~n~~   65 (655)
T TIGR00631         2 FKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMANVIAQVNRPTLVIAHNKT   65 (655)
T ss_pred             ceeccCCCCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHHHHHHhCCCEEEEECCHH
Confidence            5677778888899999999776421  2356789999999999999999999999999999853

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

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

Probab=97.64  E-value=1.6e-05  Score=59.89  Aligned_cols=55  Identities=24%  Similarity=0.213  Sum_probs=43.1

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeee-EEE---EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA-CCT---VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~-~~~---~~~~~lil~p~~~   64 (67)
                      .-.|+|-|.-++++=+-.+  ++.+++.+|+||||+++-.+ +.+   -+++.|+++|-.+
T Consensus       214 ~~eLlPVQ~laVe~GLLeG--~nllVVSaTasGKTLIgElAGi~~~l~~g~KmlfLvPLVA  272 (830)
T COG1202         214 IEELLPVQVLAVEAGLLEG--ENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLVPLVA  272 (830)
T ss_pred             cceecchhhhhhhhccccC--CceEEEeccCCCcchHHHhhCcHHHHhCCCeEEEEehhHH
Confidence            3578999999999955444  79999999999999999433 322   3689999999754

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=97.59  E-value=4.1e-06  Score=62.88  Aligned_cols=57  Identities=19%  Similarity=0.165  Sum_probs=41.5

Q ss_pred             ceeeccchhhHHHHHhc---CC---cceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFG---NG---RARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~---~~---~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~   64 (67)
                      .++.||-|.++.+++.+   .+   +++..+|-+|||+|||+-++..+..    .++|++|=++|..
T Consensus        23 ~~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k~vVIST~T~~   89 (697)
T PRK11747         23 GFIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKKKLVISTATVA   89 (697)
T ss_pred             CCCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCCeEEEEcCCHH
Confidence            58899999998777664   21   1356888899999999988754432    4678777777653

>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=97.59  E-value=2.2e-05  Score=52.67  Aligned_cols=45  Identities=27%  Similarity=0.444  Sum_probs=38.9

Q ss_pred             ccccccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637          2 TIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus         2 ~~~l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -+|+..++.+||-|.+...++.+...+.+.+..|-+|.|||.|.+
T Consensus        15 l~E~e~~iliR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI~   59 (229)
T PF12340_consen   15 LFEIESNILIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVIV   59 (229)
T ss_pred             HHHHHcCceeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchHH
Confidence            367788999999999999999986445788899999999999885

There are two conserved sequence motifs: LLE and NMG.

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

Probab=97.58  E-value=7.8e-06  Score=61.25  Aligned_cols=50  Identities=18%  Similarity=0.211  Sum_probs=37.0

Q ss_pred             hhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeecce
Q psy11637         15 QEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGV   64 (67)
Q Consensus        15 Q~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~   64 (67)
                      |++.++++.+. .++...++.+|||+|||..++..+..     .+.+++|.+||..
T Consensus         2 Q~~~~~~i~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~~~rvlIstpT~~   57 (636)
T TIGR03117         2 QALFYLNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLA   57 (636)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhccCceEEEECCcHH
Confidence            77777776653 22367888899999999888655422     3689999999864

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.

>KOG0350|consensus

Probab=97.57  E-value=3.3e-05  Score=57.14  Aligned_cols=56  Identities=29%  Similarity=0.355  Sum_probs=40.9

Q ss_pred             eeeccchhhHHHHHhcCC------cceeeeEEEeCCCCceeEeeeeEEE-E------eeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNG------RARSGVIVLPCGAGKSLVGVTACCT-V------RKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~------~~~~~~i~~pTGsGKT~i~~~~~~~-~------~~~~lil~p~~~   64 (67)
                      -.+.|-|...+..++...      ..+...+.+|||||||+.+.-.|-. +      .-|.+||+|+..
T Consensus       158 s~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~  226 (620)
T KOG0350|consen  158 SRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRE  226 (620)
T ss_pred             ccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCccceEEEEEeeHHH
Confidence            456788988888876421      2567889999999999998654432 1      247999999864

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.54  E-value=1e-05  Score=62.88  Aligned_cols=56  Identities=20%  Similarity=0.129  Sum_probs=45.1

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeecc
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSG   63 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~   63 (67)
                      ....|.|||.+++.+++... ..+.++.-.+|.|||+.+.+++..     ..+|+|||||..
T Consensus       149 ~~~~l~pHQl~~~~~vl~~~-~~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~s  209 (956)
T PRK04914        149 ARASLIPHQLYIAHEVGRRH-APRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPET  209 (956)
T ss_pred             CCCCCCHHHHHHHHHHhhcc-CCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCHH
Confidence            35679999999999887653 257889999999999999777654     246999999974

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=97.52  E-value=4.3e-06  Score=55.08  Aligned_cols=48  Identities=19%  Similarity=0.164  Sum_probs=34.8

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E---eeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V---RKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~---~~~~lil~p~~~~   65 (67)
                      +-|++++.. .+    +..+|.+..|||||.+.+.-+..    .   ..++|+++.|+.|
T Consensus         3 ~eQ~~~i~~-~~----~~~lV~a~AGSGKT~~l~~ri~~ll~~~~~~~~~Il~lTft~~a   57 (315)
T PF00580_consen    3 DEQRRIIRS-TE----GPLLVNAGAGSGKTTTLLERIAYLLYEGGVPPERILVLTFTNAA   57 (315)
T ss_dssp             HHHHHHHHS--S----SEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHH
T ss_pred             HHHHHHHhC-CC----CCEEEEeCCCCCchHHHHHHHHHhhccccCChHHheecccCHHH
Confidence            557788777 32    58899999999999988654332    1   4689999998765

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 ....

>TIGR00595 priA primosomal protein N'

Probab=97.47  E-value=3.7e-06  Score=61.14  Aligned_cols=34  Identities=26%  Similarity=0.255  Sum_probs=27.2

Q ss_pred             eEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         32 VIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ++.+|||||||.+++.++..   .++++||++|+...
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~g~~vLvlvP~i~L   37 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIAL   37 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHH
Confidence            47899999999999766643   36789999998653

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).

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=97.47  E-value=1.3e-05  Score=61.32  Aligned_cols=53  Identities=15%  Similarity=0.235  Sum_probs=39.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~   64 (67)
                      ..+|||+.+++-.+.-..  + .+..|.||+|||++++..+.   ..+..++|++||..
T Consensus        75 ~g~~p~~vQl~~~~~l~~--G-~Iaem~TGeGKTL~a~lp~~l~al~G~~v~VvTpt~~  130 (790)
T PRK09200         75 LGMRPYDVQLIGALVLHE--G-NIAEMQTGEGKTLTATMPLYLNALEGKGVHLITVNDY  130 (790)
T ss_pred             hCCCCchHHHHhHHHHcC--C-ceeeecCCCcchHHHHHHHHHHHHcCCCeEEEeCCHH
Confidence            457888777777655432  2 38899999999999876554   24788999999864

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=97.47  E-value=1.3e-05  Score=59.81  Aligned_cols=62  Identities=13%  Similarity=0.191  Sum_probs=51.3

Q ss_pred             ccccccceeeccchhhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecc
Q psy11637          2 TIDLKPSAVLRPYQEKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSG   63 (67)
Q Consensus         2 ~~~l~~~~~lR~yQ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~   63 (67)
                      .|.+...+.|++.|..+++++.+.-  ..++.++.+.+||||+++++.++...++++|||+|+.
T Consensus         4 ~~~~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia~l~~~~~r~vLIVt~~~   67 (652)
T PRK05298          4 PFKLVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMANVIARLQRPTLVLAHNK   67 (652)
T ss_pred             CcccccCCCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHHHHHHHhCCCEEEEECCH
Confidence            3678889999999999999987642  1125678999999999998888877889999999984

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.45  E-value=1.6e-05  Score=46.01  Aligned_cols=48  Identities=17%  Similarity=0.159  Sum_probs=31.1

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      -+.+.+...+........++.+|+|+|||.++..++...   +.+++++..
T Consensus         5 ~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~   55 (151)
T cd00009           5 EAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNA   55 (151)
T ss_pred             HHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEeh
Confidence            344445555544233678899999999999887776654   445554443

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.

>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=97.39  E-value=2.1e-05  Score=51.81  Aligned_cols=47  Identities=17%  Similarity=0.311  Sum_probs=32.4

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeec
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNS   62 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~   62 (67)
                      +.|+.+++.+++.   ...++.+|.|+|||+++++.+.+.     ..++++.-|.
T Consensus         7 ~~Q~~~~~al~~~---~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~   58 (205)
T PF02562_consen    7 EEQKFALDALLNN---DLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPP   58 (205)
T ss_dssp             HHHHHHHHHHHH----SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S
T ss_pred             HHHHHHHHHHHhC---CeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecC
Confidence            4799999999955   578888999999999998776542     2455555444

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

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

Probab=97.39  E-value=2.3e-05  Score=59.59  Aligned_cols=56  Identities=21%  Similarity=0.202  Sum_probs=46.2

Q ss_pred             eeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..|-+-|+.|++.+.+. +.....++.+.||||||-+++.++..   .++-+||++|...
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~GkqvLvLVPEI~  256 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIA  256 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCCEEEEEecccc
Confidence            46677899999998876 33467899999999999999998876   4778999999754

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=97.35  E-value=2.6e-05  Score=59.42  Aligned_cols=53  Identities=15%  Similarity=0.239  Sum_probs=38.2

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~   64 (67)
                      ..+|||+.+.+-.+.-.   ...+..|+||+|||++++..+.   ..+..++|++||..
T Consensus        53 lg~~p~~vQlig~~~l~---~G~Iaem~TGeGKTLva~lpa~l~aL~G~~V~VvTpt~~  108 (745)
T TIGR00963        53 LGMRPFDVQLIGGIALH---KGKIAEMKTGEGKTLTATLPAYLNALTGKGVHVVTVNDY  108 (745)
T ss_pred             hCCCccchHHhhhhhhc---CCceeeecCCCccHHHHHHHHHHHHHhCCCEEEEcCCHH
Confidence            46788877777665443   2237789999999999875543   23667999999864

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.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.34  E-value=2.2e-05  Score=59.45  Aligned_cols=56  Identities=27%  Similarity=0.235  Sum_probs=44.4

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      .+.|-+-|++|++.++..+  +..+|.+++|+|||++.-.+..   ..+.++++++||..|
T Consensus       350 ~~~Ls~~Q~~Av~~i~~s~--~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg~A  408 (744)
T TIGR02768       350 HYRLSEEQYEAVRHVTGSG--DIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKA  408 (744)
T ss_pred             cCCCCHHHHHHHHHHhcCC--CEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcHHH
Confidence            4568889999999998753  5788999999999988766543   236789999998654

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.34  E-value=2.1e-05  Score=44.91  Aligned_cols=34  Identities=18%  Similarity=0.209  Sum_probs=26.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee---eEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR---ALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~---~lil~p~   62 (67)
                      .+.++.+|+|+|||.++..++......   ++++..+
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~   39 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGE   39 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCE
Confidence            578899999999999998888876553   5555544

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.31  E-value=1.9e-05  Score=59.62  Aligned_cols=55  Identities=13%  Similarity=0.088  Sum_probs=43.1

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---Ee--eeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VR--KRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~--~~~lil~p~~~~   65 (67)
                      .+.|.+.|++|++.+..+   +..+|.+++|+|||++...++..   .+  .++++++||..|
T Consensus       321 ~~~l~~~Q~~Ai~~~~~~---~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~A  380 (720)
T TIGR01448       321 RKGLSEEQKQALDTAIQH---KVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRA  380 (720)
T ss_pred             CCCCCHHHHHHHHHHHhC---CeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHH
Confidence            467888999999998765   58889999999999988655443   34  578888998643

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.30  E-value=2.2e-05  Score=54.68  Aligned_cols=40  Identities=18%  Similarity=0.207  Sum_probs=29.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.+.|.+.+..+.+.+  .+.+|+++||||||+..-+++..
T Consensus       128 ~~~~~~~~~L~~~v~~~--~nilI~G~tGSGKTTll~aL~~~  167 (323)
T PRK13833        128 IMTEAQASVIRSAIDSR--LNIVISGGTGSGKTTLANAVIAE  167 (323)
T ss_pred             CCCHHHHHHHHHHHHcC--CeEEEECCCCCCHHHHHHHHHHH
Confidence            34456777777766654  67889999999999998666543

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=97.30  E-value=2.3e-05  Score=59.16  Aligned_cols=56  Identities=18%  Similarity=0.197  Sum_probs=42.1

Q ss_pred             eeccchhhHHHHHhcCCcce-eeeEEEeCCCCceeEeeeeEE----E---EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRAR-SGVIVLPCGAGKSLVGVTACC----T---VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~-~~~i~~pTGsGKT~i~~~~~~----~---~~~~~lil~p~~~~   65 (67)
                      ..+++|.++++......... ..++.+|||+|||..++..+.    .   ...+.+.+-|..++
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~  258 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTI  258 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHH
Confidence            34789999999988754334 788899999999998865433    2   35688888887654

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.28  E-value=2.9e-05  Score=53.24  Aligned_cols=35  Identities=20%  Similarity=0.223  Sum_probs=26.0

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+.+..+.+.+  ++.+|++|||||||+++-+++..
T Consensus       121 ~~~~L~~~v~~~--~~ilI~G~tGSGKTTll~al~~~  155 (299)
T TIGR02782       121 QRDVLREAVLAR--KNILVVGGTGSGKTTLANALLAE  155 (299)
T ss_pred             HHHHHHHHHHcC--CeEEEECCCCCCHHHHHHHHHHH
Confidence            455555555543  68899999999999998776654

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.24  E-value=3.3e-05  Score=57.30  Aligned_cols=50  Identities=14%  Similarity=0.157  Sum_probs=39.0

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~~   65 (67)
                      +.|++|+..++.+   +..+|.+++|+|||++...++..+        +.++++.+||--|
T Consensus       148 ~~Qk~A~~~al~~---~~~vitGgpGTGKTt~v~~ll~~l~~~~~~~~~~~I~l~APTGkA  205 (586)
T TIGR01447       148 NWQKVAVALALKS---NFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAAPTGKA  205 (586)
T ss_pred             HHHHHHHHHHhhC---CeEEEEcCCCCCHHHHHHHHHHHHHHhccccCCCcEEEECCcHHH
Confidence            6899999999886   689999999999999876554321        1468889998533

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.

>KOG0335|consensus

Probab=97.24  E-value=1.6e-05  Score=58.05  Aligned_cols=60  Identities=22%  Similarity=0.208  Sum_probs=45.1

Q ss_pred             cccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----------------EeeeeEEEeecceeeC
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----------------VRKRALVLCNSGVVFC   67 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----------------~~~~~lil~p~~~~v~   67 (67)
                      ...-..+-|+|+-++..+.+.   +..+.+++||||||..++..+-.                ...+.+|++||..+|+
T Consensus        91 ~~~~~~ptpvQk~sip~i~~G---rdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~lIlapTReL~~  166 (482)
T KOG0335|consen   91 RSGYTKPTPVQKYSIPIISGG---RDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRALILAPTRELVD  166 (482)
T ss_pred             cccccCCCcceeeccceeecC---CceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCceEEEeCcHHHhh
Confidence            334456788999999988876   67889999999999887654321                0246899999987764

>PRK08181 transposase; Validated

Probab=97.21  E-value=6.2e-05  Score=51.16  Aligned_cols=47  Identities=19%  Similarity=0.205  Sum_probs=31.3

Q ss_pred             eccchhhHHH---HHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         11 LRPYQEKSLR---KMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        11 lR~yQ~~av~---~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      +-..|..++.   +|.+.+  .+.++.+|+|+|||+.+.++...   .+.+++++
T Consensus        88 ~~~~~~~~L~~~~~~~~~~--~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~  140 (269)
T PRK08181         88 VSKAQVMAIAAGDSWLAKG--ANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFT  140 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcC--ceEEEEecCCCcHHHHHHHHHHHHHHcCCceeee
Confidence            3345555553   466544  67899999999999999877643   34455543

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.21  E-value=4.9e-05  Score=56.75  Aligned_cols=50  Identities=20%  Similarity=0.195  Sum_probs=38.5

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-------eeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-------RKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-------~~~~lil~p~~~~   65 (67)
                      ++|++|+...+.+   +..+|.+++|+|||++...++..+       ..++++.+||.-|
T Consensus       155 d~Qk~Av~~a~~~---~~~vItGgpGTGKTt~v~~ll~~l~~~~~~~~~~i~l~APTgkA  211 (615)
T PRK10875        155 DWQKVAAAVALTR---RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKA  211 (615)
T ss_pred             HHHHHHHHHHhcC---CeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCCcEEEEECCcHHH
Confidence            6899999988876   589999999999999875554321       2467888888543

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=97.14  E-value=4.7e-05  Score=58.32  Aligned_cols=37  Identities=19%  Similarity=0.187  Sum_probs=28.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ++.++.+|||||||+.+...+..   .++++++++||..+
T Consensus        21 ~~vvv~A~TGSGKTt~~pl~lL~~~~~~~~ilvlqPrR~a   60 (812)
T PRK11664         21 PQVLLKAPTGAGKSTWLPLQLLQHGGINGKIIMLEPRRLA   60 (812)
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHcCCcCCeEEEECChHHH
Confidence            67899999999999988544332   24689999999764

>PRK06526 transposase; Provisional

Probab=97.09  E-value=0.00011  Score=49.36  Aligned_cols=28  Identities=18%  Similarity=0.247  Sum_probs=21.9

Q ss_pred             HhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         22 MFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        22 ~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |++.+  .+.++.+|+|+|||+++.++...
T Consensus        94 fi~~~--~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         94 FVTGK--ENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             hhhcC--ceEEEEeCCCCchHHHHHHHHHH
Confidence            55443  68899999999999999876543

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

Probab=97.09  E-value=5.5e-05  Score=52.79  Aligned_cols=55  Identities=20%  Similarity=0.268  Sum_probs=41.9

Q ss_pred             eccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeeccee
Q psy11637         11 LRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNSGVV   65 (67)
Q Consensus        11 lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~~~~   65 (67)
                      |-+-|+++++.+++.   .++.+..|.+|-|+|||++.-.+....   +..+++++||-.|
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~A   62 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIA   62 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHH
Confidence            567799998887542   334678899999999999987665543   5678999998655

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

>KOG0348|consensus

Probab=97.07  E-value=6.9e-05  Score=55.99  Aligned_cols=48  Identities=19%  Similarity=0.289  Sum_probs=37.7

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----------E-eeeeEEEeecce
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----------V-RKRALVLCNSGV   64 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----------~-~~~~lil~p~~~   64 (67)
                      -|+++|=.+++.   +..+|..+||||||+.++..+-.           . +--+||+|||.-
T Consensus       163 VQkq~IP~lL~g---rD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTRE  222 (708)
T KOG0348|consen  163 VQKQAIPVLLEG---RDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTRE  222 (708)
T ss_pred             HhhcchhhhhcC---cceEEEcCCCCcccHHHHHHHHHHHHhcCccccccCCceEEEEechHH
Confidence            589999888885   78999999999999988654321           1 345899999964

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.04  E-value=6.7e-05  Score=50.19  Aligned_cols=46  Identities=9%  Similarity=0.166  Sum_probs=31.7

Q ss_pred             chhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         14 YQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        14 yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      +.++.+++.+.. ..+...++.+|+|+|||.++..+....+.+++.+
T Consensus         6 ~~~~l~~~~l~~l~~g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i   52 (262)
T TIGR02640         6 AVKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLI   52 (262)
T ss_pred             HHHHHHHHHHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEE
Confidence            344555544432 1126888999999999999988877667676655

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).

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

Probab=97.04  E-value=5.5e-05  Score=55.09  Aligned_cols=51  Identities=18%  Similarity=0.195  Sum_probs=37.7

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-EE------eee-eEEEeecce
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-TV------RKR-ALVLCNSGV   64 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~~------~~~-~lil~p~~~   64 (67)
                      +=|.|..++-.++..   ++.+..++||||||..++..+. .+      ... +||++||.-
T Consensus        52 pt~IQ~~~IP~~l~g---~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRE  110 (513)
T COG0513          52 PTPIQLAAIPLILAG---RDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRE  110 (513)
T ss_pred             CCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHH
Confidence            345799999999987   6899999999999877743222 11      112 899999964

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.02  E-value=0.00011  Score=49.50  Aligned_cols=42  Identities=21%  Similarity=0.276  Sum_probs=30.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+-+.|.+.+++++... .+..+|.+|||||||++..+++...
T Consensus        63 g~~~~~~~~l~~~~~~~-~GlilisG~tGSGKTT~l~all~~i  104 (264)
T cd01129          63 GLKPENLEIFRKLLEKP-HGIILVTGPTGSGKTTTLYSALSEL  104 (264)
T ss_pred             CCCHHHHHHHHHHHhcC-CCEEEEECCCCCcHHHHHHHHHhhh
Confidence            35566778888777542 1567889999999999887665543

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.

>KOG0947|consensus

Probab=96.97  E-value=0.00014  Score=57.09  Aligned_cols=54  Identities=17%  Similarity=0.149  Sum_probs=42.7

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeE---EEEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC---CTVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~---~~~~~~~lil~p~~~   64 (67)
                      .|.|=.+|++|+..+..+   .+.++.++|.+|||++|-.++   .....|+++-.|-.+
T Consensus       295 pFelD~FQk~Ai~~lerg---~SVFVAAHTSAGKTvVAEYAialaq~h~TR~iYTSPIKA  351 (1248)
T KOG0947|consen  295 PFELDTFQKEAIYHLERG---DSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTSPIKA  351 (1248)
T ss_pred             CCCccHHHHHHHHHHHcC---CeEEEEecCCCCcchHHHHHHHHHHhhccceEecchhhh
Confidence            456667899999998887   689999999999999995443   345778888877554

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.96  E-value=0.00031  Score=51.60  Aligned_cols=41  Identities=20%  Similarity=0.327  Sum_probs=30.1

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-++|.+.+.++++..+ +-.++.+|||||||++..+++.++
T Consensus       242 ~~~~~~~~~~~~~~~p~-GliLvTGPTGSGKTTTLY~~L~~l  282 (500)
T COG2804         242 MSPFQLARLLRLLNRPQ-GLILVTGPTGSGKTTTLYAALSEL  282 (500)
T ss_pred             CCHHHHHHHHHHHhCCC-eEEEEeCCCCCCHHHHHHHHHHHh
Confidence            35667777777777642 566777999999999887666553

>KOG0390|consensus

Probab=96.96  E-value=8.2e-05  Score=56.93  Aligned_cols=56  Identities=25%  Similarity=0.437  Sum_probs=41.3

Q ss_pred             ceeeccchhhHHHHHhcC--C-----cceeeeEEEeCCCCceeEeeeeEEEE-----e-----eeeEEEeecc
Q psy11637          8 SAVLRPYQEKSLRKMFGN--G-----RARSGVIVLPCGAGKSLVGVTACCTV-----R-----KRALVLCNSG   63 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~--~-----~~~~~~i~~pTGsGKT~i~~~~~~~~-----~-----~~~lil~p~~   63 (67)
                      ...|||||+|.++-..++  +     ..+..++.-.+|+|||+....++...     +     .+.|||+|.+
T Consensus       236 ~~~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~s  308 (776)
T KOG0390|consen  236 KKILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSS  308 (776)
T ss_pred             hhhcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcCccccccccEEEccHH
Confidence            358999999999876653  1     12345666789999999988776542     3     6889999975

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=96.96  E-value=0.00013  Score=54.95  Aligned_cols=50  Identities=16%  Similarity=0.151  Sum_probs=36.9

Q ss_pred             eeccc--hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637         10 VLRPY--QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~y--Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .+|||  |..++-.++.+    + +..|.||+|||.+++..+..   .+..++|++||..
T Consensus       101 g~~p~~VQ~~~~~~ll~G----~-Iae~~TGeGKTla~~lp~~~~al~G~~v~VvTptre  155 (656)
T PRK12898        101 GQRHFDVQLMGGLALLSG----R-LAEMQTGEGKTLTATLPAGTAALAGLPVHVITVNDY  155 (656)
T ss_pred             CCCCChHHHHHHHHHhCC----C-eeeeeCCCCcHHHHHHHHHHHhhcCCeEEEEcCcHH
Confidence            34555  77777666654    3 78899999999999755443   3678999999864

>KOG1805|consensus

Probab=96.95  E-value=8.7e-05  Score=58.02  Aligned_cols=55  Identities=18%  Similarity=0.123  Sum_probs=46.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecceee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVVF   66 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~v   66 (67)
                      .|..-|++|+.+.+...  +..+|.+=+|+|||++...++.-   .++++|+.+=|..||
T Consensus       669 ~LN~dQr~A~~k~L~ae--dy~LI~GMPGTGKTTtI~~LIkiL~~~gkkVLLtsyThsAV  726 (1100)
T KOG1805|consen  669 RLNNDQRQALLKALAAE--DYALILGMPGTGKTTTISLLIKILVALGKKVLLTSYTHSAV  726 (1100)
T ss_pred             hcCHHHHHHHHHHHhcc--chheeecCCCCCchhhHHHHHHHHHHcCCeEEEEehhhHHH
Confidence            56778999999999875  68999999999999999888765   488999988887776

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

Probab=96.95  E-value=7.4e-05  Score=47.29  Aligned_cols=37  Identities=35%  Similarity=0.320  Sum_probs=24.7

Q ss_pred             eeeeEEEeCCCCceeEee-eeEEE---EeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGV-TACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~-~~~~~---~~~~~lil~p~~~~   65 (67)
                      ...+|.+.||+|||.-.+ .++.+   .+.|+||++||.+.
T Consensus         5 ~~~~~d~hpGaGKTr~vlp~~~~~~i~~~~rvLvL~PTRvv   45 (148)
T PF07652_consen    5 ELTVLDLHPGAGKTRRVLPEIVREAIKRRLRVLVLAPTRVV   45 (148)
T ss_dssp             EEEEEE--TTSSTTTTHHHHHHHHHHHTT--EEEEESSHHH
T ss_pred             ceeEEecCCCCCCcccccHHHHHHHHHccCeEEEecccHHH
Confidence            678899999999998543 33332   46899999999764

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 ....

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=96.92  E-value=0.00014  Score=55.86  Aligned_cols=37  Identities=24%  Similarity=0.222  Sum_probs=29.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ...++.+|||||||+.+...+..   .+.+++++.|+..+
T Consensus        18 ~~vIi~a~TGSGKTT~vpl~lL~~~~~~~~ilvlqPrR~a   57 (819)
T TIGR01970        18 PQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLA   57 (819)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHhhccCCeEEEEeCcHHH
Confidence            68899999999999988544332   35689999999764

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.

>PRK10536 hypothetical protein; Provisional

Probab=96.91  E-value=0.00021  Score=48.79  Aligned_cols=34  Identities=15%  Similarity=0.175  Sum_probs=26.4

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .|...++.+.+.   ...++.+|+|+|||+++.++..
T Consensus        63 ~Q~~~l~al~~~---~lV~i~G~aGTGKT~La~a~a~   96 (262)
T PRK10536         63 AQAHYLKAIESK---QLIFATGEAGCGKTWISAAKAA   96 (262)
T ss_pred             HHHHHHHHHhcC---CeEEEECCCCCCHHHHHHHHHH
Confidence            577777766553   5888899999999999977655

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=96.91  E-value=8.5e-05  Score=47.45  Aligned_cols=31  Identities=19%  Similarity=0.284  Sum_probs=22.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      .+.++.+|+|+|||..+.+++.++   +.+++++
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~   81 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFI   81 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEE
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEe
Confidence            678889999999999998876543   4455554

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.90  E-value=9.6e-05  Score=51.25  Aligned_cols=39  Identities=13%  Similarity=0.141  Sum_probs=28.6

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +-+.|.+.++...+.+  .+.+|++|||||||+...+++..
T Consensus       133 ~~~~~~~~L~~~v~~~--~~ilI~G~tGSGKTTll~aL~~~  171 (319)
T PRK13894        133 MTAAQREAIIAAVRAH--RNILVIGGTGSGKTTLVNAIINE  171 (319)
T ss_pred             CCHHHHHHHHHHHHcC--CeEEEECCCCCCHHHHHHHHHHh
Confidence            3345667776666554  78999999999999888766643

>KOG1000|consensus

Probab=96.88  E-value=0.00013  Score=54.23  Aligned_cols=53  Identities=19%  Similarity=0.317  Sum_probs=45.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE--EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT--VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~--~~~~~lil~p~~~   64 (67)
                      .|-|||++.+.-.++++  ++.++--..|-|||+-+++++..  ...+.||+||..+
T Consensus       198 ~LlPFQreGv~faL~Rg--GR~llADeMGLGKTiQAlaIA~yyraEwplliVcPAsv  252 (689)
T KOG1000|consen  198 RLLPFQREGVIFALERG--GRILLADEMGLGKTIQALAIARYYRAEWPLLIVCPASV  252 (689)
T ss_pred             hhCchhhhhHHHHHhcC--CeEEEecccccchHHHHHHHHHHHhhcCcEEEEecHHH
Confidence            57799999999988876  78999999999999999887764  5789999999754

>KOG0392|consensus

Probab=96.87  E-value=6.7e-05  Score=59.89  Aligned_cols=56  Identities=27%  Similarity=0.441  Sum_probs=42.7

Q ss_pred             ceeeccchhhHHHH--HhcCCcceeeeEEEeCCCCceeEeeeeEEE------------EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRK--MFGNGRARSGVIVLPCGAGKSLVGVTACCT------------VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~--~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------------~~~~~lil~p~~~   64 (67)
                      +.+||.||+|.+.+  +++. .+-+|+++-..|-|||+-.+.+++.            ...|.|||||++-
T Consensus       973 ~a~LRkYQqEGVnWLaFLnk-y~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPsTL 1042 (1549)
T KOG0392|consen  973 SAKLRKYQQEGVNWLAFLNK-YKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPSTL 1042 (1549)
T ss_pred             hHHHHHHHHhccHHHHHHHH-hcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCchh
Confidence            46899999999987  4442 2368999999999999887665542            1346899999863

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.86  E-value=0.00013  Score=57.07  Aligned_cols=55  Identities=25%  Similarity=0.160  Sum_probs=42.3

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      +.|-+-|++|++.++...  +..+|.++.|+|||++.-.+..   ..+.+++.++||..|
T Consensus       345 ~~Ls~eQr~Av~~il~s~--~v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkA  402 (988)
T PRK13889        345 LVLSGEQADALAHVTDGR--DLGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIA  402 (988)
T ss_pred             CCCCHHHHHHHHHHhcCC--CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHH
Confidence            568889999999998753  4678999999999987543322   236688999998654

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.84  E-value=0.0005  Score=44.01  Aligned_cols=32  Identities=25%  Similarity=0.276  Sum_probs=22.7

Q ss_pred             HHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         20 RKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        20 ~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +++.........++.+|+|+|||+++..+...
T Consensus        30 ~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~   61 (226)
T TIGR03420        30 RQLAAGKGDRFLYLWGESGSGKSHLLQAACAA   61 (226)
T ss_pred             HHHHhcCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            33443333467889999999999998766544

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.

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=96.83  E-value=0.00016  Score=56.01  Aligned_cols=34  Identities=15%  Similarity=0.191  Sum_probs=28.2

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEe-----eeeEEEeecce
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVR-----KRALVLCNSGV   64 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~-----~~~lil~p~~~   64 (67)
                      .=|.|.||+|||.+++..+.+++     .+.+|+|||.+
T Consensus        77 iDI~METGTGKTy~YlrtmfeLhk~YG~~KFIivVPs~A  115 (985)
T COG3587          77 IDILMETGTGKTYTYLRTMFELHKKYGLFKFIIVVPSLA  115 (985)
T ss_pred             eeEEEecCCCceeeHHHHHHHHHHHhCceeEEEEeccHH
Confidence            34679999999999999888753     58999999864

>KOG0385|consensus

Probab=96.82  E-value=5.7e-05  Score=58.13  Aligned_cols=57  Identities=21%  Similarity=0.284  Sum_probs=44.4

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~   64 (67)
                      ..+|||||.+.+.+...- .-+-+|++---.|-|||+-.+++...      ..+|.||+||.++
T Consensus       165 ~g~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~P~St  228 (971)
T KOG0385|consen  165 GGELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIAPKST  228 (971)
T ss_pred             CCccchhhhccHHHHHHHHhcCcccEeehhcccchHHHHHHHHHHHHHhcCCCCCeEEEeeHhh
Confidence            378999999999986642 11267999999999999887665543      3689999999765

>KOG0951|consensus

Probab=96.81  E-value=0.00013  Score=58.51  Aligned_cols=55  Identities=18%  Similarity=0.225  Sum_probs=40.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE--------------EeeeeEEEeecceee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT--------------VRKRALVLCNSGVVF   66 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~--------------~~~~~lil~p~~~~v   66 (67)
                      .|.+-|....+..+...  .+.++++|||+|||-+++.-+.+              ...++.+++|..++|
T Consensus       309 sLNrIQS~v~daAl~~~--EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAPmKaLv  377 (1674)
T KOG0951|consen  309 SLNRIQSKVYDAALRGD--ENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAPMKALV  377 (1674)
T ss_pred             hhhHHHHHHHHHHhcCc--CcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEeeHHHHH
Confidence            35556666666666654  79999999999999999754432              134889999987654

>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=96.80  E-value=0.0001  Score=48.87  Aligned_cols=24  Identities=21%  Similarity=0.192  Sum_probs=20.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++.++.+|||||||+...+++...
T Consensus       128 ~~ili~G~tGSGKTT~l~all~~i  151 (270)
T PF00437_consen  128 GNILISGPTGSGKTTLLNALLEEI  151 (270)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             eEEEEECCCccccchHHHHHhhhc
Confidence            789999999999999987776654

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 ....

>KOG0387|consensus

Probab=96.80  E-value=0.00015  Score=55.86  Aligned_cols=56  Identities=21%  Similarity=0.421  Sum_probs=42.4

Q ss_pred             eeeccchhhHHHHHhc-CCcceeeeEEEeCCCCceeEeeeeEE------EEeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFG-NGRARSGVIVLPCGAGKSLVGVTACC------TVRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~-~~~~~~~~i~~pTGsGKT~i~~~~~~------~~~~~~lil~p~~~   64 (67)
                      -.|.|||++.+++..+ +.+...|++--..|-|||+-..++..      +..+|+|||||.+.
T Consensus       204 ~~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~Ti  266 (923)
T KOG0387|consen  204 SKLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPATI  266 (923)
T ss_pred             HHhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccHHH
Confidence            3688999999999665 22335688999999999987754433      23579999999864

>KOG1807|consensus

Probab=96.78  E-value=0.00024  Score=54.86  Aligned_cols=56  Identities=25%  Similarity=0.294  Sum_probs=44.4

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEeecceee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLCNSGVVF   66 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~p~~~~v   66 (67)
                      -..|-+.|+.|.+..+..   +-.+|.+|+|+|||++.+.++..         ...|++++|-|+-+|
T Consensus       376 ~~ildsSq~~A~qs~lty---elsliqgppGTgkt~vtlkav~tLL~n~s~~~~~epIlvvC~Tnhav  440 (1025)
T KOG1807|consen  376 LVILDSSQQFAKQSKLTY---ELSLIQGPPGTGKTLVTLKAVDTLLLNSSGYTEPEPILVVCLTNHAV  440 (1025)
T ss_pred             ceeecHHHHHHHHHHhhh---hhheeecCCCCCceeehHHHHHHHHhcccccccccceeeeehhhHHH
Confidence            345666799999998887   57899999999999999876643         256899998876554

>KOG1133|consensus

Probab=96.76  E-value=0.00061  Score=52.08  Aligned_cols=41  Identities=29%  Similarity=0.467  Sum_probs=32.0

Q ss_pred             cccccceeeccchhhHHHHHhc---CCcceeeeEEEeCCCCceeEe
Q psy11637          3 IDLKPSAVLRPYQEKSLRKMFG---NGRARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus         3 ~~l~~~~~lR~yQ~~av~~~~~---~~~~~~~~i~~pTGsGKT~i~   45 (67)
                      +++.+.+++++-|.+.++++..   .+  +.|++-.|||+|||+-.
T Consensus         8 ~~F~fPy~PYdIQ~~lM~elyrvLe~G--kIgIfESPTGTGKSLSL   51 (821)
T KOG1133|consen    8 IEFPFPYTPYDIQEDLMRELYRVLEEG--KIGIFESPTGTGKSLSL   51 (821)
T ss_pred             cccCCCCCchhHHHHHHHHHHHHHhcC--CeeeeeCCCCCCchHHH
Confidence            3566777888889999887554   44  68999999999998643

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=96.76  E-value=0.0003  Score=49.35  Aligned_cols=24  Identities=21%  Similarity=0.350  Sum_probs=20.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.+|++|||||||+..-+++...
T Consensus       163 ~nilI~G~tGSGKTTll~aLl~~i  186 (344)
T PRK13851        163 LTMLLCGPTGSGKTTMSKTLISAI  186 (344)
T ss_pred             CeEEEECCCCccHHHHHHHHHccc
Confidence            789999999999999987776653

>PRK05642 DNA replication initiation factor; Validated

Probab=96.74  E-value=0.00029  Score=46.46  Aligned_cols=31  Identities=23%  Similarity=0.147  Sum_probs=21.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      ...++.+|+|+|||+.+.++...   .+.+++++
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~   79 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYL   79 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEe
Confidence            34678899999999997665432   23455554

>PRK09183 transposase/IS protein; Provisional

Probab=96.73  E-value=0.00023  Score=47.81  Aligned_cols=31  Identities=16%  Similarity=0.247  Sum_probs=22.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .+.++.+|+|+|||+.+.++...   .+.+++++
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~  136 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFT  136 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            67889999999999999776432   34455554

>PRK10436 hypothetical protein; Provisional

Probab=96.72  E-value=0.00015  Score=52.68  Aligned_cols=41  Identities=22%  Similarity=0.242  Sum_probs=28.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+-+.|.+.+++.+... .+..++.+|||||||++..+++..
T Consensus       201 G~~~~~~~~l~~~~~~~-~GliLvtGpTGSGKTTtL~a~l~~  241 (462)
T PRK10436        201 GMTPAQLAQFRQALQQP-QGLILVTGPTGSGKTVTLYSALQT  241 (462)
T ss_pred             CcCHHHHHHHHHHHHhc-CCeEEEECCCCCChHHHHHHHHHh
Confidence            34556777777766542 256778899999999987655544

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

Probab=96.71  E-value=0.00033  Score=50.16  Aligned_cols=59  Identities=19%  Similarity=0.221  Sum_probs=45.1

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecceeeC
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVVFC   67 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~v~   67 (67)
                      ..+|-|+|+.+-...+.. .++...++.+-||+|||-+....+..   .++++.+..|+ +=||
T Consensus        95 ~G~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMif~~i~~al~~G~~vciASPR-vDVc  157 (441)
T COG4098          95 KGTLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASPR-VDVC  157 (441)
T ss_pred             ccccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhhHHHHHHHHhcCCeEEEecCc-ccch
Confidence            457889999998886653 22367889999999999998766654   57888888887 4444

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

Probab=96.71  E-value=8.4e-05  Score=56.11  Aligned_cols=55  Identities=15%  Similarity=0.241  Sum_probs=44.0

Q ss_pred             eeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecc
Q psy11637          9 AVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSG   63 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~   63 (67)
                      |+|=..|+++++++...   ...-+.++.+..|||||++++..+..   .+..+.+++||-
T Consensus       261 F~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q~ALMAPTE  321 (677)
T COG1200         261 FKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAPTE  321 (677)
T ss_pred             CCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCCeeEEeccHH
Confidence            55667899999999863   34578899999999999999766554   467888889985

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.70  E-value=0.00072  Score=44.58  Aligned_cols=49  Identities=16%  Similarity=0.222  Sum_probs=29.1

Q ss_pred             ccccccceeeccc----hhhHHH---HHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637          2 TIDLKPSAVLRPY----QEKSLR---KMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus         2 ~~~l~~~~~lR~y----Q~~av~---~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ++++++...+-++    +..++.   ++.......+.++.+|+|+|||+.+.+++.
T Consensus        12 ~~~~~~~~~fd~f~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~   67 (235)
T PRK08084         12 PLYLPDDETFASFYPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACA   67 (235)
T ss_pred             CCCCCCcCCccccccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            3445555444333    333443   333333335788899999999998866554

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=96.69  E-value=0.00026  Score=49.62  Aligned_cols=49  Identities=16%  Similarity=0.141  Sum_probs=35.6

Q ss_pred             cccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ..+.+.+++.-..++-.++..+  ++.++.+|+|+|||.++..++..++.+
T Consensus        43 ~d~~y~f~~~~~~~vl~~l~~~--~~ilL~G~pGtGKTtla~~lA~~l~~~   91 (327)
T TIGR01650        43 IDPAYLFDKATTKAICAGFAYD--RRVMVQGYHGTGKSTHIEQIAARLNWP   91 (327)
T ss_pred             CCCCccCCHHHHHHHHHHHhcC--CcEEEEeCCCChHHHHHHHHHHHHCCC
Confidence            3445667766666677766554  689999999999999998776655433

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.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.66  E-value=0.00027  Score=51.47  Aligned_cols=42  Identities=14%  Similarity=0.181  Sum_probs=29.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+-|.|.+.+++.+...+ +-.++.+|||||||++..+++...
T Consensus       225 g~~~~~~~~l~~~~~~~~-GlilitGptGSGKTTtL~a~L~~l  266 (486)
T TIGR02533       225 GMSPELLSRFERLIRRPH-GIILVTGPTGSGKTTTLYAALSRL  266 (486)
T ss_pred             CCCHHHHHHHHHHHhcCC-CEEEEEcCCCCCHHHHHHHHHhcc
Confidence            345567777777776431 456788999999999887655543

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=96.66  E-value=0.0002  Score=46.27  Aligned_cols=44  Identities=20%  Similarity=0.363  Sum_probs=30.9

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---E-eeeeEEEee
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---V-RKRALVLCN   61 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~-~~~~lil~p   61 (67)
                      .+|+.+..+  .+...+|.+|+|+|||..++.++..   . +.+++++.-
T Consensus         7 ~LD~~l~GGip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~   56 (226)
T PF06745_consen    7 GLDELLGGGIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSF   56 (226)
T ss_dssp             THHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEES
T ss_pred             hHHHhhcCCCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEe
Confidence            467777543  2456888899999999999877654   2 678887763

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 ....

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.60  E-value=0.00072  Score=42.92  Aligned_cols=39  Identities=18%  Similarity=0.140  Sum_probs=29.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+-+.|.+.++..++.+  ...++++|||||||+..-+++.
T Consensus         9 ~~~~~~~~~l~~~v~~g--~~i~I~G~tGSGKTTll~aL~~   47 (186)
T cd01130           9 TFSPLQAAYLWLAVEAR--KNILISGGTGSGKTTLLNALLA   47 (186)
T ss_pred             CCCHHHHHHHHHHHhCC--CEEEEECCCCCCHHHHHHHHHh
Confidence            44456777777777765  6889999999999987755443

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.

>KOG0345|consensus

Probab=96.60  E-value=0.00038  Score=51.32  Aligned_cols=50  Identities=20%  Similarity=0.312  Sum_probs=36.2

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----------eeeeEEEeecce
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----------RKRALVLCNSGV   64 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----------~~~~lil~p~~~   64 (67)
                      =|-|..++=-++++   ...++.+|||||||..++..+.+.           +--.|||+||.-
T Consensus        30 TpVQa~tIPlll~~---KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRE   90 (567)
T KOG0345|consen   30 TPVQAATIPLLLKN---KDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRE   90 (567)
T ss_pred             CHHHHhhhHHHhcC---CceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEEecCcHH
Confidence            45677777777776   678899999999999886544321           124799999863

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.59  E-value=0.00025  Score=55.03  Aligned_cols=53  Identities=15%  Similarity=0.222  Sum_probs=36.4

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..+|||=.+.+-.+.-+   ..-+..|+||+|||+++...+..   .+..++|++||..
T Consensus        79 lg~~~ydvQliGg~~Lh---~G~Iaem~TGeGKTL~a~Lpa~~~al~G~~V~VvTpn~y  134 (896)
T PRK13104         79 LGLRHFDVQLIGGMVLH---EGNIAEMRTGEGKTLVATLPAYLNAISGRGVHIVTVNDY  134 (896)
T ss_pred             cCCCcchHHHhhhhhhc---cCccccccCCCCchHHHHHHHHHHHhcCCCEEEEcCCHH
Confidence            45667766655554333   34467899999999998755542   3567999999864

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.57  E-value=0.00065  Score=50.12  Aligned_cols=43  Identities=19%  Similarity=0.173  Sum_probs=30.1

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..+.|.|.+.+++.+... .+..++.+|||||||++..+++...
T Consensus       298 lg~~~~~~~~l~~~~~~~-~Glilv~G~tGSGKTTtl~a~l~~~  340 (564)
T TIGR02538       298 LGFEPDQKALFLEAIHKP-QGMVLVTGPTGSGKTVSLYTALNIL  340 (564)
T ss_pred             cCCCHHHHHHHHHHHHhc-CCeEEEECCCCCCHHHHHHHHHHhh
Confidence            345566777787776542 1567788999999998876555443

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.

>KOG0330|consensus

Probab=96.57  E-value=0.00044  Score=50.06  Aligned_cols=49  Identities=20%  Similarity=0.132  Sum_probs=37.2

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecce
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGV   64 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~   64 (67)
                      +-|++++=-.+.+   ++.+..+.||||||..++..+..      ...+.||++||.-
T Consensus        86 ~IQ~~aiP~~L~g---~dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRE  140 (476)
T KOG0330|consen   86 KIQSEAIPVALGG---RDVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRE  140 (476)
T ss_pred             hhhhhhcchhhCC---CcEEEEeccCCCchhhhHHHHHHHHHcCCCCceEEEecCcHH
Confidence            3577777777765   68889999999999988765542      2357999999863

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=96.56  E-value=0.0011  Score=40.71  Aligned_cols=41  Identities=20%  Similarity=0.268  Sum_probs=25.5

Q ss_pred             ccchhhHHHHHhc---CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFG---NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~---~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+.|.+.+...++   .+.....+|.++.|+|||.+...+....
T Consensus         5 R~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~   48 (185)
T PF13191_consen    5 REEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRL   48 (185)
T ss_dssp             -HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            7788888888773   2335678899999999998876555443

>KOG0948|consensus

Probab=96.56  E-value=0.00041  Score=53.68  Aligned_cols=54  Identities=19%  Similarity=0.252  Sum_probs=43.3

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~   64 (67)
                      .|+|-|+|..++..+-+.   .+.++++-|.+|||++|.-+|.   +-+.|+++-.|-.+
T Consensus       127 PF~LDpFQ~~aI~Cidr~---eSVLVSAHTSAGKTVVAeYAIA~sLr~kQRVIYTSPIKA  183 (1041)
T KOG0948|consen  127 PFTLDPFQSTAIKCIDRG---ESVLVSAHTSAGKTVVAEYAIAMSLREKQRVIYTSPIKA  183 (1041)
T ss_pred             CcccCchHhhhhhhhcCC---ceEEEEeecCCCcchHHHHHHHHHHHhcCeEEeeChhhh
Confidence            478889999999887765   6999999999999999965444   34778888877554

>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=96.55  E-value=0.00013  Score=42.64  Aligned_cols=24  Identities=25%  Similarity=0.199  Sum_probs=18.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEee
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      -+|.+|+|||||+++-.++...+-
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~   25 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGF   25 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
Confidence            368899999999999777665443

...

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.54  E-value=0.00049  Score=47.95  Aligned_cols=24  Identities=17%  Similarity=0.124  Sum_probs=20.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.+|++|||||||+..-+++...
T Consensus       161 ~nili~G~tgSGKTTll~aL~~~i  184 (332)
T PRK13900        161 KNIIISGGTSTGKTTFTNAALREI  184 (332)
T ss_pred             CcEEEECCCCCCHHHHHHHHHhhC
Confidence            789999999999999887666543

>KOG1806|consensus

Probab=96.53  E-value=0.0012  Score=52.43  Aligned_cols=50  Identities=24%  Similarity=0.328  Sum_probs=39.1

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~   65 (67)
                      |-|-+++......   +-.++++|+|.|||.++..++.-.     ..+++|++|++.|
T Consensus       741 ~~qveai~sg~qp---gltmvvgppgtgktd~avqil~~lyhn~p~qrTlivthsnqa  795 (1320)
T KOG1806|consen  741 PTQVEAILSGMQP---GLTMVVGPPGTGKTDVAVQILSVLYHNSPNQRTLIVTHSNQA  795 (1320)
T ss_pred             HHHHHHHHhcCCC---CceeeecCCCCCCcchhhhhhhhhhhcCCCcceEEEEecccc
Confidence            3566666654444   688999999999999998877653     5799999999865

>KOG0949|consensus

Probab=96.49  E-value=0.00061  Score=53.88  Aligned_cols=54  Identities=24%  Similarity=0.311  Sum_probs=41.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecceee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVVF   66 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~v   66 (67)
                      .+-.+|++.++-.=..   .+++|++||-+|||++..-++.+.     .+=+++++|+.++|
T Consensus       511 ~Pd~WQ~elLDsvDr~---eSavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLV  569 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRN---ESAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALV  569 (1330)
T ss_pred             CCcHHHHHHhhhhhcc---cceEEEeeccCCceeccHHHHHHHHhhcCCCEEEEecchHHHh
Confidence            3344788877764443   799999999999999998777653     45688999998775

>KOG0386|consensus

Probab=96.48  E-value=0.00023  Score=55.94  Aligned_cols=59  Identities=17%  Similarity=0.277  Sum_probs=47.5

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecceee
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVVF   66 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~v   66 (67)
                      ..+||+||...+++...- +.+-+|++---+|-|||+-.++++..      ..+|.||+||+.+++
T Consensus       392 GG~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~K~~~GP~LvivPlstL~  457 (1157)
T KOG0386|consen  392 GGELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEHKQMQGPFLIIVPLSTLV  457 (1157)
T ss_pred             CCCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHHcccCCCeEEeccccccC
Confidence            468999999999986541 22268999999999999888777654      478999999998764

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.41  E-value=0.0011  Score=44.72  Aligned_cols=38  Identities=13%  Similarity=0.068  Sum_probs=24.8

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...+.+.++++.+...+.++.+|+|+|||+++..++..
T Consensus        22 ~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~   59 (337)
T PRK12402         22 EVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARE   59 (337)
T ss_pred             HHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            33444444555542236889999999999988665443

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.40  E-value=0.00059  Score=44.88  Aligned_cols=45  Identities=11%  Similarity=0.174  Sum_probs=32.8

Q ss_pred             hhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         16 EKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .+.+|+.+..+  .+...+|.+|+|+|||+.++.++..   .+.+++++.
T Consensus         7 i~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877         7 IPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             cHhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            35677777653  2456788899999999999876653   366777775

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.

>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=96.37  E-value=0.00026  Score=43.93  Aligned_cols=31  Identities=13%  Similarity=0.091  Sum_probs=24.0

Q ss_pred             eeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      .+|.+|+|+|||.+++.++..   .+++++++.-
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~   35 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTL   35 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEEC
Confidence            478899999999999876553   4677887753

A related protein is found in archaea.

>PHA02244 ATPase-like protein

Probab=96.34  E-value=0.00048  Score=49.25  Aligned_cols=41  Identities=10%  Similarity=0.118  Sum_probs=29.9

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ..+.+|++.+  ...++.+|||+|||.++.+++...+.+.+.+
T Consensus       110 ~ri~r~l~~~--~PVLL~GppGtGKTtLA~aLA~~lg~pfv~I  150 (383)
T PHA02244        110 ADIAKIVNAN--IPVFLKGGAGSGKNHIAEQIAEALDLDFYFM  150 (383)
T ss_pred             HHHHHHHhcC--CCEEEECCCCCCHHHHHHHHHHHhCCCEEEE
Confidence            3445666665  6788999999999999987776666554443

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.34  E-value=0.00044  Score=54.71  Aligned_cols=56  Identities=23%  Similarity=0.201  Sum_probs=43.7

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      .+.|-+-|++|++.+...+  +..+|.++.|+|||++.-.+..   ..+.+++.++||..|
T Consensus       379 ~~~Ls~eQ~~Av~~i~~~~--r~~~v~G~AGTGKTt~l~~~~~~~e~~G~~V~g~ApTgkA  437 (1102)
T PRK13826        379 HARLSDEQKTAIEHVAGPA--RIAAVVGRAGAGKTTMMKAAREAWEAAGYRVVGGALAGKA  437 (1102)
T ss_pred             CCCCCHHHHHHHHHHhccC--CeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEcCcHHH
Confidence            3578889999999986443  6788999999999998866544   346788888988644

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=96.34  E-value=0.0017  Score=45.93  Aligned_cols=48  Identities=17%  Similarity=0.166  Sum_probs=36.1

Q ss_pred             cccceeeccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637          5 LKPSAVLRPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +++...-|+-|.+.+..++.    ++...+.+|.+|||+|||.++-.++.++
T Consensus        15 iP~~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l   66 (366)
T COG1474          15 IPEELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEEL   66 (366)
T ss_pred             CcccccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHH
Confidence            34456778889988887664    3445679999999999999887666553

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=96.33  E-value=0.0014  Score=44.87  Aligned_cols=45  Identities=24%  Similarity=0.168  Sum_probs=32.5

Q ss_pred             cceeeccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637          7 PSAVLRPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+.-|+.|.+.+..++.    .+...+.+|.+|+|+|||.++-.+...
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~   63 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKE   63 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            345567788888877664    223467899999999999988666543

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=96.32  E-value=0.00029  Score=50.13  Aligned_cols=27  Identities=22%  Similarity=0.351  Sum_probs=21.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      .+.++++|||||||+.+..++..++-|
T Consensus        98 SNILLiGPTGsGKTlLAqTLAk~LnVP  124 (408)
T COG1219          98 SNILLIGPTGSGKTLLAQTLAKILNVP  124 (408)
T ss_pred             ccEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            478899999999999987776655444

>cd01394 radB RadB

Probab=96.29  E-value=0.00059  Score=43.83  Aligned_cols=44  Identities=23%  Similarity=0.400  Sum_probs=32.0

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +.+|+.+..+  .+....|.+++|+|||..++.++..   .+++++++.
T Consensus         6 ~~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~   54 (218)
T cd01394           6 KGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID   54 (218)
T ss_pred             hHHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            4577777643  2356788899999999999887754   356777763

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>KOG1132|consensus

Probab=96.28  E-value=0.00096  Score=51.89  Aligned_cols=43  Identities=23%  Similarity=0.289  Sum_probs=34.0

Q ss_pred             ccccceeeccchhhHHHHHhcCC-cceeeeEEEeCCCCceeEee
Q psy11637          4 DLKPSAVLRPYQEKSLRKMFGNG-RARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus         4 ~l~~~~~lR~yQ~~av~~~~~~~-~~~~~~i~~pTGsGKT~i~~   46 (67)
                      +..+.++++|-|...+.+++... ...++++-.|||+|||+-.+
T Consensus        15 ~V~fP~qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLL   58 (945)
T KOG1132|consen   15 PVEFPFQPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLL   58 (945)
T ss_pred             eeeccCCcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHH
Confidence            44567788999999999988752 23679999999999997554

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=96.25  E-value=0.00018  Score=41.96  Aligned_cols=29  Identities=14%  Similarity=0.124  Sum_probs=22.3

Q ss_pred             eEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         32 VIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      ++++|+|+|||.++-.++...+.+++.+.
T Consensus         2 ll~G~~G~GKT~l~~~la~~l~~~~~~i~   30 (132)
T PF00004_consen    2 LLHGPPGTGKTTLARALAQYLGFPFIEID   30 (132)
T ss_dssp             EEESSTTSSHHHHHHHHHHHTTSEEEEEE
T ss_pred             EEECcCCCCeeHHHHHHHhhccccccccc
Confidence            68899999999998877776665554443

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 ....

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=96.24  E-value=0.0016  Score=43.50  Aligned_cols=36  Identities=17%  Similarity=0.220  Sum_probs=24.0

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |.++++.   +++.+...+.++.+|+|+|||.++..++.
T Consensus        22 ~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~   60 (319)
T PRK00440         22 QEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALAR   60 (319)
T ss_pred             cHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            5555544   44443334578999999999988865544

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.23  E-value=0.00035  Score=52.78  Aligned_cols=53  Identities=23%  Similarity=0.248  Sum_probs=38.9

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~   65 (67)
                      +..|.+.|++|+..   ..  ++.+|.+..|||||.+...-+..       ...++|+++.++.|
T Consensus       194 ~~~L~~~Q~~av~~---~~--~~~lV~agaGSGKT~vl~~r~ayLl~~~~~~~~~IL~ltft~~A  253 (684)
T PRK11054        194 SSPLNPSQARAVVN---GE--DSLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRQA  253 (684)
T ss_pred             CCCCCHHHHHHHhC---CC--CCeEEEEeCCCCHHHHHHHHHHHHHHhCCCCHHHeEEEeccHHH
Confidence            45788899998863   21  46789999999999998765422       24588988887644

>PLN03025 replication factor C subunit; Provisional

Probab=96.20  E-value=0.00083  Score=45.91  Aligned_cols=38  Identities=16%  Similarity=0.233  Sum_probs=26.2

Q ss_pred             chhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|.++++.   +...+...+.++.+|+|+|||..+..++..
T Consensus        17 g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~   57 (319)
T PLN03025         17 GNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHE   57 (319)
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            46666554   444433346789999999999888766554

>PLN02165 adenylate isopentenyltransferase

Probab=96.19  E-value=0.00037  Score=48.99  Aligned_cols=25  Identities=28%  Similarity=0.318  Sum_probs=20.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ...+|.+|||||||.++..++...+
T Consensus        44 ~iivIiGPTGSGKStLA~~LA~~l~   68 (334)
T PLN02165         44 KVVVIMGATGSGKSRLSVDLATRFP   68 (334)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHcC
Confidence            5678889999999999987766544

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.18  E-value=0.00038  Score=45.13  Aligned_cols=32  Identities=19%  Similarity=0.298  Sum_probs=21.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      +..++++|||+|||++..-++.+.   +.++.+++
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis   36 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLKGKKVALIS   36 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhccccceeec
Confidence            346789999999999987666542   44554443

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 ....

>PRK08727 hypothetical protein; Validated

Probab=96.18  E-value=0.00097  Score=43.92  Aligned_cols=31  Identities=19%  Similarity=0.361  Sum_probs=21.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      ...++.+|+|+|||+.+.+++..   .+.+++++
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~   75 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYL   75 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            34788899999999988776443   23455544

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.17  E-value=0.0023  Score=41.42  Aligned_cols=24  Identities=17%  Similarity=0.061  Sum_probs=19.3

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+..++.+|+|+|||+.+.++...
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            357888999999999988766543

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.17  E-value=0.00065  Score=45.67  Aligned_cols=32  Identities=19%  Similarity=0.297  Sum_probs=24.7

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ..+.++.+|+|+|||+++.++..++   +.+++|+
T Consensus       105 ~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~  139 (254)
T COG1484         105 GENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFI  139 (254)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEE
Confidence            3789999999999999998876653   3455554

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

Probab=96.16  E-value=0.00048  Score=54.56  Aligned_cols=58  Identities=22%  Similarity=0.259  Sum_probs=44.9

Q ss_pred             ceeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .+.-=|=|..|++++.+.   +..-..+|++..|.|||-||+-++-.   -++-+.|+|||+.+
T Consensus       592 PyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~GKQVAvLVPTTlL  655 (1139)
T COG1197         592 PYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDGKQVAVLVPTTLL  655 (1139)
T ss_pred             CCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCCCeEEEEcccHHh
Confidence            344445599999998863   44577899999999999999866554   36789999999754

>KOG0340|consensus

Probab=96.16  E-value=0.0016  Score=46.86  Aligned_cols=51  Identities=22%  Similarity=0.221  Sum_probs=39.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----eeeeEEEeecc
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----RKRALVLCNSG   63 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----~~~~lil~p~~   63 (67)
                      +.-|-|+.++-+++++   ++.+-.+-||||||.-+..-+.. +     +-..+|+.||.
T Consensus        29 ~pTpiQ~~cIpkILeG---rdcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTPTr   85 (442)
T KOG0340|consen   29 KPTPIQQACIPKILEG---RDCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTPTR   85 (442)
T ss_pred             CCCchHhhhhHHHhcc---cccccccccCCCcchhhhHHHHHhhccCCCcceEEEecchH
Confidence            4457799999999987   68888999999999877554432 2     44789999885

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=96.16  E-value=0.00095  Score=43.12  Aligned_cols=45  Identities=24%  Similarity=0.356  Sum_probs=32.5

Q ss_pred             hhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         16 EKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .+.+|+.+..+  .+....+.+|+|+|||.+++.++..   .+.+++++.
T Consensus         9 i~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~   58 (225)
T PRK09361          9 CKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYID   58 (225)
T ss_pred             cHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            34578888643  2456788999999999999877653   356777664

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.15  E-value=0.00081  Score=47.68  Aligned_cols=23  Identities=26%  Similarity=0.323  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +..+|++|||||||+...+++..
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~  172 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQH  172 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            56788999999999998776543

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).

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=96.14  E-value=0.00051  Score=43.78  Aligned_cols=42  Identities=21%  Similarity=0.359  Sum_probs=29.3

Q ss_pred             HHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         20 RKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        20 ~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      |+++..+  .+....|.+|+|+|||..++.++..   .+.+++++.-
T Consensus         2 D~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~   48 (209)
T TIGR02237         2 DELLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDT   48 (209)
T ss_pred             hhhhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            4555543  2466888899999999999877653   3567777653

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=96.10  E-value=0.0028  Score=46.23  Aligned_cols=43  Identities=12%  Similarity=0.236  Sum_probs=34.1

Q ss_pred             HHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--eeeeEEEeec
Q psy11637         20 RKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--RKRALVLCNS   62 (67)
Q Consensus        20 ~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--~~~~lil~p~   62 (67)
                      +++|..+.+...+|.+.+|+|||+.++.++..+  ..+++++..+
T Consensus         2 ~~FF~~~~G~TLLIKG~PGTGKTtfaLelL~~l~~~~~v~YISTR   46 (484)
T PF07088_consen    2 KRFFTQEPGQTLLIKGEPGTGKTTFALELLNSLKDHGNVMYISTR   46 (484)
T ss_pred             chhhcCCCCcEEEEecCCCCCceeeehhhHHHHhccCCeEEEEec
Confidence            467766555788889999999999999888765  4567888766

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.09  E-value=0.0009  Score=44.36  Aligned_cols=44  Identities=23%  Similarity=0.394  Sum_probs=32.9

Q ss_pred             HHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeec
Q psy11637         19 LRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNS   62 (67)
Q Consensus        19 v~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~   62 (67)
                      +++++..+  .++..+|.+++|+|||+.++.++..   .+.|+++++-.
T Consensus        12 lD~~l~GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~   60 (260)
T COG0467          12 LDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE   60 (260)
T ss_pred             hHHHhcCCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEec
Confidence            56777642  3467888999999999999887764   36788887643

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=96.09  E-value=0.00037  Score=46.90  Aligned_cols=28  Identities=21%  Similarity=0.332  Sum_probs=20.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      -+|.+|||+|||-.+..++.+.+.++++
T Consensus         4 ~~i~GpT~tGKt~~ai~lA~~~g~pvI~   31 (233)
T PF01745_consen    4 YLIVGPTGTGKTALAIALAQKTGAPVIS   31 (233)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH--EEEE
T ss_pred             EEEECCCCCChhHHHHHHHHHhCCCEEE
Confidence            4688999999999998888877777654

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.08  E-value=0.0015  Score=44.68  Aligned_cols=23  Identities=17%  Similarity=0.109  Sum_probs=19.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.++++|||||||+..-+++..
T Consensus       145 ~~ili~G~tGsGKTTll~al~~~  167 (308)
T TIGR02788       145 KNIIISGGTGSGKTTFLKSLVDE  167 (308)
T ss_pred             CEEEEECCCCCCHHHHHHHHHcc
Confidence            68999999999999987665544

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.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.05  E-value=0.0004  Score=52.07  Aligned_cols=51  Identities=14%  Similarity=0.197  Sum_probs=36.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E---eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V---RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~---~~~~lil~p~~~~   65 (67)
                      .|.|-|++|+...  .   +..+|.+.+|||||.+...-+..    .   ..++|+++-|+-|
T Consensus         2 ~Ln~~Q~~av~~~--~---g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v~p~~IL~lTFT~kA   59 (672)
T PRK10919          2 RLNPGQQQAVEFV--T---GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKA   59 (672)
T ss_pred             CCCHHHHHHHhCC--C---CCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeeeEechHHH
Confidence            4678899988742  2   57889999999999887543332    1   3568888877643

>KOG0328|consensus

Probab=96.05  E-value=0.017  Score=40.88  Aligned_cols=48  Identities=17%  Similarity=0.288  Sum_probs=37.4

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----eeeeEEEeecce
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----RKRALVLCNSGV   64 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----~~~~lil~p~~~   64 (67)
                      -|+.|+-.++++   ++.+..+-.|+|||.++.--+.. .     .-.+||+.||.-
T Consensus        53 IQqrAi~~IlkG---rdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRE  106 (400)
T KOG0328|consen   53 IQQRAIPQILKG---RDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRE  106 (400)
T ss_pred             HHhhhhhhhhcc---cceEEEecCCCCceEEEEeeeeeecccccceeeEEEecChHH
Confidence            499999999987   68888999999999887543332 1     346899999863

>PF12846 AAA_10: AAA-like domain

Probab=96.05  E-value=0.00044  Score=45.20  Aligned_cols=31  Identities=16%  Similarity=0.176  Sum_probs=22.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .+.+|.++||+|||+.+..++..   .+.+++++
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l~~~~~~~g~~~~i~   35 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNLLEQLIRRGPRVVIF   35 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHcCCCEEEE
Confidence            57899999999999888766553   24444444

>KOG0389|consensus

Probab=96.03  E-value=0.00049  Score=53.16  Aligned_cols=61  Identities=18%  Similarity=0.219  Sum_probs=46.5

Q ss_pred             cccceeeccchhhHHHHHh-cCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637          5 LKPSAVLRPYQEKSLRKMF-GNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~-~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      +++.++|.|||.-.+.+.. -+.++-+|++--..|-|||.-+.++...     ..+|=|||||+++.
T Consensus       394 l~s~i~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsSTl  460 (941)
T KOG0389|consen  394 LSSGIQLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSSTL  460 (941)
T ss_pred             cCCCCcccchhhhhHHHHHHHHHccccceehhhccCcchhHHHHHHHHHHHcCCCCCcEEEecchhH
Confidence            5567899999999999843 1222368999999999999877655443     26799999998753

>PRK13342 recombination factor protein RarA; Reviewed

Probab=96.00  E-value=0.00099  Score=47.15  Aligned_cols=39  Identities=26%  Similarity=0.310  Sum_probs=26.7

Q ss_pred             HHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         19 LRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        19 v~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      +.++++.+...+.++.+|+|+|||+++..++...+.+.+
T Consensus        27 L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~   65 (413)
T PRK13342         27 LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFE   65 (413)
T ss_pred             HHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            444555544457889999999999998776654444333

>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=95.99  E-value=0.00046  Score=41.34  Aligned_cols=28  Identities=18%  Similarity=0.290  Sum_probs=21.4

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      .++.+|+|+|||.++-.++...+.+.+.
T Consensus         2 vlL~G~~G~GKt~l~~~la~~~~~~~~~   29 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAALLGRPVIR   29 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHHHHTCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhcceEE
Confidence            5789999999999987777665555433

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.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.98  E-value=0.00068  Score=47.77  Aligned_cols=24  Identities=21%  Similarity=0.153  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-.++.+|||||||++.++.+...
T Consensus       126 GLILVTGpTGSGKSTTlAamId~i  149 (353)
T COG2805         126 GLILVTGPTGSGKSTTLAAMIDYI  149 (353)
T ss_pred             ceEEEeCCCCCcHHHHHHHHHHHH
Confidence            345566999999999988877654

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.94  E-value=0.0013  Score=45.67  Aligned_cols=33  Identities=21%  Similarity=0.158  Sum_probs=22.9

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.+++... .+..+|.+|||||||++..+++..
T Consensus       113 ~l~~~~~~~-~g~ili~G~tGSGKTT~l~al~~~  145 (343)
T TIGR01420       113 VLRELAERP-RGLILVTGPTGSGKSTTLASMIDY  145 (343)
T ss_pred             HHHHHHhhc-CcEEEEECCCCCCHHHHHHHHHHh
Confidence            344444322 267889999999999998766553

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=95.93  E-value=0.00027  Score=57.25  Aligned_cols=33  Identities=24%  Similarity=0.385  Sum_probs=23.9

Q ss_pred             EEEeCCCCceeEeee-eEEE---------------EeeeeEEEeeccee
Q psy11637         33 IVLPCGAGKSLVGVT-ACCT---------------VRKRALVLCNSGVV   65 (67)
Q Consensus        33 i~~pTGsGKT~i~~~-~~~~---------------~~~~~lil~p~~~~   65 (67)
                      |++|||||||.++.. ++.+               .+.++|||+|++++
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKAL   49 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKAL   49 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHH
Confidence            478999999999865 2211               13579999998754

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=95.93  E-value=0.00062  Score=39.94  Aligned_cols=24  Identities=29%  Similarity=0.238  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +..+|.+|+|+|||.++..++...
T Consensus         5 ~~~~i~G~~G~GKT~~~~~~~~~~   28 (131)
T PF13401_consen    5 RILVISGPPGSGKTTLIKRLARQL   28 (131)
T ss_dssp             --EEEEE-TTSSHHHHHHHHHHHH
T ss_pred             cccEEEcCCCCCHHHHHHHHHHHh
Confidence            578899999999999887776653

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.91  E-value=0.0014  Score=54.28  Aligned_cols=57  Identities=12%  Similarity=0.064  Sum_probs=42.2

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeee----eE---EEEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVT----AC---CTVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~----~~---~~~~~~~lil~p~~~~   65 (67)
                      ...|-+.|++|++.++.... +..+|.++.|+|||++...    +.   ...+.+++.++||..|
T Consensus      1017 ~~~Lt~~Q~~Ai~~il~~~~-~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~~g~~v~glApT~~A 1080 (1960)
T TIGR02760      1017 LERLTHGQKQAIHLIISTKD-RFVAVQGLAGVGKTTMLESRYKPVLQAFESEQLQVIGLAPTHEA 1080 (1960)
T ss_pred             cCCCCHHHHHHHHHHHhCCC-cEEEEEeCCCCCHHHhHHHHHHHHHHHHHhcCCeEEEEeChHHH
Confidence            45688899999999986531 5678889999999998832    21   1235678889998755

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.

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=95.89  E-value=0.00077  Score=51.91  Aligned_cols=53  Identities=17%  Similarity=0.250  Sum_probs=35.2

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..+|||=.+.+-.+.-+   ...+.-|.||+|||+++...+..   .+..+.+++|+..
T Consensus        77 ~g~~~~dvQlig~l~l~---~G~iaEm~TGEGKTLvA~l~a~l~al~G~~v~vvT~ney  132 (796)
T PRK12906         77 LGLRPFDVQIIGGIVLH---EGNIAEMKTGEGKTLTATLPVYLNALTGKGVHVVTVNEY  132 (796)
T ss_pred             hCCCCchhHHHHHHHHh---cCCcccccCCCCCcHHHHHHHHHHHHcCCCeEEEeccHH
Confidence            34566644444443322   22377899999999999765543   4778889998864

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.88  E-value=0.0013  Score=47.67  Aligned_cols=44  Identities=16%  Similarity=0.295  Sum_probs=33.1

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~   60 (67)
                      +.+|+++..+  .+...+|.+|+|+|||+.++.++..    .+++.+++.
T Consensus         8 ~gLD~il~GGlp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs   57 (484)
T TIGR02655         8 EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVT   57 (484)
T ss_pred             hhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEE
Confidence            4577777653  3467888999999999999887654    256887775

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.

>KOG0344|consensus

Probab=95.83  E-value=0.0022  Score=47.94  Aligned_cols=52  Identities=25%  Similarity=0.322  Sum_probs=38.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----------EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----------VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----------~~~~~lil~p~~~   64 (67)
                      .+-|-|.+|+--++..   +..+.++|||+|||+-+..-+..           .+-+.+|+.|+..
T Consensus       158 ~Pt~iq~~aipvfl~~---r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptre  220 (593)
T KOG0344|consen  158 EPTPIQKQAIPVFLEK---RDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTRE  220 (593)
T ss_pred             CCCcccchhhhhhhcc---cceEEeccCCCcchhhhhhHHHHHHHHhhcccCccceEEEEecchHH
Confidence            3446688888777776   68999999999998777543321           2357899998753

>KOG0342|consensus

Probab=95.82  E-value=0.0021  Score=47.49  Aligned_cols=50  Identities=18%  Similarity=0.377  Sum_probs=37.1

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----------eeeeEEEeecce
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----------RKRALVLCNSGV   64 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~~lil~p~~~   64 (67)
                      =+-|+..+..++..   ++.+..+-||+|||+.++-.+-+.          +-.++|++||.-
T Consensus       106 T~VQ~~ti~pll~g---kDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRE  165 (543)
T KOG0342|consen  106 TPVQQKTIPPLLEG---KDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRE  165 (543)
T ss_pred             hHHHHhhcCccCCC---ccceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHH
Confidence            34577777777776   588999999999999887544321          336899999863

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=95.81  E-value=0.0016  Score=45.58  Aligned_cols=35  Identities=17%  Similarity=0.120  Sum_probs=24.3

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+.++.+.+.+  .+.+++++||+|||+...+++..
T Consensus       167 ~~~~L~~~v~~~--~~ili~G~tGsGKTTll~al~~~  201 (340)
T TIGR03819       167 VARLLRAIVAAR--LAFLISGGTGSGKTTLLSALLAL  201 (340)
T ss_pred             HHHHHHHHHhCC--CeEEEECCCCCCHHHHHHHHHcc
Confidence            344444444443  68999999999999877655544

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.

>KOG0391|consensus

Probab=95.81  E-value=0.00048  Score=55.45  Aligned_cols=58  Identities=19%  Similarity=0.320  Sum_probs=44.2

Q ss_pred             ceeeccchhhHHHHHhc-CCcceeeeEEEeCCCCceeEeeeeEEEE------eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFG-NGRARSGVIVLPCGAGKSLVGVTACCTV------RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~-~~~~~~~~i~~pTGsGKT~i~~~~~~~~------~~~~lil~p~~~~   65 (67)
                      ...||+||...+++... +.++-+|++.--.|-|||+-.+++..++      =++-||||||.+.
T Consensus       613 rGqLReYQkiGLdWLatLYeknlNGILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsvi  677 (1958)
T KOG0391|consen  613 RGQLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVI  677 (1958)
T ss_pred             HHHHHHHHHhhHHHHHHHHHhcccceehhhhcccchhHHHHHHHHHHhcccCCCCceEEeechhh
Confidence            46899999999998553 2223789999999999998776544332      3688999999764

>PRK04328 hypothetical protein; Provisional

Probab=95.80  E-value=0.0016  Score=43.28  Aligned_cols=44  Identities=11%  Similarity=0.172  Sum_probs=31.6

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +.+|+.+..+  .+...+|.+|+|+|||..++.++..   .+.+++++.
T Consensus        10 ~~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis   58 (249)
T PRK04328         10 PGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVA   58 (249)
T ss_pred             hhHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            4677877653  2456778899999999998876653   356777664

>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=95.77  E-value=0.0019  Score=49.72  Aligned_cols=37  Identities=30%  Similarity=0.419  Sum_probs=25.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      .+|+|-.--++..+..   +-.+|++|||||||++.-++.
T Consensus        10 Nf~S~~~~~~~~~f~~---gi~lI~G~nGsGKSSIldAI~   46 (908)
T COG0419          10 NFRSFKDIDIEKLFDS---GIFLIVGPNGAGKSSILDAIT   46 (908)
T ss_pred             ccccccccceeecCCC---CeEEEECCCCCcHHHHHHHHH
Confidence            4677763333333443   688999999999999875543

>PRK06893 DNA replication initiation factor; Validated

Probab=95.75  E-value=0.0024  Score=41.91  Aligned_cols=22  Identities=18%  Similarity=-0.156  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.+|+|+|||+.+.+++..
T Consensus        41 ~l~l~G~~G~GKThL~~ai~~~   62 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNH   62 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999998777654

>PRK04195 replication factor C large subunit; Provisional

Probab=95.75  E-value=0.0019  Score=46.61  Aligned_cols=32  Identities=16%  Similarity=0.176  Sum_probs=24.0

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ....++.+|+|+|||+++.+++...+..++.+
T Consensus        39 ~~~lLL~GppG~GKTtla~ala~el~~~~iel   70 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLAHALANDYGWEVIEL   70 (482)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCEEEE
Confidence            46788999999999999877766655444433

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=95.74  E-value=0.0016  Score=47.20  Aligned_cols=38  Identities=29%  Similarity=0.349  Sum_probs=28.0

Q ss_pred             hhhHH------HHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         15 QEKSL------RKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        15 Q~~av------~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+..+      .+.++.++-.+.++-+|+|+|||+++-.++...
T Consensus        29 Q~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~   72 (436)
T COG2256          29 QEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT   72 (436)
T ss_pred             hHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh
Confidence            77666      345565556789999999999999986655443

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=95.73  E-value=0.00099  Score=51.93  Aligned_cols=52  Identities=21%  Similarity=0.256  Sum_probs=35.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~   64 (67)
                      .+|||=.+.+-.+.-+   ..-+.-|.||.|||+++...+.   ..+..+.|++|+..
T Consensus        80 Gm~~ydVQliGg~~Lh---~G~iaEM~TGEGKTLvA~l~a~l~al~G~~VhvvT~ndy  134 (913)
T PRK13103         80 GMRHFDVQLIGGMTLH---EGKIAEMRTGEGKTLVGTLAVYLNALSGKGVHVVTVNDY  134 (913)
T ss_pred             CCCcchhHHHhhhHhc---cCccccccCCCCChHHHHHHHHHHHHcCCCEEEEeCCHH
Confidence            4566655555543333   3456679999999999875554   35788999998864

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=95.73  E-value=0.0013  Score=44.12  Aligned_cols=26  Identities=15%  Similarity=0.137  Sum_probs=20.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .+.++.+|+|+|||..+..++...+.
T Consensus        31 ~~~ll~Gp~G~GKT~la~~ia~~~~~   56 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLAHIIANEMGV   56 (305)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            46889999999999998777665543

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.72  E-value=0.0021  Score=43.01  Aligned_cols=33  Identities=21%  Similarity=0.043  Sum_probs=25.4

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +...+|.+|+|+|||..++.++..   .+++++++.
T Consensus        36 gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis   71 (259)
T TIGR03878        36 YSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVT   71 (259)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            356778899999999999876553   356787775

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.68  E-value=0.0015  Score=42.35  Aligned_cols=42  Identities=17%  Similarity=0.211  Sum_probs=29.1

Q ss_pred             HHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         19 LRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        19 v~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      +++++.+ ..+...+|.+++|+|||..++.++...    +.+++++.
T Consensus         3 LD~~~~Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s   49 (242)
T cd00984           3 LDNLTGGLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFS   49 (242)
T ss_pred             hhhhhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEe
Confidence            4455542 123567889999999999988776542    66777775

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.

>KOG0384|consensus

Probab=95.68  E-value=0.00091  Score=53.53  Aligned_cols=57  Identities=19%  Similarity=0.223  Sum_probs=43.4

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~   64 (67)
                      .-+||+||-+.+.+.+.. -...++++.--.|-|||+-...++..      ..+|.||++|-.+
T Consensus       368 g~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst  431 (1373)
T KOG0384|consen  368 GNELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLST  431 (1373)
T ss_pred             cchhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhh
Confidence            368999999999874421 11268999999999999887655443      5789999999754

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=95.67  E-value=0.0012  Score=51.54  Aligned_cols=53  Identities=17%  Similarity=0.217  Sum_probs=35.0

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      +.+|||=.+.+-.+.-+   ..-+..|+||.|||++++..+..   .+..++|++|+..
T Consensus        79 lgm~~ydVQliGgl~L~---~G~IaEm~TGEGKTL~a~lp~~l~al~g~~VhIvT~ndy  134 (908)
T PRK13107         79 FEMRHFDVQLLGGMVLD---SNRIAEMRTGEGKTLTATLPAYLNALTGKGVHVITVNDY  134 (908)
T ss_pred             hCCCcCchHHhcchHhc---CCccccccCCCCchHHHHHHHHHHHhcCCCEEEEeCCHH
Confidence            34566655555443332   34567899999999998755542   3567899998864

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.67  E-value=0.0016  Score=45.41  Aligned_cols=50  Identities=20%  Similarity=0.192  Sum_probs=32.0

Q ss_pred             eeccchhhHHHH---HhcC--CcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         10 VLRPYQEKSLRK---MFGN--GRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        10 ~lR~yQ~~av~~---~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ..|.+++.+++.   |.+.  ....+.++.+|||+|||+.+.+++..+   +..++++
T Consensus       160 ~~~~~~~~~~~~~~~f~~~f~~~~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~  217 (329)
T PRK06835        160 SPRKNMEKILEKCKNFIENFDKNNENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYR  217 (329)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEE
Confidence            445556666653   3331  122678889999999999998776653   3455544

>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=95.66  E-value=0.0021  Score=37.21  Aligned_cols=19  Identities=21%  Similarity=0.097  Sum_probs=15.1

Q ss_pred             eEEEeCCCCceeEeeeeEE
Q psy11637         32 VIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~   50 (67)
                      +|.+++|||||+++-.+..
T Consensus         2 ~i~G~~GsGKtTia~~L~~   20 (129)
T PF13238_consen    2 GISGIPGSGKTTIAKELAE   20 (129)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            5789999999998865443

...

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.66  E-value=0.002  Score=45.40  Aligned_cols=23  Identities=22%  Similarity=0.085  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +..+|++|||||||++..+++..
T Consensus       135 glilI~GpTGSGKTTtL~aLl~~  157 (358)
T TIGR02524       135 GIVFITGATGSGKSTLLAAIIRE  157 (358)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            67888999999999988766543

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.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.64  E-value=0.00073  Score=40.18  Aligned_cols=30  Identities=13%  Similarity=0.295  Sum_probs=21.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      .+|.+|+|+|||.++..++...   +++++++.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~   34 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVD   34 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEE
Confidence            4688999999999887665543   45666554

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.63  E-value=0.0018  Score=46.90  Aligned_cols=45  Identities=22%  Similarity=0.299  Sum_probs=32.8

Q ss_pred             hhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         16 EKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .+.+|+.+..+  .+...+|.+|+|+|||+.++.++..   .+.+++++.
T Consensus       249 i~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s  298 (484)
T TIGR02655       249 VVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFA  298 (484)
T ss_pred             hHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            44567777653  2456788899999999999887764   356777764

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.

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

Probab=95.62  E-value=0.0015  Score=45.18  Aligned_cols=34  Identities=24%  Similarity=0.405  Sum_probs=27.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecc
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSG   63 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~   63 (67)
                      ..+|.+.+|||||++++.++..+     +.+.++++++.
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~   41 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNH   41 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecc
Confidence            46788999999999999887765     56777887764

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

>PHA02774 E1; Provisional

Probab=95.60  E-value=0.0025  Score=47.96  Aligned_cols=46  Identities=20%  Similarity=0.234  Sum_probs=33.9

Q ss_pred             HHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecc
Q psy11637         18 SLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSG   63 (67)
Q Consensus        18 av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~   63 (67)
                      +++.|++... ....++.+|+|+|||..+++++..++++++-.++..
T Consensus       423 ~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~  469 (613)
T PHA02774        423 ALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSK  469 (613)
T ss_pred             HHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECc
Confidence            3455665433 245778899999999999999988877777666654

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.60  E-value=0.0014  Score=53.66  Aligned_cols=56  Identities=20%  Similarity=0.118  Sum_probs=41.9

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---E----EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---T----VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~----~~~~~lil~p~~~~   65 (67)
                      ..|-+-|++|+..++.... +..+|.+..|+|||++.-.++.   .    .+.+++.++||.-|
T Consensus       834 ~~Lt~~Qr~Av~~iLts~d-r~~~IqG~AGTGKTT~l~~i~~~~~~l~e~~g~~V~glAPTgkA  896 (1623)
T PRK14712        834 EKLTSGQRAATRMILETSD-RFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRA  896 (1623)
T ss_pred             cccCHHHHHHHHHHHhCCC-ceEEEEeCCCCCHHHHHHHHHHHHHHHhhccCceEEEEechHHH
Confidence            4678899999999997531 6788999999999998643322   1    24568889998655

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.60  E-value=0.0024  Score=53.01  Aligned_cols=57  Identities=12%  Similarity=0.151  Sum_probs=44.6

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~~   65 (67)
                      .+.|-+-|++|+..++.... +..+|.++.|+|||.+.-.+..   ..+.+++.++||..|
T Consensus       427 ~~~Ls~~Q~~Av~~il~s~~-~v~ii~G~aGTGKTt~l~~l~~~~~~~G~~V~~lAPTgrA  486 (1960)
T TIGR02760       427 EFALSPSNKDAVSTLFTSTK-RFIIINGFGGTGSTEIAQLLLHLASEQGYEIQIITAGSLS  486 (1960)
T ss_pred             cCCCCHHHHHHHHHHHhCCC-CeEEEEECCCCCHHHHHHHHHHHHHhcCCeEEEEeCCHHH
Confidence            35677889999999987531 6788899999999998865543   347789999998643

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.

>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=95.59  E-value=0.0023  Score=38.04  Aligned_cols=20  Identities=25%  Similarity=0.282  Sum_probs=15.9

Q ss_pred             eeEEEeCCCCceeEeeeeEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .++++|+|||||+.+-.+..
T Consensus         2 ii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            36789999999998866553

...

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.57  E-value=0.0021  Score=44.74  Aligned_cols=41  Identities=22%  Similarity=0.430  Sum_probs=32.4

Q ss_pred             eeccchhhHHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         10 VLRPYQEKSLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+.|+|+...++++..+. .+.-++.+|.|.|||.++..++.
T Consensus         3 ~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~   44 (328)
T PRK05707          3 EIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAA   44 (328)
T ss_pred             cCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHH
Confidence            458999999999997654 34567899999999988865543

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=95.56  E-value=0.0016  Score=44.57  Aligned_cols=27  Identities=15%  Similarity=0.128  Sum_probs=21.2

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .++.++.+|+|+|||.++..++...+.
T Consensus        51 ~~~~ll~GppG~GKT~la~~ia~~l~~   77 (328)
T PRK00080         51 LDHVLLYGPPGLGKTTLANIIANEMGV   77 (328)
T ss_pred             CCcEEEECCCCccHHHHHHHHHHHhCC
Confidence            357889999999999998776655443

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=95.56  E-value=0.00091  Score=41.10  Aligned_cols=21  Identities=24%  Similarity=0.371  Sum_probs=16.8

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++++|+|+|||+++-.+....
T Consensus         2 ~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         2 VLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             EEECCCCCCHHHHHHHHHHhc
Confidence            578999999999987665544

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.56  E-value=0.0031  Score=40.51  Aligned_cols=23  Identities=22%  Similarity=0.133  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +-.+|++|||||||++...++..
T Consensus         2 GlilI~GptGSGKTTll~~ll~~   24 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY   24 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999998765544

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=95.56  E-value=0.0018  Score=43.66  Aligned_cols=47  Identities=19%  Similarity=0.294  Sum_probs=28.7

Q ss_pred             chhhHHH---HHhcCCcceeeeE-EEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         14 YQEKSLR---KMFGNGRARSGVI-VLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        14 yQ~~av~---~~~~~~~~~~~~i-~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      .|++..+   .+.+.+.-.+.++ .+|+|+|||..+..++...+..++.+-
T Consensus        25 ~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~   75 (316)
T PHA02544         25 LPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVN   75 (316)
T ss_pred             CcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEec
Confidence            4665544   4454443234445 799999999988776655544444443

>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=95.56  E-value=0.0042  Score=44.03  Aligned_cols=37  Identities=19%  Similarity=0.173  Sum_probs=26.5

Q ss_pred             ceeeeEEEeCCCCceeEe-----eeeEEEEeeeeEEEeecce
Q psy11637         28 ARSGVIVLPCGAGKSLVG-----VTACCTVRKRALVLCNSGV   64 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~-----~~~~~~~~~~~lil~p~~~   64 (67)
                      .-.++|.+|||+|||-..     ..++.-..+-+.||+|..=
T Consensus        87 P~I~~VYGPTG~GKSqLlRNLis~~lI~P~PETVfFItP~~~  128 (369)
T PF02456_consen   87 PFIGVVYGPTGSGKSQLLRNLISCQLIQPPPETVFFITPQKD  128 (369)
T ss_pred             ceEEEEECCCCCCHHHHHHHhhhcCcccCCCCceEEECCCCC
Confidence            345888999999999543     3444445677889998753

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

>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed

Probab=95.55  E-value=0.00096  Score=46.18  Aligned_cols=25  Identities=24%  Similarity=0.299  Sum_probs=20.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      -.+|++|||||||.++..++...+.
T Consensus         6 ~i~i~GptgsGKt~la~~la~~~~~   30 (307)
T PRK00091          6 VIVIVGPTASGKTALAIELAKRLNG   30 (307)
T ss_pred             EEEEECCCCcCHHHHHHHHHHhCCC
Confidence            4678899999999999888776544

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.55  E-value=0.003  Score=40.54  Aligned_cols=45  Identities=20%  Similarity=0.328  Sum_probs=31.7

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---Ee------eeeEEEee
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VR------KRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~------~~~lil~p   61 (67)
                      +.+|+++..+  .+....|.+|+|+|||.+++.++..   .+      .+++++..
T Consensus         6 ~~lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~   61 (226)
T cd01393           6 KALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDT   61 (226)
T ss_pred             HHHHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEec
Confidence            4567777542  2467888999999999999876643   22      66777654

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=95.53  E-value=0.0021  Score=41.89  Aligned_cols=45  Identities=22%  Similarity=0.281  Sum_probs=32.2

Q ss_pred             hhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         16 EKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .+.+|+.+..+  .+...++.+|+|+|||+.+..++..   .+++++++.
T Consensus        11 i~~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~   60 (234)
T PRK06067         11 NEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVIT   60 (234)
T ss_pred             CHHHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEE
Confidence            45677777653  2356777899999999999877643   356777664

>PRK12377 putative replication protein; Provisional

Probab=95.52  E-value=0.0017  Score=43.77  Aligned_cols=24  Identities=17%  Similarity=0.097  Sum_probs=20.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.++.+|+|+|||+++.+++..+
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l  125 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRL  125 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            467888999999999998877654

>KOG0334|consensus

Probab=95.50  E-value=0.0073  Score=47.58  Aligned_cols=51  Identities=22%  Similarity=0.275  Sum_probs=40.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----------eee-eEEEeecc
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----------RKR-ALVLCNSG   63 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~-~lil~p~~   63 (67)
                      .++|-|.+|+=.+..+   +..|.++-||||||+-++..+.+.          .+| .+|++||.
T Consensus       387 k~~~IQ~qAiP~ImsG---rdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtr  448 (997)
T KOG0334|consen  387 KPTPIQAQAIPAIMSG---RDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTR  448 (997)
T ss_pred             CCcchhhhhcchhccC---cceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCH
Confidence            6788999999999987   689999999999999886554432          233 68899986

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=95.48  E-value=0.0022  Score=41.43  Aligned_cols=44  Identities=16%  Similarity=0.212  Sum_probs=29.9

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~   60 (67)
                      +.+|+.+..+  .+...+|.+|+|+|||..+..++.   ..+.+++++.
T Consensus         7 ~~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881         7 EGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             hhHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            4567776532  246788889999999998876543   2355666664

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.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=95.46  E-value=0.0014  Score=41.65  Aligned_cols=32  Identities=9%  Similarity=0.048  Sum_probs=25.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEeeeeEEEeec
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVRKRALVLCNS   62 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~   62 (67)
                      .+|.+++|||||..+..++...+.+.++++-.
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~   33 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATA   33 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEcc
Confidence            36789999999999988877766788887543

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.

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=95.44  E-value=0.0072  Score=44.49  Aligned_cols=39  Identities=21%  Similarity=0.247  Sum_probs=27.1

Q ss_pred             eecc--chhhHHHHHhc-CCcceeeeEEEeCCCCceeEeeee
Q psy11637         10 VLRP--YQEKSLRKMFG-NGRARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        10 ~lR~--yQ~~av~~~~~-~~~~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      .|+|  .|+.|-+...- ...+++.++.+|+|||||.++.-+
T Consensus       177 D~~DV~GQ~~AKrAleiAAAGgHnLl~~GpPGtGKTmla~Rl  218 (490)
T COG0606         177 DFKDVKGQEQAKRALEIAAAGGHNLLLVGPPGTGKTMLASRL  218 (490)
T ss_pred             chhhhcCcHHHHHHHHHHHhcCCcEEEecCCCCchHHhhhhh
Confidence            4555  48887776432 111278899999999999888544

>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]

Probab=95.43  E-value=0.0011  Score=46.21  Aligned_cols=26  Identities=19%  Similarity=0.229  Sum_probs=21.8

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      -.+|.+||++|||-+++.++.+.++.
T Consensus         5 ~i~I~GPTAsGKT~lai~LAk~~~~e   30 (308)
T COG0324           5 LIVIAGPTASGKTALAIALAKRLGGE   30 (308)
T ss_pred             EEEEECCCCcCHHHHHHHHHHHcCCc
Confidence            46788999999999998888877664

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.43  E-value=0.0012  Score=44.33  Aligned_cols=46  Identities=22%  Similarity=0.240  Sum_probs=29.4

Q ss_pred             chhhHHHHHhc---C-Cc-ceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         14 YQEKSLRKMFG---N-GR-ARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        14 yQ~~av~~~~~---~-~~-~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      .|+.++..+.+   . .. ....++.+++|+|||+++.+++..+   +.+++++
T Consensus        80 ~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~i  133 (244)
T PRK07952         80 GQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLII  133 (244)
T ss_pred             hHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            45556654332   2 11 1356788999999999998877654   4455554

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=95.42  E-value=0.0016  Score=50.43  Aligned_cols=53  Identities=17%  Similarity=0.218  Sum_probs=34.5

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~   64 (67)
                      ..+|||=.+.+-.+.-+   ..-+..|.||+|||+++...+.   ..+..+.|++||..
T Consensus        78 lg~~~~dvQlig~l~L~---~G~Iaem~TGeGKTLva~lpa~l~aL~G~~V~IvTpn~y  133 (830)
T PRK12904         78 LGMRHFDVQLIGGMVLH---EGKIAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVNDY  133 (830)
T ss_pred             hCCCCCccHHHhhHHhc---CCchhhhhcCCCcHHHHHHHHHHHHHcCCCEEEEecCHH
Confidence            34566655455443322   2346789999999999876553   23566888998864

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.41  E-value=0.0014  Score=44.47  Aligned_cols=23  Identities=22%  Similarity=0.213  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +..++++|||+|||+++..++..
T Consensus       195 ~vi~~vGptGvGKTTt~~kLa~~  217 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTLAKLAAR  217 (282)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            46778899999999999877654

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.41  E-value=0.0014  Score=40.00  Aligned_cols=22  Identities=27%  Similarity=0.235  Sum_probs=17.7

Q ss_pred             eEEEeCCCCceeEeeeeEEEEe
Q psy11637         32 VIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +|++|+|+|||.++..+.....
T Consensus         3 ~i~GpsGsGKstl~~~L~~~~~   24 (137)
T cd00071           3 VLSGPSGVGKSTLLKRLLEEFD   24 (137)
T ss_pred             EEECCCCCCHHHHHHHHHhcCC
Confidence            5789999999998877766543

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.

>KOG0745|consensus

Probab=95.41  E-value=0.0016  Score=48.03  Aligned_cols=30  Identities=20%  Similarity=0.317  Sum_probs=24.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      -+.++.+|||||||+++..++.-++-|+.|
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~ldVPfaI  256 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVLDVPFAI  256 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHhCCCeEE
Confidence            578899999999999998777766666543

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.41  E-value=0.0036  Score=43.91  Aligned_cols=45  Identities=24%  Similarity=0.358  Sum_probs=32.9

Q ss_pred             chhhHHHH------HhcC----C--cceeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         14 YQEKSLRK------MFGN----G--RARSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        14 yQ~~av~~------~~~~----~--~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      .|++|-.+      ++++    +  ..++.+..+|+|+|||.++-+++.+.+-+.+.
T Consensus       125 GqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~kvp~l~  181 (368)
T COG1223         125 GQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLL  181 (368)
T ss_pred             chHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhcccCCceEE
Confidence            47777643      4543    1  25799999999999999998888776666543

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=95.40  E-value=0.003  Score=40.72  Aligned_cols=44  Identities=25%  Similarity=0.353  Sum_probs=30.5

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEE---------eeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTV---------RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---------~~~~lil~   60 (67)
                      ..+|+++..+  .+....|.+|+|+|||..++.++...         +++++++.
T Consensus         6 ~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~   60 (235)
T cd01123           6 KALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID   60 (235)
T ss_pred             hhhHhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEe
Confidence            3567777643  24667889999999999997765321         25677665

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 .

>PRK05973 replicative DNA helicase; Provisional

Probab=95.40  E-value=0.0015  Score=43.80  Aligned_cols=32  Identities=16%  Similarity=0.264  Sum_probs=24.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      ...+|.+++|+|||+.++.++..   .+++++|+.
T Consensus        65 sl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfS   99 (237)
T PRK05973         65 DLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFT   99 (237)
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            45678899999999999877653   366777774

>KOG1002|consensus

Probab=95.39  E-value=0.0013  Score=49.24  Aligned_cols=57  Identities=19%  Similarity=0.285  Sum_probs=43.1

Q ss_pred             ceeeccchhhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE--EEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC--TVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~--~~~~~~lil~p~~~   64 (67)
                      .+.|-|||.|.+.+.....  .-..|++.-..|-|||+-+.++..  .-+.++|+++|+.+
T Consensus       182 ii~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~~ra~tLVvaP~VA  242 (791)
T KOG1002|consen  182 IIPLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEVDRAPTLVVAPTVA  242 (791)
T ss_pred             eecchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhccccCCeeEEccHHH
Confidence            3678999999998866532  235688899999999987765443  34678999999854

>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=95.38  E-value=0.0095  Score=40.41  Aligned_cols=33  Identities=27%  Similarity=0.371  Sum_probs=24.3

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++-+++.+  +..++++|+|+|||.+.......
T Consensus        24 ~ll~~l~~~~--~pvLl~G~~GtGKT~li~~~l~~   56 (272)
T PF12775_consen   24 YLLDLLLSNG--RPVLLVGPSGTGKTSLIQNFLSS   56 (272)
T ss_dssp             HHHHHHHHCT--EEEEEESSTTSSHHHHHHHHHHC
T ss_pred             HHHHHHHHcC--CcEEEECCCCCchhHHHHhhhcc
Confidence            3445566655  78999999999999988665543

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.36  E-value=0.0012  Score=40.26  Aligned_cols=25  Identities=28%  Similarity=0.254  Sum_probs=20.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ...++++|+|||||+++-.++..++
T Consensus         5 ~~i~l~G~~GsGKstla~~La~~l~   29 (175)
T PRK00131          5 PNIVLIGFMGAGKSTIGRLLAKRLG   29 (175)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHhC
Confidence            4678889999999999977766553

>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=95.35  E-value=0.0063  Score=40.03  Aligned_cols=40  Identities=20%  Similarity=0.193  Sum_probs=29.1

Q ss_pred             ccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+...+.+.+++..  +..+...|+++.|.|||.++..++..
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~   42 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARD   42 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCH
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccc
Confidence            55666777666654  33466788899999999999877755

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.

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=95.34  E-value=0.0017  Score=46.89  Aligned_cols=43  Identities=26%  Similarity=0.335  Sum_probs=31.0

Q ss_pred             chhhHHHH------HhcCC--cceeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         14 YQEKSLRK------MFGNG--RARSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        14 yQ~~av~~------~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      .|.+|-++      ..+.+  .++-.++++|+|+|||-++++++.+++.-+
T Consensus        43 GQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dv   93 (450)
T COG1224          43 GQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIARELGEDV   93 (450)
T ss_pred             chHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHHHhCCCC
Confidence            48888776      22333  235567789999999999999888876433

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.33  E-value=0.0012  Score=50.17  Aligned_cols=32  Identities=22%  Similarity=0.324  Sum_probs=25.1

Q ss_pred             eEEEeCCCCceeEeeeeEEEE----eeeeEEEeecc
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV----RKRALVLCNSG   63 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~----~~~~lil~p~~   63 (67)
                      +..|+||||||.+++++|.+.    -+..|+.|+..
T Consensus         1 lf~matgsgkt~~ma~lil~~y~kgyr~flffvnq~   36 (812)
T COG3421           1 LFEMATGSGKTLVMAGLILECYKKGYRNFLFFVNQA   36 (812)
T ss_pred             CcccccCCChhhHHHHHHHHHHHhchhhEEEEecch
Confidence            357999999999999998763    35678887753

>PRK08118 topology modulation protein; Reviewed

Probab=95.33  E-value=0.001  Score=41.87  Aligned_cols=23  Identities=17%  Similarity=0.190  Sum_probs=18.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.+|++|+|||||+++-.+....
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l   25 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL   25 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46788999999999886665543

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.29  E-value=0.0037  Score=40.37  Aligned_cols=44  Identities=20%  Similarity=0.345  Sum_probs=31.1

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      .+++.+..+  .+...+|.+++|+|||..++.++..   .+++++++.-
T Consensus         4 ~LD~~l~gGi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~   52 (224)
T TIGR03880         4 GLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISL   52 (224)
T ss_pred             hhHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            466777543  2456788899999999998877643   3667777653

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.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=95.28  E-value=0.0014  Score=49.41  Aligned_cols=51  Identities=14%  Similarity=0.079  Sum_probs=36.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E---eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V---RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~---~~~~lil~p~~~~   65 (67)
                      .|-|.|++|+...  .   +..+|.+.+|||||.+...=+..    .   ..++|+++-|+-|
T Consensus         9 ~Ln~~Q~~av~~~--~---g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v~p~~IL~lTFT~kA   66 (721)
T PRK11773          9 SLNDKQREAVAAP--L---GNMLVLAGAGSGKTRVLVHRIAWLMQVENASPYSIMAVTFTNKA   66 (721)
T ss_pred             hcCHHHHHHHhCC--C---CCEEEEecCCCCHHHHHHHHHHHHHHcCCCChhHeEeeeccHHH
Confidence            5788999998732  2   57889999999999887543332    1   3568888877644

>PRK07261 topology modulation protein; Provisional

Probab=95.26  E-value=0.0015  Score=41.21  Aligned_cols=22  Identities=23%  Similarity=0.160  Sum_probs=17.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+|++++|||||+.+-.+...
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~   23 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQH   23 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999766544

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=95.26  E-value=0.0034  Score=42.61  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=29.0

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEe
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLC   60 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~   60 (67)
                      .+++++..+  .+....|.+|+|+|||..++.++..         .++++++|.
T Consensus        83 ~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~  136 (310)
T TIGR02236        83 ELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYID  136 (310)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEE
Confidence            355666543  2345678899999999998776543         234777765

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.25  E-value=0.0077  Score=41.65  Aligned_cols=44  Identities=20%  Similarity=0.114  Sum_probs=30.1

Q ss_pred             eeeccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637          9 AVLRPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.-|+-|.+.+..++.    .+...+.+|.+|+|+|||.+.-.+....
T Consensus        32 l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l   79 (394)
T PRK00411         32 LPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEEL   79 (394)
T ss_pred             CCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3346666666666552    2234678999999999999887766543

>KOG4439|consensus

Probab=95.24  E-value=0.0031  Score=48.62  Aligned_cols=58  Identities=21%  Similarity=0.344  Sum_probs=44.0

Q ss_pred             ccceeeccchhhHHHHHhc--CCcceeeeEEEeCCCCceeEeeeeEEEE-------------eeeeEEEeecc
Q psy11637          6 KPSAVLRPYQEKSLRKMFG--NGRARSGVIVLPCGAGKSLVGVTACCTV-------------RKRALVLCNSG   63 (67)
Q Consensus         6 ~~~~~lR~yQ~~av~~~~~--~~~~~~~~i~~pTGsGKT~i~~~~~~~~-------------~~~~lil~p~~   63 (67)
                      .....|-|+|+.++.+..-  ...+..|++-...|-|||.++.+++...             ..+||||||-+
T Consensus       321 g~~v~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaS  393 (901)
T KOG4439|consen  321 GLKVELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPAS  393 (901)
T ss_pred             cceeecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcHH
Confidence            3467889999999988553  3335679999999999999887776531             12699999954

>KOG0989|consensus

Probab=95.24  E-value=0.002  Score=45.49  Aligned_cols=40  Identities=15%  Similarity=0.117  Sum_probs=29.3

Q ss_pred             chhhHHHHHhc---CCcceeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         14 YQEKSLRKMFG---NGRARSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        14 yQ~~av~~~~~---~~~~~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +|+..+....+   ++..-+-++.+|+|+|||.++.+++..+.
T Consensus        40 gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~   82 (346)
T KOG0989|consen   40 GQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALN   82 (346)
T ss_pred             chHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhc
Confidence            68888876543   22234678899999999999987776543

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=95.23  E-value=0.0017  Score=45.01  Aligned_cols=22  Identities=23%  Similarity=0.012  Sum_probs=19.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      -.+|.+|||||||-+++.++.+
T Consensus         6 ii~I~GpTasGKS~LAl~LA~~   27 (300)
T PRK14729          6 IVFIFGPTAVGKSNILFHFPKG   27 (300)
T ss_pred             EEEEECCCccCHHHHHHHHHHh
Confidence            4678899999999999888776

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=95.21  E-value=0.0021  Score=52.95  Aligned_cols=56  Identities=20%  Similarity=0.109  Sum_probs=42.0

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~   65 (67)
                      ..|-+-|++|++.++... ++..+|.+..|+|||++.-.++..       .+.+++.++||.-|
T Consensus       966 ~~Lt~~Q~~Av~~il~s~-dr~~~I~G~AGTGKTT~l~~v~~~~~~l~~~~~~~V~glAPTgrA 1028 (1747)
T PRK13709        966 EGLTSGQRAATRMILEST-DRFTVVQGYAGVGKTTQFRAVMSAVNTLPESERPRVVGLGPTHRA 1028 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCC-CcEEEEEeCCCCCHHHHHHHHHHHHHHhhcccCceEEEECCcHHH
Confidence            457788999999999753 267889999999999987544332       13467888998654

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.21  E-value=0.0043  Score=41.25  Aligned_cols=21  Identities=19%  Similarity=0.056  Sum_probs=17.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      .+.++.+|+|+|||.++-.++
T Consensus        43 ~~vll~GppGtGKTtlA~~ia   63 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARILG   63 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHHH
Confidence            467899999999999985554

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.

>TIGR01075 uvrD DNA helicase II

Probab=95.20  E-value=0.0013  Score=49.41  Aligned_cols=51  Identities=12%  Similarity=0.068  Sum_probs=36.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E---eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V---RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~---~~~~lil~p~~~~   65 (67)
                      .|-|.|++++...  .   +..+|.+.+|||||.+...=+..    .   ..++|+++-|+-|
T Consensus         4 ~Ln~~Q~~av~~~--~---g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v~p~~IL~lTFTnkA   61 (715)
T TIGR01075         4 GLNDKQREAVAAP--P---GNLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFTNKA   61 (715)
T ss_pred             ccCHHHHHHHcCC--C---CCEEEEecCCCCHHHHHHHHHHHHHHcCCCCHHHeEeeeccHHH
Confidence            4788899998641  2   57899999999999887543322    1   3568888877643

Designed to identify uvrD members of the uvrD/rep subfamily.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=95.19  E-value=0.0047  Score=33.78  Aligned_cols=18  Identities=33%  Similarity=0.329  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ...+|.+|+|||||++.=
T Consensus        24 ~~tli~G~nGsGKSTllD   41 (62)
T PF13555_consen   24 DVTLITGPNGSGKSTLLD   41 (62)
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            368899999999998763

>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=95.16  E-value=0.0021  Score=46.21  Aligned_cols=41  Identities=27%  Similarity=0.385  Sum_probs=27.5

Q ss_pred             chhhHHHH------HhcCCc--ceeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         14 YQEKSLRK------MFGNGR--ARSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        14 yQ~~av~~------~~~~~~--~~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .|.+|-++      ..+.++  ++..++.+|+|+|||-++++++.+++.
T Consensus        28 GQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~   76 (398)
T PF06068_consen   28 GQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAKELGE   76 (398)
T ss_dssp             S-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHHHCTT
T ss_pred             ChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHHHhCC
Confidence            37777765      223332  466778899999999999998888764

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.

>PRK13764 ATPase; Provisional

Probab=95.14  E-value=0.0035  Score=47.05  Aligned_cols=24  Identities=25%  Similarity=0.105  Sum_probs=19.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++.++++|||||||+++.+++...
T Consensus       258 ~~ILIsG~TGSGKTTll~AL~~~i  281 (602)
T PRK13764        258 EGILIAGAPGAGKSTFAQALAEFY  281 (602)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            578899999999999887766543

>PRK08233 hypothetical protein; Provisional

Probab=95.12  E-value=0.002  Score=39.81  Aligned_cols=24  Identities=17%  Similarity=0.171  Sum_probs=18.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      -..|.+++|||||+.+..++..+.
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCC
Confidence            345679999999999977776553

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=95.10  E-value=0.0031  Score=44.50  Aligned_cols=29  Identities=17%  Similarity=0.306  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ...++.+|+|+|||.++-+++...+.+.+
T Consensus       166 ~gvLL~GppGtGKT~lAkaia~~~~~~~i  194 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLAKAVAHETNATFI  194 (389)
T ss_pred             CceEEECCCCCChHHHHHHHHHHhCCCEE
Confidence            56788899999999998776665544433

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.10  E-value=0.0019  Score=40.08  Aligned_cols=24  Identities=29%  Similarity=0.099  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|+|||.++-.++...
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~~~   25 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEED   25 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHccC
Confidence            356788999999999887766643

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.

>PRK14532 adenylate kinase; Provisional

Probab=95.09  E-value=0.0019  Score=40.61  Aligned_cols=24  Identities=17%  Similarity=0.061  Sum_probs=19.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +.++.+|+|||||+++..++...+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g   25 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERG   25 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            357889999999999977765543

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=95.04  E-value=0.0018  Score=49.71  Aligned_cols=51  Identities=27%  Similarity=0.427  Sum_probs=34.8

Q ss_pred             eeeccc--hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPY--QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~y--Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..+|||  |.-.....+.+     -+.-|.||.|||+++..++..   .++.+.|++|+..
T Consensus        75 lg~r~ydvQlig~l~Ll~G-----~VaEM~TGEGKTLvA~l~a~l~AL~G~~VhvvT~Ndy  130 (764)
T PRK12326         75 LGLRPFDVQLLGALRLLAG-----DVIEMATGEGKTLAGAIAAAGYALQGRRVHVITVNDY  130 (764)
T ss_pred             cCCCcchHHHHHHHHHhCC-----CcccccCCCCHHHHHHHHHHHHHHcCCCeEEEcCCHH
Confidence            345666  54444444432     356899999999999766553   4778888888754

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=95.03  E-value=0.011  Score=47.67  Aligned_cols=29  Identities=14%  Similarity=0.166  Sum_probs=19.9

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEe
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~   45 (67)
                      +..+.++.+.++   +..+|+++||||||+..
T Consensus        78 ~r~~Il~ai~~~---~VviI~GeTGSGKTTql  106 (1294)
T PRK11131         78 KKQDILEAIRDH---QVVIVAGETGSGKTTQL  106 (1294)
T ss_pred             HHHHHHHHHHhC---CeEEEECCCCCCHHHHH
Confidence            444445554443   56778899999999854

>KOG4284|consensus

Probab=94.98  E-value=0.047  Score=42.34  Aligned_cols=47  Identities=15%  Similarity=0.254  Sum_probs=36.6

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecc
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSG   63 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~   63 (67)
                      -|..||-.++..   -..+|.+-.|+|||.++.-++..      ..-..||++||.
T Consensus        51 iQaaAIP~~~~k---mDliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTR  103 (980)
T KOG4284|consen   51 IQAAAIPAIFSK---MDLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTR  103 (980)
T ss_pred             hhhhhhhhhhcc---cceEEEecCCCCceEEEEeeeehhcCcccCcceeEEEecch
Confidence            477777777765   57888899999999999766654      245689999986

>PRK14530 adenylate kinase; Provisional

Probab=94.97  E-value=0.0018  Score=41.85  Aligned_cols=24  Identities=17%  Similarity=0.088  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.+|.+|+|||||+++-.++...
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            467788999999999987665544

>PRK04296 thymidine kinase; Provisional

Probab=94.95  E-value=0.002  Score=41.26  Aligned_cols=33  Identities=18%  Similarity=0.107  Sum_probs=25.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      ...++.+|+|+|||+.++.++.+.   +.+++++-|
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEec
Confidence            346788999999999888776653   567777755

>TIGR00174 miaA tRNA isopentenyltransferase (miaA)

Probab=94.95  E-value=0.002  Score=44.39  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=19.0

Q ss_pred             eEEEeCCCCceeEeeeeEEEEee
Q psy11637         32 VIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      +|++|||+|||.++..++...+.
T Consensus         3 ~i~G~t~~GKs~la~~l~~~~~~   25 (287)
T TIGR00174         3 FIMGPTAVGKSQLAIQLAKKLNA   25 (287)
T ss_pred             EEECCCCCCHHHHHHHHHHhCCC
Confidence            67899999999999888766543

Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=94.95  E-value=0.0019  Score=40.31  Aligned_cols=22  Identities=18%  Similarity=0.169  Sum_probs=17.8

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|.+|+|||||+++..++...
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            4788999999999987766554

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=94.94  E-value=0.0037  Score=39.52  Aligned_cols=25  Identities=16%  Similarity=0.119  Sum_probs=19.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ...+|++|+|+|||+++-.+.....
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~   27 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQ   27 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCC
Confidence            4678899999999999876655443

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=94.90  E-value=0.013  Score=47.23  Aligned_cols=36  Identities=14%  Similarity=0.059  Sum_probs=22.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEeecce
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV----RKRALVLCNSGV   64 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~p~~~   64 (67)
                      ...+|.++||||||+..=.++...    .+++++.-|+..
T Consensus        83 ~vvii~g~TGSGKTTqlPq~lle~~~~~~~~I~~tQPRRl  122 (1283)
T TIGR01967        83 QVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRL  122 (1283)
T ss_pred             ceEEEeCCCCCCcHHHHHHHHHHcCCCCCceEecCCccHH
Confidence            578888999999998653333222    234444555544

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.

>KOG1131|consensus

Probab=94.88  E-value=0.0092  Score=45.03  Aligned_cols=39  Identities=18%  Similarity=0.296  Sum_probs=26.8

Q ss_pred             ccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         12 RPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        12 R~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .|.|.+-..++-+. +..+++++-||+|+|||+..++++-
T Consensus        18 YPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~   57 (755)
T KOG1131|consen   18 YPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLII   57 (755)
T ss_pred             CHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHH
Confidence            44577666554332 2237999999999999987766553

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.83  E-value=0.002  Score=40.15  Aligned_cols=21  Identities=14%  Similarity=0.097  Sum_probs=17.2

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++.+|+|||||+++..++.+.
T Consensus         3 ~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         3 FVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEECCCCCCHHHHHHHHHHHc
Confidence            678999999999987766554

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=94.82  E-value=0.0016  Score=41.43  Aligned_cols=32  Identities=13%  Similarity=0.057  Sum_probs=25.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEeeeeEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRKRALVLCN   61 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p   61 (67)
                      ..+|.+|+|||||..+..++...+.+.++++.
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat   34 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIAT   34 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcC
Confidence            46788999999999998887776666666654

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=94.78  E-value=0.011  Score=36.66  Aligned_cols=19  Identities=21%  Similarity=0.106  Sum_probs=15.4

Q ss_pred             EEEeCCCCceeEeeeeEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~   51 (67)
                      +++|||+|||.++-.++..
T Consensus        58 fHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   58 FHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             eecCCCCcHHHHHHHHHHH
Confidence            4599999999998766654

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

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=94.77  E-value=0.0049  Score=47.03  Aligned_cols=41  Identities=24%  Similarity=0.289  Sum_probs=27.3

Q ss_pred             chhhHH------HHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         14 YQEKSL------RKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        14 yQ~~av------~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .|+..+      .++++.+...+.++.+|+|+|||+++..+....+.
T Consensus        32 GQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~~~   78 (725)
T PRK13341         32 GQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRA   78 (725)
T ss_pred             CcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            366554      33444443457899999999999988766554433

>KOG0331|consensus

Probab=94.76  E-value=0.0035  Score=46.39  Aligned_cols=49  Identities=22%  Similarity=0.216  Sum_probs=33.3

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E----------E-eeeeEEEeecce
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T----------V-RKRALVLCNSGV   64 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~----------~-~~~~lil~p~~~   64 (67)
                      |-|...+--.+..   ++.+..+-||||||+-++-.+- +          . ...+||++||.-
T Consensus       116 pIQaq~wp~~l~G---rD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRE  176 (519)
T KOG0331|consen  116 PIQAQGWPIALSG---RDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRE  176 (519)
T ss_pred             hhhhcccceeccC---CceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHH
Confidence            3455555555554   6889999999999998863221 1          1 235999999964

>CHL00095 clpC Clp protease ATP binding subunit

Probab=94.76  E-value=0.01  Score=45.55  Aligned_cols=40  Identities=13%  Similarity=0.231  Sum_probs=30.0

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+.+.+.+.+++......+.++++|+|.|||.++-.++..
T Consensus       184 r~~ei~~~~~~L~r~~~~n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        184 REKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             cHHHHHHHHHHHcccccCCeEEECCCCCCHHHHHHHHHHH
Confidence            5556666666776544568999999999999998766554

>PF13479 AAA_24: AAA domain

Probab=94.76  E-value=0.0085  Score=38.89  Aligned_cols=20  Identities=25%  Similarity=0.308  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      -+.+|.+|+|+|||..+..+
T Consensus         4 ~~~lIyG~~G~GKTt~a~~~   23 (213)
T PF13479_consen    4 IKILIYGPPGSGKTTLAASL   23 (213)
T ss_pred             eEEEEECCCCCCHHHHHHhC
Confidence            57889999999999988766

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.75  E-value=0.0035  Score=44.62  Aligned_cols=24  Identities=17%  Similarity=0.223  Sum_probs=20.1

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++..++++|||+|||+++..++..
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~  160 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAAR  160 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            467889999999999999877654

>PRK08939 primosomal protein DnaI; Reviewed

Probab=94.74  E-value=0.0041  Score=42.93  Aligned_cols=24  Identities=17%  Similarity=0.138  Sum_probs=19.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|+|||+++.+++..+
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l  180 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANEL  180 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            456788999999999998876653

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.73  E-value=0.0032  Score=45.83  Aligned_cols=29  Identities=14%  Similarity=0.239  Sum_probs=22.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ++.++.+|||+|||.++-.++...+.+.+
T Consensus        48 ~~ILLiGppG~GKT~lAraLA~~l~~~fi   76 (441)
T TIGR00390        48 KNILMIGPTGVGKTEIARRLAKLANAPFI   76 (441)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCeEE
Confidence            57889999999999998777665554433

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.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=94.72  E-value=0.0035  Score=45.13  Aligned_cols=28  Identities=21%  Similarity=0.318  Sum_probs=21.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      .+.++.+|||+|||.++-.++..++.+.
T Consensus       117 ~~iLL~GP~GsGKT~lAraLA~~l~~pf  144 (413)
T TIGR00382       117 SNILLIGPTGSGKTLLAQTLARILNVPF  144 (413)
T ss_pred             ceEEEECCCCcCHHHHHHHHHHhcCCCe
Confidence            4688899999999999977665554443

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.

>PRK13947 shikimate kinase; Provisional

Probab=94.72  E-value=0.0022  Score=39.49  Aligned_cols=25  Identities=28%  Similarity=0.305  Sum_probs=19.8

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      +.++.+++|+|||+++-.++..++-
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~   27 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSF   27 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCC
Confidence            4678899999999999777665543

>PRK03839 putative kinase; Provisional

Probab=94.69  E-value=0.0022  Score=40.13  Aligned_cols=23  Identities=22%  Similarity=0.091  Sum_probs=17.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..++.+++|||||+++-.++...
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~   24 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            35678999999999987665543

>KOG2373|consensus

Probab=94.69  E-value=0.031  Score=40.61  Aligned_cols=31  Identities=23%  Similarity=0.238  Sum_probs=21.8

Q ss_pred             HHHHHhcCC-cceeeeEEEeCCCCceeEeeee
Q psy11637         18 SLRKMFGNG-RARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        18 av~~~~~~~-~~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      .+.+++++. .+.-.++.+|||||||+.....
T Consensus       262 vLNk~LkGhR~GElTvlTGpTGsGKTTFlsEY  293 (514)
T KOG2373|consen  262 VLNKYLKGHRPGELTVLTGPTGSGKTTFLSEY  293 (514)
T ss_pred             HHHHHhccCCCCceEEEecCCCCCceeEehHh
Confidence            345566653 3456888999999999876543

>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=94.68  E-value=0.01  Score=39.36  Aligned_cols=33  Identities=24%  Similarity=0.337  Sum_probs=20.4

Q ss_pred             chhhHHHHHhc--CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG--NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~--~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      .|+++..++.-  .+ .++.++.+|+|+|||.++-.
T Consensus         7 GQe~aKrAL~iAAaG-~h~lLl~GppGtGKTmlA~~   41 (206)
T PF01078_consen    7 GQEEAKRALEIAAAG-GHHLLLIGPPGTGKTMLARR   41 (206)
T ss_dssp             STHHHHHHHHHHHHC-C--EEEES-CCCTHHHHHHH
T ss_pred             CcHHHHHHHHHHHcC-CCCeEEECCCCCCHHHHHHH
Confidence            36666665332  12 26899999999999988743

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.

>PRK06217 hypothetical protein; Validated

Probab=94.66  E-value=0.0026  Score=40.10  Aligned_cols=24  Identities=17%  Similarity=0.205  Sum_probs=19.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +.+|.+++|||||+++-.+...++
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~   26 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLD   26 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            467889999999999977766543

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=94.64  E-value=0.0026  Score=45.63  Aligned_cols=28  Identities=21%  Similarity=0.311  Sum_probs=21.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      .+.++.+|||+|||.++-.++...+.+.
T Consensus       109 ~~iLl~Gp~GtGKT~lAr~lA~~l~~pf  136 (412)
T PRK05342        109 SNILLIGPTGSGKTLLAQTLARILDVPF  136 (412)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHhCCCc
Confidence            5688999999999999876665544443

>KOG0346|consensus

Probab=94.62  E-value=0.0057  Score=45.16  Aligned_cols=47  Identities=15%  Similarity=0.148  Sum_probs=33.1

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE------------EEeeeeEEEeecce
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC------------TVRKRALVLCNSGV   64 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~------------~~~~~~lil~p~~~   64 (67)
                      |+.||--++++   .+.+.-+.||||||..++-.+.            +.+-..+|++||.-
T Consensus        46 Qs~aIplaLEg---KDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkE  104 (569)
T KOG0346|consen   46 QSSAIPLALEG---KDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKE  104 (569)
T ss_pred             hhcccchhhcC---cceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEEEechHH
Confidence            66666656655   5788889999999988754322            12457899999863

>TIGR02012 tigrfam_recA protein RecA

Probab=94.60  E-value=0.005  Score=43.03  Aligned_cols=44  Identities=27%  Similarity=0.308  Sum_probs=31.1

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      ...+|..+. .+  .+....|.+|+|+|||..++.++..   .+++++++
T Consensus        40 i~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yI   89 (321)
T TIGR02012        40 SLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFI   89 (321)
T ss_pred             CHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEE
Confidence            346677776 43  2456778899999999998876654   35666665

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.58  E-value=0.0032  Score=44.90  Aligned_cols=22  Identities=27%  Similarity=0.345  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...++++|||+|||+++..++.
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~  196 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAA  196 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5677889999999999976654

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=94.57  E-value=0.0072  Score=41.38  Aligned_cols=43  Identities=19%  Similarity=0.286  Sum_probs=28.4

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEE---------eeeeEEEe
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTV---------RKRALVLC   60 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---------~~~~lil~   60 (67)
                      .++.++..+  .+....|.+|+|+|||..++.++...         +++++++.
T Consensus        90 ~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~  143 (317)
T PRK04301         90 ELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID  143 (317)
T ss_pred             HHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEe
Confidence            345555542  23557788999999999988766431         34677664

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.56  E-value=0.0032  Score=38.08  Aligned_cols=20  Identities=35%  Similarity=0.424  Sum_probs=16.3

Q ss_pred             eEEEeCCCCceeEeeeeEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++.+++|||||+++-.+...
T Consensus         3 ~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           3 VVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             EEEcCCCCCHHHHHHHHHhh
Confidence            67899999999998765554

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.51  E-value=0.005  Score=46.83  Aligned_cols=36  Identities=25%  Similarity=0.294  Sum_probs=26.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE----E-----EeeeeEEEeecce
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC----T-----VRKRALVLCNSGV   64 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~----~-----~~~~~lil~p~~~   64 (67)
                      .-.++.+..|||||.+++.=+.    .     ..+++||+.|+.+
T Consensus       227 ~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~v  271 (747)
T COG3973         227 KILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNRV  271 (747)
T ss_pred             CeEEEecCCCCCchhHHHHHHHHHHhccccccccCceEEEcCcHH
Confidence            4566779999999999975222    1     1456999999753

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=94.50  E-value=0.0037  Score=42.41  Aligned_cols=32  Identities=19%  Similarity=0.093  Sum_probs=22.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +..++++|+|+|||+++..++..   .+.+++++.
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~  107 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAA  107 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEe
Confidence            45667799999999998776643   245666554

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.

>KOG0731|consensus

Probab=94.49  E-value=0.0061  Score=46.98  Aligned_cols=31  Identities=19%  Similarity=0.267  Sum_probs=24.9

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      .+..++++|+|+|||+.|-+++-+.+-|++-
T Consensus       344 PkGvLL~GPPGTGKTLLAKAiAGEAgVPF~s  374 (774)
T KOG0731|consen  344 PKGVLLVGPPGTGKTLLAKAIAGEAGVPFFS  374 (774)
T ss_pred             cCceEEECCCCCcHHHHHHHHhcccCCceee
Confidence            5678999999999999998888776555443

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.46  E-value=0.031  Score=36.50  Aligned_cols=25  Identities=24%  Similarity=0.333  Sum_probs=19.8

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      -++-+|.|||||++.+..-....+-
T Consensus         5 ~IvaG~NGsGKstv~~~~~~~~~~~   29 (187)
T COG4185           5 DIVAGPNGSGKSTVYASTLAPLLPG   29 (187)
T ss_pred             EEEecCCCCCceeeeeccchhhcCC
Confidence            4667999999999998877766553

>PHA00729 NTP-binding motif containing protein

Probab=94.46  E-value=0.0076  Score=40.37  Aligned_cols=23  Identities=26%  Similarity=0.265  Sum_probs=19.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.+|.+++|+|||+++..++..
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            57888999999999999876554

>KOG0338|consensus

Probab=94.46  E-value=0.0063  Score=45.68  Aligned_cols=50  Identities=18%  Similarity=0.170  Sum_probs=33.2

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEeecce
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLCNSGV   64 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~p~~~   64 (67)
                      -|-|...|=-.+-+   +...-++.||||||-.++..+.+         .-.|+||++||.-
T Consensus       205 TpIQ~a~IPvallg---kDIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTRE  263 (691)
T KOG0338|consen  205 TPIQVATIPVALLG---KDICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTRE  263 (691)
T ss_pred             CchhhhcccHHhhc---chhhheecccCCchhhhHHHHHHHHhcCcccCcceeEEEEeccHH
Confidence            34566666544443   45667899999998766544432         1358999999963

>PRK00300 gmk guanylate kinase; Provisional

Probab=94.44  E-value=0.0037  Score=39.62  Aligned_cols=24  Identities=29%  Similarity=0.113  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...+|++|+|||||.++-.++...
T Consensus         6 ~~i~i~G~sGsGKstl~~~l~~~~   29 (205)
T PRK00300          6 LLIVLSGPSGAGKSTLVKALLERD   29 (205)
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhC
Confidence            567788999999999876665543

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.44  E-value=0.0038  Score=43.33  Aligned_cols=32  Identities=19%  Similarity=0.078  Sum_probs=23.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      ...++++|+|+|||+++..++..   .+++++++.
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~  149 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAA  149 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEe
Confidence            45677899999999998766554   245666654

>KOG0922|consensus

Probab=94.43  E-value=0.0091  Score=45.35  Aligned_cols=49  Identities=16%  Similarity=0.128  Sum_probs=31.4

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      |-.+.++.+-++   ...+|++.||||||+-.-....+    ..+++-+--|+.+|
T Consensus        55 ~r~~il~~ve~n---qvlIviGeTGsGKSTQipQyL~eaG~~~~g~I~~TQPRRVA  107 (674)
T KOG0922|consen   55 YRDQILYAVEDN---QVLIVIGETGSGKSTQIPQYLAEAGFASSGKIACTQPRRVA  107 (674)
T ss_pred             HHHHHHHHHHHC---CEEEEEcCCCCCccccHhHHHHhcccccCCcEEeecCchHH
Confidence            333444444444   68889999999999887554433    24456666666655

>PRK06762 hypothetical protein; Provisional

Probab=94.43  E-value=0.0028  Score=39.00  Aligned_cols=23  Identities=17%  Similarity=0.117  Sum_probs=17.8

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -.++.+++|||||+++-.+....
T Consensus         4 li~i~G~~GsGKST~A~~L~~~l   26 (166)
T PRK06762          4 LIIIRGNSGSGKTTIAKQLQERL   26 (166)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            35678999999999887665544

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=94.43  E-value=0.0053  Score=40.51  Aligned_cols=33  Identities=12%  Similarity=0.029  Sum_probs=25.0

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLC   60 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~   60 (67)
                      +...+|.+|+|+|||..+..++..    .+.+++++.
T Consensus        30 g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS   66 (271)
T cd01122          30 GELIILTAGTGVGKTTFLREYALDLITQHGVRVGTIS   66 (271)
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEE
Confidence            356788999999999988766554    256777775

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=94.41  E-value=0.008  Score=43.51  Aligned_cols=46  Identities=13%  Similarity=0.267  Sum_probs=32.6

Q ss_pred             hhhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---E-eeeeEEEe
Q psy11637         15 QEKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---V-RKRALVLC   60 (67)
Q Consensus        15 Q~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~-~~~~lil~   60 (67)
                      =.+.+++++..+  .+...+|.+++|+|||+.++.++..   . +.+++++.
T Consensus        16 GI~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis   67 (509)
T PRK09302         16 GIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVT   67 (509)
T ss_pred             CchhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEE
Confidence            455678888643  2356788899999999999876543   2 56777764

>PRK09354 recA recombinase A; Provisional

Probab=94.38  E-value=0.0073  Score=42.72  Aligned_cols=45  Identities=24%  Similarity=0.279  Sum_probs=32.0

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      ...+|.++. .+  .++...|.+|+|+|||.+++.++..   .+++++|+-
T Consensus        45 i~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId   95 (349)
T PRK09354         45 SLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFID   95 (349)
T ss_pred             cHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEC
Confidence            346677777 43  2456778899999999999877653   356666654

>PLN02748 tRNA dimethylallyltransferase

Probab=94.38  E-value=0.0041  Score=45.47  Aligned_cols=26  Identities=27%  Similarity=0.374  Sum_probs=20.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      ...+|.+|||+|||.++..++...+.
T Consensus        23 ~~i~i~GptgsGKs~la~~la~~~~~   48 (468)
T PLN02748         23 KVVVVMGPTGSGKSKLAVDLASHFPV   48 (468)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCe
Confidence            34677799999999999887766543

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=94.37  E-value=0.0029  Score=40.09  Aligned_cols=21  Identities=24%  Similarity=0.183  Sum_probs=16.3

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .|.+|+|||||+++-.+....
T Consensus         3 gi~G~~GsGKSTl~~~l~~~l   23 (198)
T cd02023           3 GIAGGSGSGKTTVAEEIIEQL   23 (198)
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            478999999999986655443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>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=94.37  E-value=0.0028  Score=39.36  Aligned_cols=29  Identities=21%  Similarity=0.256  Sum_probs=20.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      .++.+|+|+|||.++..++...   +.+++++
T Consensus         3 ~~~~G~~G~GKTt~~~~la~~~~~~g~~v~~i   34 (173)
T cd03115           3 ILLVGLQGVGKTTTAAKLALYLKKKGKKVLLV   34 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            4678999999999987766543   3455544

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.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.36  E-value=0.0062  Score=42.66  Aligned_cols=46  Identities=22%  Similarity=0.251  Sum_probs=32.9

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      ...+|..+. .+  .++...|.+|+|+|||..++.++..   .+++++++-.
T Consensus        40 i~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~   91 (325)
T cd00983          40 SLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDA   91 (325)
T ss_pred             CHHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECc
Confidence            456777877 43  2456778899999999999887654   3567776643

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK14531 adenylate kinase; Provisional

Probab=94.31  E-value=0.0028  Score=40.05  Aligned_cols=24  Identities=25%  Similarity=0.387  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.++.+|+|||||+.+..++...
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            357889999999999987665543

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=94.31  E-value=0.0043  Score=40.10  Aligned_cols=31  Identities=19%  Similarity=0.178  Sum_probs=22.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE----eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV----RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil   59 (67)
                      ++..|.+-||||||..+..++.++    +.+++|+
T Consensus        24 ~H~~I~G~TGsGKS~~~~~ll~~l~~~~~~~~ii~   58 (229)
T PF01935_consen   24 RHIAIFGTTGSGKSNTVKVLLEELLKKKGAKVIIF   58 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCCCEEEE
Confidence            477799999999998887666543    3455554

It contains several conserved aspartates and histidines that could be metal ligands.

>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]

Probab=94.30  E-value=0.068  Score=36.15  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=17.0

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      =+.+|.|+|||+++.+++-..
T Consensus        34 GLLGPNGAGKTT~Fymi~Glv   54 (243)
T COG1137          34 GLLGPNGAGKTTTFYMIVGLV   54 (243)
T ss_pred             EEECCCCCCceeEEEEEEEEE
Confidence            356999999999998876543

>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup

Probab=94.30  E-value=0.061  Score=37.45  Aligned_cols=34  Identities=12%  Similarity=-0.038  Sum_probs=22.1

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .|.+...+..++||||||+++..
T Consensus        68 tq~~vy~~~~~p~v~~~l~G~n~ti~aYGqtGSGKTyTm~G  108 (345)
T cd01368          68 TQKEFFEGTALPLVQDLLKGKNSLLFTYGVTNSGKTYTMQG  108 (345)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCCeEEecC
Confidence            46666655321       23334555669999999999864

Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, a

>PRK14737 gmk guanylate kinase; Provisional

Probab=94.28  E-value=0.0032  Score=40.43  Aligned_cols=24  Identities=21%  Similarity=0.083  Sum_probs=19.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .-.+|++|+|+|||.++-.++...
T Consensus         5 ~~ivl~GpsG~GK~tl~~~l~~~~   28 (186)
T PRK14737          5 KLFIISSVAGGGKSTIIQALLEEH   28 (186)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhcC
Confidence            456788999999999998777654

>TIGR01351 adk adenylate kinases

Probab=94.28  E-value=0.0034  Score=40.38  Aligned_cols=22  Identities=23%  Similarity=0.200  Sum_probs=17.7

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|.+|+|||||+++..++.+.
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            4688999999999987766543

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=94.28  E-value=0.015  Score=44.05  Aligned_cols=37  Identities=16%  Similarity=0.278  Sum_probs=25.8

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |++-+++   ++.+....+.++++|+|.|||.++-.++.+
T Consensus       187 r~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       187 REDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             cHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHH
Confidence            4444444   444444468999999999999998666554

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.27  E-value=0.0041  Score=47.64  Aligned_cols=43  Identities=21%  Similarity=0.207  Sum_probs=28.7

Q ss_pred             chhhHHHHHhcC-----------Cc-ceeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         14 YQEKSLRKMFGN-----------GR-ARSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        14 yQ~~av~~~~~~-----------~~-~~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      .|.+|++.+.+.           ++ ..+.++.+|||+|||.++-.++..++.+.
T Consensus       462 GQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~  516 (758)
T PRK11034        462 GQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIEL  516 (758)
T ss_pred             CcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhCCCc
Confidence            388888764321           11 23578899999999999876666554443

>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=94.26  E-value=0.0057  Score=41.26  Aligned_cols=42  Identities=17%  Similarity=0.133  Sum_probs=25.8

Q ss_pred             chhhHHHH---Hhc----CC-cceeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         14 YQEKSLRK---MFG----NG-RARSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        14 yQ~~av~~---~~~----~~-~~~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      .|+..++.   +++    .+ .-.+.++.+|+|.|||+.+.-++.+.+..
T Consensus        28 GQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~   77 (233)
T PF05496_consen   28 GQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANELGVN   77 (233)
T ss_dssp             S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHCT--
T ss_pred             CcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhccCCC
Confidence            38888765   221    21 23578999999999999887666555443

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.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=94.26  E-value=0.0069  Score=43.21  Aligned_cols=29  Identities=17%  Similarity=0.279  Sum_probs=21.9

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      .+..++.+|+|+|||+++-+++...+.+.
T Consensus       179 pkgvLL~GppGTGKT~LAkalA~~l~~~f  207 (398)
T PTZ00454        179 PRGVLLYGPPGTGKTMLAKAVAHHTTATF  207 (398)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhcCCCE
Confidence            46688889999999999876665544433

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=94.20  E-value=0.0064  Score=37.51  Aligned_cols=20  Identities=35%  Similarity=0.335  Sum_probs=16.9

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +-.+|.+|+|+|||.++-++
T Consensus        20 g~~vi~G~Ng~GKStil~ai   39 (202)
T PF13476_consen   20 GLNVIYGPNGSGKSTILEAI   39 (202)
T ss_dssp             EEEEEEESTTSSHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            57889999999999988554

>PRK06921 hypothetical protein; Provisional

Probab=94.19  E-value=0.0053  Score=41.49  Aligned_cols=32  Identities=19%  Similarity=0.119  Sum_probs=23.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      .+.++.+|+|+|||+.+.+++..+    +..++++.
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~  153 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFP  153 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEE
Confidence            578889999999999998776653    34455543

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=94.19  E-value=0.0035  Score=45.62  Aligned_cols=28  Identities=14%  Similarity=0.214  Sum_probs=21.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      ++.++.+|||+|||.++-.++...+.++
T Consensus        51 ~~ILliGp~G~GKT~LAr~LAk~l~~~f   78 (443)
T PRK05201         51 KNILMIGPTGVGKTEIARRLAKLANAPF   78 (443)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCChh
Confidence            6788999999999998876666554443

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=94.18  E-value=0.019  Score=36.05  Aligned_cols=41  Identities=17%  Similarity=0.263  Sum_probs=26.0

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |....+.+.+++..+.....+|.+|-|+|||.....++...
T Consensus         4 R~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~   44 (234)
T PF01637_consen    4 REKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINEL   44 (234)
T ss_dssp             -HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHh
Confidence            33444555666654434678888999999998776555443

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=94.13  E-value=0.023  Score=41.06  Aligned_cols=23  Identities=26%  Similarity=0.293  Sum_probs=18.6

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ++...+++|||.|||++.+-++.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAa  225 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAA  225 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHH
Confidence            47788999999999998765543

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=94.12  E-value=0.01  Score=36.86  Aligned_cols=21  Identities=33%  Similarity=0.214  Sum_probs=16.8

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..+|.+|+|||||+++-.++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~   23 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARA   23 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467889999999999855444

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=94.12  E-value=0.011  Score=40.10  Aligned_cols=19  Identities=21%  Similarity=0.176  Sum_probs=15.8

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      +.++.+|+|+|||+++-.+
T Consensus        60 ~vll~G~pGTGKT~lA~~i   78 (284)
T TIGR02880        60 HMSFTGNPGTGKTTVALRM   78 (284)
T ss_pred             eEEEEcCCCCCHHHHHHHH
Confidence            5778899999999998444

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.

>KOG0388|consensus

Probab=94.10  E-value=0.0022  Score=49.82  Aligned_cols=57  Identities=19%  Similarity=0.321  Sum_probs=45.7

Q ss_pred             ceeeccchhhHHHHHhc-CCcceeeeEEEeCCCCceeEeeeeEEEE------eeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFG-NGRARSGVIVLPCGAGKSLVGVTACCTV------RKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~-~~~~~~~~i~~pTGsGKT~i~~~~~~~~------~~~~lil~p~~~   64 (67)
                      ..+|..||-..+.+..+ .+++-+|++.-..|-|||+-++++...+      -+|+||++|.++
T Consensus       565 ~ctLKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpaSt  628 (1185)
T KOG0388|consen  565 KCTLKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPAST  628 (1185)
T ss_pred             hhhhHHHhhccHHHHHHHHHccccceehhhhccchhHHHHHHHHHHHHhccCCCceEEeehHHH
Confidence            36789999999987654 2445899999999999999998776543      579999999765

>PLN02840 tRNA dimethylallyltransferase

Probab=94.09  E-value=0.0039  Score=45.08  Aligned_cols=26  Identities=31%  Similarity=0.340  Sum_probs=20.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .-.+|.+|||+|||.++..++...+.
T Consensus        22 ~vi~I~GptgsGKTtla~~La~~~~~   47 (421)
T PLN02840         22 KVIVISGPTGAGKSRLALELAKRLNG   47 (421)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHCCC
Confidence            34667799999999999887776544

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=94.08  E-value=0.013  Score=40.57  Aligned_cols=44  Identities=18%  Similarity=0.271  Sum_probs=29.8

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~   60 (67)
                      +.+|+++..+  .+....|.+|+|+|||.+++.++..         .+++++++-
T Consensus        83 ~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYId  137 (313)
T TIGR02238        83 QALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYID  137 (313)
T ss_pred             HHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEE
Confidence            3467777653  2456778899999999998765421         245777764

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>KOG2228|consensus

Probab=94.07  E-value=0.042  Score=39.55  Aligned_cols=52  Identities=25%  Similarity=0.358  Sum_probs=33.1

Q ss_pred             cceeeccchhh--HHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEE
Q psy11637          7 PSAVLRPYQEK--SLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALV   58 (67)
Q Consensus         7 ~~~~lR~yQ~~--av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~li   58 (67)
                      +...|+-+|.+  -+++|++    .++.++.++++|-|||||...-....   +.++.+++
T Consensus        22 ~~~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~   82 (408)
T KOG2228|consen   22 PHINLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLL   82 (408)
T ss_pred             CCcceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEE
Confidence            34566666544  3455665    35567899999999999987643322   34555554

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=94.06  E-value=0.0029  Score=37.66  Aligned_cols=21  Identities=33%  Similarity=0.360  Sum_probs=16.7

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +|.+++|||||.++-.+....
T Consensus         3 ~i~G~~GsGKst~a~~la~~~   23 (147)
T cd02020           3 AIDGPAGSGKSTVAKLLAKKL   23 (147)
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            578999999999887665543

>PRK06696 uridine kinase; Validated

Probab=94.05  E-value=0.0066  Score=39.51  Aligned_cols=24  Identities=13%  Similarity=-0.046  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ....|.+++|||||+++-.++..+
T Consensus        23 ~iI~I~G~sgsGKSTlA~~L~~~l   46 (223)
T PRK06696         23 LRVAIDGITASGKTTFADELAEEI   46 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            345567999999999998777665

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=94.05  E-value=0.02  Score=42.54  Aligned_cols=48  Identities=15%  Similarity=0.210  Sum_probs=32.9

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E---eeeeEEEeecc
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V---RKRALVLCNSG   63 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~---~~~~lil~p~~   63 (67)
                      |.|-|++++..  ..   +..+|.+.+|||||.+...-+..    .   .+++|+++-|+
T Consensus         2 Ln~~Q~~av~~--~~---~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~~p~~IL~vTFt~   56 (664)
T TIGR01074         2 LNPQQQEAVEY--VT---GPCLVLAGAGSGKTRVITNKIAYLIQNCGYKARNIAAVTFTN   56 (664)
T ss_pred             CCHHHHHHHhC--CC---CCEEEEecCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccH
Confidence            66788888764  12   57899999999999888643332    1   24567776554

Designed to identify rep members of the uvrD/rep subfamily.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=94.04  E-value=0.0044  Score=39.07  Aligned_cols=24  Identities=38%  Similarity=0.498  Sum_probs=19.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.++++|+|+|||+++-.++...
T Consensus         5 ~~I~liG~~GaGKStl~~~La~~l   28 (172)
T PRK05057          5 RNIFLVGPMGAGKSTIGRQLAQQL   28 (172)
T ss_pred             CEEEEECCCCcCHHHHHHHHHHHc
Confidence            467788999999999997766544

>PRK06547 hypothetical protein; Provisional

Probab=94.03  E-value=0.0069  Score=38.52  Aligned_cols=23  Identities=17%  Similarity=0.153  Sum_probs=17.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...+|.+++|||||+++-.+...
T Consensus        16 ~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         16 ITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            44556689999999998666544

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=94.02  E-value=0.0053  Score=42.65  Aligned_cols=27  Identities=19%  Similarity=0.322  Sum_probs=20.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ...++.+|+|+|||+++-+++...+.+
T Consensus       157 ~gvLL~GppGtGKT~lakaia~~l~~~  183 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLAKAVAHETNAT  183 (364)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhCCCC
Confidence            457889999999999987776655443

Many proteins may score above the trusted cutoff because an internal

>PRK05480 uridine/cytidine kinase; Provisional

Probab=93.99  E-value=0.006  Score=39.04  Aligned_cols=24  Identities=25%  Similarity=0.095  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ....|.+|+|||||+++-.+....
T Consensus         7 ~iI~I~G~sGsGKTTl~~~l~~~l   30 (209)
T PRK05480          7 IIIGIAGGSGSGKTTVASTIYEEL   30 (209)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh
Confidence            456688999999999986665554

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=93.99  E-value=0.011  Score=42.84  Aligned_cols=29  Identities=21%  Similarity=0.323  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ...++.+|+|+|||+++-+++.....+.+
T Consensus       218 ~gVLL~GPPGTGKT~LAraIA~el~~~fi  246 (438)
T PTZ00361        218 KGVILYGPPGTGKTLLAKAVANETSATFL  246 (438)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhhCCCEE
Confidence            56788899999999998777665544433

>CHL00181 cbbX CbbX; Provisional

Probab=93.98  E-value=0.011  Score=40.28  Aligned_cols=22  Identities=18%  Similarity=0.102  Sum_probs=17.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+.++.+|+|+|||.++-.++.
T Consensus        60 ~~ill~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            3468889999999999976644

>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=93.98  E-value=0.0036  Score=37.63  Aligned_cols=22  Identities=32%  Similarity=0.330  Sum_probs=17.5

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .++++++|+|||+++-.+...+
T Consensus         2 i~l~G~~GsGKstla~~la~~l   23 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKAL   23 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHh
Confidence            4688999999999987665543

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.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=93.94  E-value=0.011  Score=36.67  Aligned_cols=21  Identities=24%  Similarity=-0.004  Sum_probs=16.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..++.+|+|||||+++..++.
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            466789999999998865553

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=93.92  E-value=0.0061  Score=39.93  Aligned_cols=22  Identities=27%  Similarity=0.341  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .-+++.+|.|+|||..++.++.
T Consensus         2 ~~~ll~g~~G~GKS~lal~la~   23 (239)
T cd01125           2 YVSALVAPGGTGKSSLLLVLAL   23 (239)
T ss_pred             ceeEEEcCCCCCHHHHHHHHHH
Confidence            3578999999999999976653

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.

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.89  E-value=0.043  Score=38.28  Aligned_cols=17  Identities=24%  Similarity=0.284  Sum_probs=13.9

Q ss_pred             eeeEEEeCCCCceeEee
Q psy11637         30 SGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~   46 (67)
                      +.++++|||||||....
T Consensus         1 H~lv~g~tGsGKt~~~v   17 (384)
T cd01126           1 HVLVFAPTRSGKGVGFV   17 (384)
T ss_pred             CeeEecCCCCCCccEEE
Confidence            35789999999997654

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=93.88  E-value=0.0099  Score=42.88  Aligned_cols=45  Identities=20%  Similarity=0.271  Sum_probs=31.8

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      +-+|+.+..+  .+...+|.+++|+|||+.++.++...   +++++++.-
T Consensus        67 ~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~  116 (446)
T PRK11823         67 GELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSG  116 (446)
T ss_pred             HHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEc
Confidence            3456677643  23567888999999999988776542   567887753

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.88  E-value=0.022  Score=39.77  Aligned_cols=38  Identities=16%  Similarity=0.154  Sum_probs=25.8

Q ss_pred             chhhHHHHHh---cCCc-ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRKMF---GNGR-ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~~~---~~~~-~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|+.+++.+.   ..+. .+.-++.+|.|+|||+++..++..
T Consensus        20 Gq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~   61 (363)
T PRK14961         20 GQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKS   61 (363)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHH
Confidence            5888776543   3332 233489999999999988665544

>KOG0090|consensus

Probab=93.87  E-value=0.056  Score=36.58  Aligned_cols=25  Identities=12%  Similarity=0.021  Sum_probs=21.6

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +...++++|++||||.++..++...
T Consensus        38 ~~~Vll~Gl~dSGKT~LF~qL~~gs   62 (238)
T KOG0090|consen   38 QNAVLLVGLSDSGKTSLFTQLITGS   62 (238)
T ss_pred             CCcEEEEecCCCCceeeeeehhcCC
Confidence            3678999999999999999888764

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=93.86  E-value=0.013  Score=38.30  Aligned_cols=25  Identities=20%  Similarity=0.045  Sum_probs=20.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +..++.+|+|+|||+++..+.....
T Consensus        44 ~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            4678899999999999876665543

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=93.84  E-value=0.0097  Score=45.09  Aligned_cols=41  Identities=17%  Similarity=0.242  Sum_probs=27.0

Q ss_pred             chhhHHHHHhcC------C------cceeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         14 YQEKSLRKMFGN------G------RARSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        14 yQ~~av~~~~~~------~------~~~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .|.++++.+.+.      +      ...+.++.+|||+|||.++-.++..+..
T Consensus       458 GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~  510 (731)
T TIGR02639       458 GQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGV  510 (731)
T ss_pred             CcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcC
Confidence            488888764321      1      1134688999999999888666555443

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=93.83  E-value=0.014  Score=37.49  Aligned_cols=22  Identities=32%  Similarity=0.304  Sum_probs=17.6

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+|.+|+|||||+.+-.++.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999988665543

>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins

Probab=93.79  E-value=0.09  Score=36.63  Aligned_cols=33  Identities=21%  Similarity=0.145  Sum_probs=21.6

Q ss_pred             hhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         15 QEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        15 Q~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      |++..+++..       .|.+...+..++||||||++...
T Consensus        69 q~~vf~~~~~p~v~~~l~G~n~~i~ayGqtGSGKT~Tm~G  108 (356)
T cd01365          69 QEDVFEDLGRELLDHAFEGYNVCLFAYGQTGSGKSYTMMG  108 (356)
T ss_pred             HHHHHHHHHHHHHHHHhCCCceEEEEecCCCCCCeEEecC
Confidence            7777655321       23334455569999999998863

KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=93.78  E-value=0.011  Score=35.93  Aligned_cols=19  Identities=26%  Similarity=0.281  Sum_probs=15.5

Q ss_pred             EEEeCCCCceeEeeeeEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+|+|||||+++..++.+
T Consensus         1 i~G~PgsGK~t~~~~la~~   19 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKR   19 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHh
Confidence            5799999999988766554

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=93.77  E-value=0.0049  Score=39.85  Aligned_cols=25  Identities=28%  Similarity=0.296  Sum_probs=20.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+.+++++.|+|||+++-.++..++
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~   27 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALN   27 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcC
Confidence            4678999999999999977765543

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=93.74  E-value=0.0047  Score=40.15  Aligned_cols=23  Identities=22%  Similarity=0.075  Sum_probs=18.1

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEe
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ..|.+|+|||||+++-.++...+
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~g   25 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLG   25 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhC
Confidence            35789999999999977666543

>cd01373 KISc_KLP2_like Kinesin motor domain, KLP2-like subgroup

Probab=93.73  E-value=0.084  Score=36.62  Aligned_cols=34  Identities=21%  Similarity=0.144  Sum_probs=22.2

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.+..       .+.+...+..+.||||||.++..
T Consensus        54 ~q~~vy~~~~~p~v~~~~~G~n~ti~aYGqTGSGKTyTm~G   94 (337)
T cd01373          54 NQEDVFQSVGKPLVEDCLSGYNGSIFAYGQTGSGKTYTMMG   94 (337)
T ss_pred             CHHHHHHHHHHHHHHHHhCCCceeEEEeCCCCCCceEEecC
Confidence            47776665432       23233455559999999999865

Members of this subgroup seem to play a role in mitosis and meiosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second

>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup

Probab=93.73  E-value=0.076  Score=36.86  Aligned_cols=34  Identities=24%  Similarity=0.169  Sum_probs=21.6

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .|.+...+..++||||||.++..
T Consensus        67 ~q~~vf~~~~~plv~~~~~G~n~~i~ayGqtGSGKTyTm~G  107 (338)
T cd01370          67 TQEEVYENTTKPLVDGVLNGYNATVFAYGATGAGKTHTMLG  107 (338)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCceEEeeCCCCCCCeEEEcC
Confidence            36666654331       13234455569999999999855

The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a sec

>KOG0341|consensus

Probab=93.72  E-value=0.034  Score=40.93  Aligned_cols=51  Identities=25%  Similarity=0.307  Sum_probs=33.8

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeee----EE---------EE-eeeeEEEeecce
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA----CC---------TV-RKRALVLCNSGV   64 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~----~~---------~~-~~~~lil~p~~~   64 (67)
                      +-|-|.+.+--+++.   +..+-.+-||||||+++...    +.         +. +.--||+||+.-
T Consensus       193 PTpIQvQGlPvvLsG---RDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRE  257 (610)
T KOG0341|consen  193 PTPIQVQGLPVVLSG---RDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRE  257 (610)
T ss_pred             CCceeecCcceEeec---CceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHH
Confidence            344566666556654   67777899999999998532    11         11 335799999863

>PRK10865 protein disaggregation chaperone; Provisional

Probab=93.72  E-value=0.011  Score=45.68  Aligned_cols=38  Identities=13%  Similarity=0.249  Sum_probs=27.9

Q ss_pred             hhhHHHHHh---cCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         15 QEKSLRKMF---GNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        15 Q~~av~~~~---~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+.-+++++   .+....+.++++|+|.|||.++-.++...
T Consensus       183 r~~ei~~~i~iL~r~~~~n~lL~G~pGvGKT~l~~~la~~i  223 (857)
T PRK10865        183 RDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRI  223 (857)
T ss_pred             CHHHHHHHHHHHhcCCcCceEEECCCCCCHHHHHHHHHHHh
Confidence            555566644   34445789999999999999987666543

>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup

Probab=93.72  E-value=0.093  Score=36.05  Aligned_cols=34  Identities=21%  Similarity=0.241  Sum_probs=22.4

Q ss_pred             cchhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         13 PYQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        13 ~yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      .-|++..++        +++ +.+...+..++||||||.+...
T Consensus        59 ~~q~~vy~~~~~plv~~~~~-G~n~~i~ayG~tgSGKTyTm~G  100 (319)
T cd01376          59 CTQEDIFSREVKPIVPHLLS-GQNATVFAYGSTGAGKTHTMLG  100 (319)
T ss_pred             CCHHHHHHHHHHHHHHHHhC-CCceEEEEECCCCCCCcEEEeC
Confidence            347776665        333 3334455569999999999864

Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=93.72  E-value=0.013  Score=41.50  Aligned_cols=44  Identities=20%  Similarity=0.254  Sum_probs=30.7

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .-+|+.+..+  .+.-.++.+++|+|||++++.++..   .+++++++.
T Consensus        69 ~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs  117 (372)
T cd01121          69 EELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVS  117 (372)
T ss_pred             HHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            4456666543  2356778899999999998877654   245777764

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.

>TIGR02746 TraC-F-type type-IV secretion system protein TraC

Probab=93.70  E-value=0.0064  Score=45.86  Aligned_cols=31  Identities=23%  Similarity=0.165  Sum_probs=22.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .+.+|.++||||||+....++..   .+.+++|+
T Consensus       431 ~n~~I~G~tGsGKS~~~~~l~~~~~~~g~~v~ii  464 (797)
T TIGR02746       431 YNIAVVGGSGAGKSFFMQELIVDNLSRGGKVWVI  464 (797)
T ss_pred             cceEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEE
Confidence            57999999999999988655433   24455554

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.

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=93.70  E-value=0.026  Score=42.56  Aligned_cols=49  Identities=18%  Similarity=0.231  Sum_probs=34.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-------eeeeEEEeecc
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-------RKRALVLCNSG   63 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-------~~~~lil~p~~   63 (67)
                      .|.|.|++++...  .   +..+|.+..|||||.+...-+..+       ..++|+++=|+
T Consensus         4 ~Ln~~Q~~av~~~--~---g~~lV~AgaGSGKT~~l~~ria~Li~~~~i~P~~IL~lTFT~   59 (726)
T TIGR01073         4 HLNPEQREAVKTT--E---GPLLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWNILAITFTN   59 (726)
T ss_pred             ccCHHHHHHHhCC--C---CCEEEEeCCCCCHHHHHHHHHHHHHHcCCCCHHHeeeeeccH
Confidence            5788999998742  2   578999999999998886433321       24677776553

Designed to identify pcrA members of the uvrD/rep subfamily.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=93.68  E-value=0.015  Score=36.37  Aligned_cols=24  Identities=21%  Similarity=0.133  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +..++++|+|||||+++-.+....
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhh
Confidence            456788999999999997665543

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK13873 conjugal transfer ATPase TrbE; Provisional

Probab=93.67  E-value=0.0076  Score=46.10  Aligned_cols=23  Identities=30%  Similarity=0.378  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++.+|.+|||||||+....++..
T Consensus       442 gn~~I~G~tGsGKS~l~~~l~~~  464 (811)
T PRK13873        442 GHTLVVGPTGAGKSVLLALMALQ  464 (811)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999988665543

>PRK08116 hypothetical protein; Validated

Probab=93.65  E-value=0.0049  Score=41.63  Aligned_cols=30  Identities=10%  Similarity=0.171  Sum_probs=22.5

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ..++.+++|+|||+.+.+++..+   +.+++++
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~  148 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFV  148 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            36788999999999998877653   4455554

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=93.65  E-value=0.012  Score=42.69  Aligned_cols=44  Identities=25%  Similarity=0.411  Sum_probs=31.0

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +.+|+.+..+  .+...+|.+|+|+|||..++.++..   .+.+++++.
T Consensus       260 ~~lD~~l~GG~~~g~~~li~G~~G~GKT~l~~~~~~~~~~~g~~~~yis  308 (509)
T PRK09302        260 PDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFA  308 (509)
T ss_pred             HHHHHhhcCCCCCCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEE
Confidence            3456666532  2356778899999999999877653   367777775

>PHA02624 large T antigen; Provisional

Probab=93.62  E-value=0.014  Score=44.22  Aligned_cols=41  Identities=17%  Similarity=0.173  Sum_probs=30.6

Q ss_pred             HHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         19 LRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        19 v~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ++.++++-. .+-.++.+|.|+|||..+.+++..++++++-+
T Consensus       421 lk~~l~giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsV  462 (647)
T PHA02624        421 LKLIVENVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNV  462 (647)
T ss_pred             HHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEe
Confidence            444555422 34567779999999999999999998877663

>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=93.62  E-value=0.0093  Score=40.28  Aligned_cols=33  Identities=18%  Similarity=0.208  Sum_probs=23.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe---eeeEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR---KRALVLCN   61 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~---~~~lil~p   61 (67)
                      -+.+|++++|||||...+.++....   ..+.+++|
T Consensus        14 fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITP   49 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEec
Confidence            5788999999999998877766432   34444444

This is thought to be an ATPase involved in viral DNA packaging [].

>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=93.61  E-value=0.0046  Score=40.60  Aligned_cols=20  Identities=20%  Similarity=0.124  Sum_probs=15.7

Q ss_pred             EEEeCCCCceeEeeeeEEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |.+|+|||||+++-.+...+
T Consensus         4 I~G~sGSGKTTla~~L~~~l   23 (220)
T cd02025           4 IAGSVAVGKSTTARVLQALL   23 (220)
T ss_pred             eeCCCCCCHHHHHHHHHHHH
Confidence            67999999999986555443

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PRK13949 shikimate kinase; Provisional

Probab=93.60  E-value=0.0052  Score=38.73  Aligned_cols=23  Identities=26%  Similarity=0.267  Sum_probs=18.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.+|++|+|+|||+++-.++...
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l   25 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAREL   25 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            56788999999999987665544

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=93.60  E-value=0.015  Score=41.32  Aligned_cols=47  Identities=19%  Similarity=0.199  Sum_probs=30.7

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--eeeeEEEeec
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--RKRALVLCNS   62 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--~~~~lil~p~   62 (67)
                      -|-+.+..+.+..  .+.++++-||||||+..-++....  .+|++.+-.|
T Consensus       161 ~~a~~L~~av~~r--~NILisGGTGSGKTTlLNal~~~i~~~eRvItiEDt  209 (355)
T COG4962         161 RAAKFLRRAVGIR--CNILISGGTGSGKTTLLNALSGFIDSDERVITIEDT  209 (355)
T ss_pred             HHHHHHHHHHhhc--eeEEEeCCCCCCHHHHHHHHHhcCCCcccEEEEeeh
Confidence            3444445555543  589999999999999886665543  3466555443

>PF05729 NACHT: NACHT domain

Probab=93.59  E-value=0.0073  Score=36.17  Aligned_cols=22  Identities=23%  Similarity=-0.031  Sum_probs=18.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      -.+|.+++|+|||.++..++..
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~   23 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQ   23 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHH
Confidence            3578899999999998777654

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=93.59  E-value=0.0082  Score=43.12  Aligned_cols=22  Identities=23%  Similarity=0.244  Sum_probs=18.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +..++++|||+|||+++..++.
T Consensus       222 ~~i~~vGptGvGKTTt~~kLA~  243 (424)
T PRK05703        222 GVVALVGPTGVGKTTTLAKLAA  243 (424)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4678889999999998876654

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=93.58  E-value=0.0067  Score=46.97  Aligned_cols=24  Identities=29%  Similarity=0.239  Sum_probs=19.8

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+++|.+|||||||+....++..
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q  498 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQ  498 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999988666544

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=93.57  E-value=0.026  Score=40.21  Aligned_cols=23  Identities=22%  Similarity=0.115  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-.++.+|+|+|||+++-.++..
T Consensus        79 ~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       79 QILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            34578899999999999776554

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

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

Probab=93.56  E-value=0.0048  Score=45.92  Aligned_cols=57  Identities=23%  Similarity=0.332  Sum_probs=41.4

Q ss_pred             ceeeccchhhHHHHHhc--CCcceeeeEEEeCCCCceeEeeeeEEE---E----eeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFG--NGRARSGVIVLPCGAGKSLVGVTACCT---V----RKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~--~~~~~~~~i~~pTGsGKT~i~~~~~~~---~----~~~~lil~p~~~   64 (67)
                      ...+||||.+.+.+...  ......+++.-..|.|||+..++++..   .    .++.++++|+..
T Consensus       336 ~~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~  401 (866)
T COG0553         336 SAELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASL  401 (866)
T ss_pred             hhhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHHH
Confidence            46799999999955331  112367888899999999888766532   1    358999999754

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=93.55  E-value=0.014  Score=37.17  Aligned_cols=21  Identities=24%  Similarity=0.324  Sum_probs=16.8

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -|.+|+|||||+++-.+...+
T Consensus         3 gI~G~sgSGKTTla~~L~~~L   23 (194)
T PF00485_consen    3 GIAGPSGSGKTTLAKRLAQIL   23 (194)
T ss_dssp             EEEESTTSSHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHh
Confidence            378999999999997666544

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 ....

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.54  E-value=0.026  Score=39.89  Aligned_cols=38  Identities=21%  Similarity=0.161  Sum_probs=25.4

Q ss_pred             chhhHHHH---HhcCCc-ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRK---MFGNGR-ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~---~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|+.+++.   +++.+. .+.-++.+|.|.|||.++..++..
T Consensus        20 Gq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~   61 (397)
T PRK14955         20 AQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKA   61 (397)
T ss_pred             ChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHH
Confidence            47776654   444433 234678899999999998665543

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.51  E-value=0.014  Score=41.13  Aligned_cols=44  Identities=18%  Similarity=0.245  Sum_probs=29.7

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEee
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLCN   61 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~p   61 (67)
                      .+|+++..+  .+....|.+|+|+|||.+++.++..         .+++++|+--
T Consensus       114 ~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdT  168 (344)
T PLN03187        114 ALDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDT  168 (344)
T ss_pred             hHHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEc
Confidence            466777653  2456778899999999988765421         1357777653

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=93.51  E-value=0.004  Score=39.23  Aligned_cols=25  Identities=32%  Similarity=0.357  Sum_probs=20.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +-.+|++|.|+|||.++-.++....
T Consensus         3 r~ivl~Gpsg~GK~~l~~~L~~~~~   27 (183)
T PF00625_consen    3 RPIVLVGPSGSGKSTLAKRLIQEFP   27 (183)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHST
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcc
Confidence            4678899999999999987777654

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 ....

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=93.51  E-value=0.012  Score=40.94  Aligned_cols=40  Identities=18%  Similarity=0.273  Sum_probs=30.4

Q ss_pred             eccchhhHHHHHhcC-Cc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         11 LRPYQEKSLRKMFGN-GR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        11 lR~yQ~~av~~~~~~-~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +.|+|++..+++... +. .+.-++.+|.|.|||..+..++.
T Consensus         2 ~yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~~a~   43 (325)
T PRK08699          2 IYPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARFAAQ   43 (325)
T ss_pred             CCCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHHHHH
Confidence            479999999998753 22 35677899999999988865543

>PTZ00088 adenylate kinase 1; Provisional

Probab=93.50  E-value=0.0056  Score=40.68  Aligned_cols=24  Identities=17%  Similarity=0.009  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.++.+|+|||||+++..++...
T Consensus         7 mrIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          7 LKIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            357888999999999987665543

>PRK00279 adk adenylate kinase; Reviewed

Probab=93.50  E-value=0.0057  Score=39.48  Aligned_cols=23  Identities=22%  Similarity=0.174  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.+|.+|+|||||+++..++...
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            35788999999999887666543

>PRK14528 adenylate kinase; Provisional

Probab=93.49  E-value=0.0052  Score=39.14  Aligned_cols=23  Identities=26%  Similarity=0.374  Sum_probs=18.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.++.+|+|||||+++..++...
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            56788999999999987665443

>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group

Probab=93.49  E-value=0.091  Score=36.19  Aligned_cols=31  Identities=23%  Similarity=0.347  Sum_probs=20.7

Q ss_pred             hhhHHHH--------HhcCCcceeeeEEEeCCCCceeEee
Q psy11637         15 QEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        15 Q~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      |++..++        +++ +.+...+..++||||||.++.
T Consensus        65 q~~vf~~~~~plv~~~~~-G~n~~i~ayGqtGSGKTyTm~  103 (322)
T cd01367          65 NEEVYRSTVKPLIPHVFE-GGVATCFAYGQTGSGKTYTML  103 (322)
T ss_pred             HHHHHHHHHHHHHHHHhC-CCceEEEeccCCCCCCceEec
Confidence            6666655        333 333445555999999999987

KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and lo

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=93.48  E-value=0.0066  Score=43.92  Aligned_cols=30  Identities=20%  Similarity=0.297  Sum_probs=22.2

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      .+..++.+|+|+|||.++-+++...+.+.+
T Consensus        88 ~~giLL~GppGtGKT~la~alA~~~~~~~~  117 (495)
T TIGR01241        88 PKGVLLVGPPGTGKTLLAKAVAGEAGVPFF  117 (495)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHcCCCee
Confidence            346888999999999998766655544443

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.

>PRK06620 hypothetical protein; Validated

Probab=93.43  E-value=0.017  Score=37.85  Aligned_cols=21  Identities=19%  Similarity=0.105  Sum_probs=16.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ...++.+|+|+|||+.+.++.
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~   65 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQ   65 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHH
Confidence            457889999999999886543

>TIGR00416 sms DNA repair protein RadA

Probab=93.42  E-value=0.015  Score=42.11  Aligned_cols=44  Identities=23%  Similarity=0.358  Sum_probs=30.2

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      +-+|+++..+  .+.-.+|.+++|+|||+.++.++...   +++++++.
T Consensus        81 ~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs  129 (454)
T TIGR00416        81 GELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVS  129 (454)
T ss_pred             HHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEE
Confidence            3456666543  23557788999999999998775542   45777765

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)).

>KOG1533|consensus

Probab=93.34  E-value=0.037  Score=38.16  Aligned_cols=16  Identities=38%  Similarity=0.455  Sum_probs=13.1

Q ss_pred             eeEEEeCCCCceeEee
Q psy11637         31 GVIVLPCGAGKSLVGV   46 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~   46 (67)
                      .+|++|+|||||+--.
T Consensus         5 qvVIGPPgSGKsTYc~   20 (290)
T KOG1533|consen    5 QVVIGPPGSGKSTYCN   20 (290)
T ss_pred             eEEEcCCCCCccchhh
Confidence            5789999999997544

>TIGR03689 pup_AAA proteasome ATPase

Probab=93.34  E-value=0.0099  Score=43.90  Aligned_cols=25  Identities=20%  Similarity=0.410  Sum_probs=19.6

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+..++.+|+|+|||.++-+++..+
T Consensus       216 p~GILLyGPPGTGKT~LAKAlA~eL  240 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIAKAVANSL  240 (512)
T ss_pred             CcceEEECCCCCcHHHHHHHHHHhh
Confidence            3568889999999999886665554

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.

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=93.34  E-value=0.037  Score=40.91  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ++|+|.+.||+|||++-..+++
T Consensus        20 RHGLIaGATGTGKTvTLqvlAE   41 (502)
T PF05872_consen   20 RHGLIAGATGTGKTVTLQVLAE   41 (502)
T ss_pred             ccceeeccCCCCceehHHHHHH
Confidence            7999999999999987654443

This family is restricted to bacterial proteins, none of which have currently been characterised.

>CHL00195 ycf46 Ycf46; Provisional

Probab=93.32  E-value=0.008  Score=44.02  Aligned_cols=32  Identities=28%  Similarity=0.219  Sum_probs=23.4

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .+..++.+|+|+|||.++-+++...+-+.+.+
T Consensus       259 pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l  290 (489)
T CHL00195        259 PRGLLLVGIQGTGKSLTAKAIANDWQLPLLRL  290 (489)
T ss_pred             CceEEEECCCCCcHHHHHHHHHHHhCCCEEEE
Confidence            35678889999999999877766655554443

>PRK14738 gmk guanylate kinase; Provisional

Probab=93.32  E-value=0.0094  Score=38.50  Aligned_cols=23  Identities=30%  Similarity=0.157  Sum_probs=18.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...+|++|.|+|||.++-.+...
T Consensus        14 ~~ivi~GpsG~GK~tl~~~L~~~   36 (206)
T PRK14738         14 LLVVISGPSGVGKDAVLARMRER   36 (206)
T ss_pred             eEEEEECcCCCCHHHHHHHHHhc
Confidence            56778899999999988666543

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=93.32  E-value=0.013  Score=42.11  Aligned_cols=26  Identities=19%  Similarity=0.333  Sum_probs=20.4

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+..++.+|+|+|||+++=+++.+.+
T Consensus       185 PKGVLLYGPPGTGKTLLAkAVA~~T~  210 (406)
T COG1222         185 PKGVLLYGPPGTGKTLLAKAVANQTD  210 (406)
T ss_pred             CCceEeeCCCCCcHHHHHHHHHhccC
Confidence            46678889999999999876665543

>PRK02496 adk adenylate kinase; Provisional

Probab=93.31  E-value=0.0062  Score=38.18  Aligned_cols=23  Identities=26%  Similarity=0.284  Sum_probs=17.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.++.+|+|||||+++-.++...
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~   25 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHL   25 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46788999999999886665443

>PRK04841 transcriptional regulator MalT; Provisional

Probab=93.29  E-value=0.017  Score=43.50  Aligned_cols=30  Identities=17%  Similarity=0.090  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .-.+|.+|.|+|||+.........+ ++.++
T Consensus        33 ~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~   62 (903)
T PRK04841         33 RLVLVTSPAGYGKTTLISQWAAGKN-NLGWY   62 (903)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC-CeEEE
Confidence            5688999999999998876554433 44444

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=93.29  E-value=0.015  Score=42.07  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=31.2

Q ss_pred             ceeecc---chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637          8 SAVLRP---YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus         8 ~~~lR~---yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      -|.+||   +|.-|++..+..+- +-..+.++.|||||..++++..+
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI-~lV~L~G~AGtGKTlLALaAgle  268 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDI-DLVSLGGKAGTGKTLLALAAGLE  268 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCC-CeEEeeccCCccHhHHHHHHHHH
Confidence            355555   68888888887531 34556699999999999876554

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.28  E-value=0.015  Score=40.92  Aligned_cols=23  Identities=26%  Similarity=0.138  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +-.+++++||||||+..++.+..
T Consensus       128 GLviiVGaTGSGKSTtmAaMi~y  150 (375)
T COG5008         128 GLVIIVGATGSGKSTTMAAMIGY  150 (375)
T ss_pred             ceEEEECCCCCCchhhHHHHhcc
Confidence            35677899999999988776654

>PRK04182 cytidylate kinase; Provisional

Probab=93.27  E-value=0.0055  Score=37.65  Aligned_cols=23  Identities=26%  Similarity=0.206  Sum_probs=18.5

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEe
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+|.+++|||||+++-.++..++
T Consensus         3 I~i~G~~GsGKstia~~la~~lg   25 (180)
T PRK04182          3 ITISGPPGSGKTTVARLLAEKLG   25 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            46789999999999977766544

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=93.26  E-value=0.012  Score=41.46  Aligned_cols=22  Identities=18%  Similarity=-0.011  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.+|+|+|||+++.++..+
T Consensus       138 ~l~l~G~~G~GKThL~~ai~~~  159 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLLHAIGNE  159 (405)
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            3578999999999998776654

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).

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

Probab=93.24  E-value=0.051  Score=42.42  Aligned_cols=36  Identities=14%  Similarity=0.019  Sum_probs=23.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecce
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGV   64 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~   64 (67)
                      ...+|++|||||||+-.=..+.+    ..+.+.+.-|+..
T Consensus        66 ~vvii~getGsGKTTqlP~~lle~g~~~~g~I~~tQPRRl  105 (845)
T COG1643          66 QVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRL  105 (845)
T ss_pred             CEEEEeCCCCCChHHHHHHHHHhhhcccCCeEEecCchHH
Confidence            68889999999999866333322    2345555555543

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=93.21  E-value=0.013  Score=40.70  Aligned_cols=29  Identities=17%  Similarity=0.154  Sum_probs=22.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      -..++.+++|+|||.++..++.+++.+.+
T Consensus        93 ~iIlI~G~sgsGKStlA~~La~~l~~~~v  121 (301)
T PRK04220         93 IIILIGGASGVGTSTIAFELASRLGIRSV  121 (301)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            45677899999999999888877665543

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=93.21  E-value=0.099  Score=33.22  Aligned_cols=29  Identities=14%  Similarity=0.036  Sum_probs=20.7

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      .+++.+++. .+...+..++||||||.+..
T Consensus        14 ~~v~~~~~G-~n~~i~~yG~tGsGKT~Tm~   42 (186)
T cd01363          14 PLLQSALDG-YNVCIFAYGQTGSGKTYTME   42 (186)
T ss_pred             HHHHHHhCC-cceeEEEECCCCCcceEecC
Confidence            556666654 33456667999999998875

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=93.18  E-value=0.011  Score=36.53  Aligned_cols=24  Identities=17%  Similarity=0.034  Sum_probs=19.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.++.|+|||+..-.++..+
T Consensus        23 ~~i~l~G~lGaGKTtl~~~l~~~l   46 (133)
T TIGR00150        23 TVVLLKGDLGAGKTTLVQGLLQGL   46 (133)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            567788999999999886666554

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PRK01184 hypothetical protein; Provisional

Probab=93.16  E-value=0.016  Score=36.18  Aligned_cols=16  Identities=25%  Similarity=0.059  Sum_probs=13.4

Q ss_pred             eeEEEeCCCCceeEee
Q psy11637         31 GVIVLPCGAGKSLVGV   46 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~   46 (67)
                      .++++|+|||||+++-
T Consensus         4 i~l~G~~GsGKsT~a~   19 (184)
T PRK01184          4 IGVVGMPGSGKGEFSK   19 (184)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            4678999999999764

>cd01375 KISc_KIF9_like Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling

Probab=93.15  E-value=0.095  Score=36.28  Aligned_cols=35  Identities=20%  Similarity=0.165  Sum_probs=22.9

Q ss_pred             cchhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         13 PYQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        13 ~yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      .-|++..+.+..       .|.+...+..++||||||.+...
T Consensus        59 ~~q~~vy~~~~~p~v~~~~~G~n~~i~ayG~tgSGKTyTm~G  100 (334)
T cd01375          59 ASQEEVYETVAKPVVDSALDGYNGTIFAYGQTGAGKTFTMTG  100 (334)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCccceeeecCCCCCCeEEccC
Confidence            457776665332       23334555669999999999865

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=93.14  E-value=0.053  Score=38.54  Aligned_cols=18  Identities=28%  Similarity=0.407  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      .+.++++|||||||.-..
T Consensus        45 ~h~lvig~tgSGKt~~~v   62 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFV   62 (469)
T ss_pred             eEEEEEeCCCCCccceee
Confidence            468999999999997653

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=93.13  E-value=0.0082  Score=43.67  Aligned_cols=31  Identities=16%  Similarity=0.248  Sum_probs=22.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      +...+++|||+|||+++..++..+   +.++.++
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI  275 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFI  275 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEE
Confidence            466789999999999987776543   3345444

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=93.11  E-value=0.033  Score=40.56  Aligned_cols=31  Identities=19%  Similarity=0.218  Sum_probs=23.1

Q ss_pred             hhHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         16 EKSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      .+.++.|+....+-..+|.+|-||||+-+.+
T Consensus         5 ~~~L~~wL~e~~~TFIvV~GPrGSGK~elV~   35 (431)
T PF10443_consen    5 IEQLKSWLNENPNTFIVVQGPRGSGKRELVM   35 (431)
T ss_pred             HHHHHHHHhcCCCeEEEEECCCCCCccHHHH
Confidence            4556778876544567777999999987664

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK08356 hypothetical protein; Provisional

Probab=93.11  E-value=0.017  Score=36.79  Aligned_cols=19  Identities=26%  Similarity=0.048  Sum_probs=15.8

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      ..++++|+|||||+++-.+
T Consensus         7 ~i~~~G~~gsGK~t~a~~l   25 (195)
T PRK08356          7 IVGVVGKIAAGKTTVAKFF   25 (195)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4567899999999998666

>KOG0923|consensus

Probab=93.11  E-value=0.059  Score=41.73  Aligned_cols=38  Identities=21%  Similarity=0.248  Sum_probs=27.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....+|-.+.++++-++   .-.+|++.||||||+-.=...
T Consensus       264 LPVy~ykdell~av~e~---QVLiI~GeTGSGKTTQiPQyL  301 (902)
T KOG0923|consen  264 LPVYPYKDELLKAVKEH---QVLIIVGETGSGKTTQIPQYL  301 (902)
T ss_pred             CCchhhHHHHHHHHHhC---cEEEEEcCCCCCccccccHHH
Confidence            34456667777776665   578889999999998764433

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=93.09  E-value=0.0094  Score=39.31  Aligned_cols=33  Identities=12%  Similarity=-0.030  Sum_probs=24.4

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +...++.+|+|+|||+.++.++..   .+.+++++.
T Consensus        24 g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         24 GSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            357888899999999998665543   245667665

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=93.06  E-value=0.009  Score=43.26  Aligned_cols=32  Identities=13%  Similarity=0.109  Sum_probs=23.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++++|+|||+++..++..+   +.+++++.
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~  130 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVA  130 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEec
Confidence            457888999999999997776543   34555544

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=93.05  E-value=0.0064  Score=37.13  Aligned_cols=23  Identities=26%  Similarity=0.232  Sum_probs=18.1

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEe
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+|.+++|||||.++-.+...++
T Consensus         3 I~i~G~~GSGKstia~~la~~lg   25 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLS   25 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcC
Confidence            46789999999999877765544

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=93.03  E-value=0.036  Score=42.84  Aligned_cols=37  Identities=14%  Similarity=0.240  Sum_probs=26.6

Q ss_pred             hhhHHHHHh---cCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMF---GNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~---~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |++-++++.   .+....+.++++|+|.|||.++-.++.+
T Consensus       178 r~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       178 RDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             cHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHH
Confidence            555565544   3444478999999999999988766554

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=93.02  E-value=0.074  Score=40.13  Aligned_cols=25  Identities=16%  Similarity=0.167  Sum_probs=18.5

Q ss_pred             HhcCCcceeeeEEEeCCCCceeEee
Q psy11637         22 MFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        22 ~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      ++.++...+.++++|||||||+-..
T Consensus       169 ~L~~~g~~HvlviapTgSGKgvg~V  193 (636)
T PRK13880        169 YLRHNGPEHVLTYAPTRSGKGVGLV  193 (636)
T ss_pred             eEEeCCCceEEEEecCCCCCceEEE
Confidence            3444334789999999999998553

>PRK10867 signal recognition particle protein; Provisional

Probab=93.01  E-value=0.0079  Score=43.53  Aligned_cols=32  Identities=22%  Similarity=0.233  Sum_probs=22.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      ...++++|+|+|||+++..++..+    +.+++++.
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV~lV~  136 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVA  136 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhcCCcEEEEE
Confidence            346788999999999987776542    44555543

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=92.98  E-value=0.014  Score=39.31  Aligned_cols=35  Identities=23%  Similarity=0.323  Sum_probs=25.0

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++|.++--+++.+.+|.+|.|+|||+++-.+....
T Consensus         6 ~id~~~~i~~Gqr~~I~G~~G~GKTTLlr~I~n~l   40 (249)
T cd01128           6 VVDLFAPIGKGQRGLIVAPPKAGKTTLLQSIANAI   40 (249)
T ss_pred             heeeecccCCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            45555544455899999999999998776655443

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK09087 hypothetical protein; Validated

Probab=92.98  E-value=0.046  Score=36.02  Aligned_cols=20  Identities=25%  Similarity=0.288  Sum_probs=16.4

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ...|.+|+|+|||+....+.
T Consensus        46 ~l~l~G~~GsGKThLl~~~~   65 (226)
T PRK09087         46 VVVLAGPVGSGKTHLASIWR   65 (226)
T ss_pred             eEEEECCCCCCHHHHHHHHH
Confidence            47899999999999886544

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.98  E-value=0.035  Score=40.88  Aligned_cols=39  Identities=15%  Similarity=0.285  Sum_probs=26.5

Q ss_pred             chhhHHHH---HhcCCc-ceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         14 YQEKSLRK---MFGNGR-ARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        14 yQ~~av~~---~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .|+.++..   +++.+. .+.-++.+|.|+|||.++-.++..+
T Consensus        22 GQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~L   64 (484)
T PRK14956         22 HQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRL   64 (484)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            57777654   444432 2335899999999999986665543

>TIGR00929 VirB4_CagE type IV secretion/conjugal transfer ATPase, VirB4 family

Probab=92.94  E-value=0.011  Score=44.34  Aligned_cols=34  Identities=15%  Similarity=0.111  Sum_probs=23.9

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE---Eee-eeEEEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT---VRK-RALVLCN   61 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~---~~~-~~lil~p   61 (67)
                      ..+.+|.++||+|||+....++..   .+. +++++=|
T Consensus       434 ~~n~~I~G~tGsGKS~~~~~l~~~~~~~~~~~v~iiD~  471 (785)
T TIGR00929       434 LGHTLIFGPTGSGKTTLLNFLLAQMQKYGGMTIFAFDK  471 (785)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhhccCCCeEEEEeC
Confidence            368999999999999888655443   234 5555543

Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation).

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.94  E-value=0.0098  Score=43.23  Aligned_cols=22  Identities=23%  Similarity=0.232  Sum_probs=18.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++++|+|+|||+++..++..
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4678899999999999877653

>PRK13531 regulatory ATPase RavA; Provisional

Probab=92.85  E-value=0.028  Score=41.59  Aligned_cols=36  Identities=19%  Similarity=0.164  Sum_probs=25.1

Q ss_pred             hhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |++.++.++.. ..+++.++.+|+|+|||.++-.+..
T Consensus        25 re~vI~lll~aalag~hVLL~GpPGTGKT~LAraLa~   61 (498)
T PRK13531         25 RSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKF   61 (498)
T ss_pred             cHHHHHHHHHHHccCCCEEEECCCChhHHHHHHHHHH
Confidence            55666654431 1237999999999999999865554

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.83  E-value=0.02  Score=43.28  Aligned_cols=31  Identities=16%  Similarity=0.309  Sum_probs=22.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      +..++.+|+|+|||.++-+++...+.+.+.+
T Consensus       488 ~giLL~GppGtGKT~lakalA~e~~~~fi~v  518 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLLAKAVATESGANFIAV  518 (733)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhcCCCEEEE
Confidence            4568889999999999877776655544433

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.

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=92.81  E-value=0.012  Score=36.67  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=18.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .-.++.+|+|+|||.+++.++.
T Consensus        33 ~l~~i~g~~g~GKT~~~~~l~~   54 (193)
T PF13481_consen   33 ELTLIAGPPGSGKTTLALQLAA   54 (193)
T ss_dssp             SEEEEEECSTSSHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHH
Confidence            5789999999999998876554

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=92.80  E-value=0.085  Score=40.18  Aligned_cols=24  Identities=33%  Similarity=0.490  Sum_probs=17.9

Q ss_pred             hcCCcceeeeEEEeCCCCceeEee
Q psy11637         23 FGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        23 ~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      +.++...+.++++|||||||+-..
T Consensus       134 lr~~~~~hvlviApTgSGKgvg~V  157 (670)
T PRK13850        134 LTNGEQPHSLVVAPTRAGKGVGVV  157 (670)
T ss_pred             cccCCCceEEEEecCCCCceeeeh
Confidence            333334688999999999998663

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=92.77  E-value=0.017  Score=39.59  Aligned_cols=40  Identities=15%  Similarity=0.131  Sum_probs=27.8

Q ss_pred             hhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         15 QEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        15 Q~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      +++.+...+.. ..+++.++.+|+|.|||..+-.++...+.
T Consensus        29 ~~~~~~~~l~a~~~~~~vll~G~PG~gKT~la~~lA~~l~~   69 (329)
T COG0714          29 DEEVIELALLALLAGGHVLLEGPPGVGKTLLARALARALGL   69 (329)
T ss_pred             cHHHHHHHHHHHHcCCCEEEECCCCccHHHHHHHHHHHhCC
Confidence            55555554321 11278999999999999998777766553

>smart00072 GuKc Guanylate kinase homologues

Probab=92.76  E-value=0.013  Score=37.04  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=19.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-.++++|.|+||+.++-.++...
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhcC
Confidence            456788999999999887776664

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=92.76  E-value=0.067  Score=39.70  Aligned_cols=54  Identities=13%  Similarity=0.070  Sum_probs=43.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~   64 (67)
                      ..-|||.+.++.+-..+ -+...+..+.-+|||.+++..+..    ...++|++.||.-
T Consensus        16 ~~~Py~~eimd~~~~~~-v~~Vv~~k~aQ~GkT~~~~n~~g~~i~~~P~~~l~v~Pt~~   73 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPS-VREVVVMKSAQVGKTELLLNWIGYSIDQDPGPMLYVQPTDD   73 (557)
T ss_pred             CCChhHHHHHHhcCCcC-ccEEEEEEcchhhHhHHHHhhceEEEEeCCCCEEEEEEcHH
Confidence            66799999999988754 357778899999999988766554    3578999999853

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PTZ00301 uridine kinase; Provisional

Probab=92.68  E-value=0.019  Score=37.67  Aligned_cols=21  Identities=24%  Similarity=0.172  Sum_probs=16.2

Q ss_pred             eeEEEeCCCCceeEeeeeEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-|.+|+|||||+++..+..+
T Consensus         6 IgIaG~SgSGKTTla~~l~~~   26 (210)
T PTZ00301          6 IGISGASGSGKSSLSTNIVSE   26 (210)
T ss_pred             EEEECCCcCCHHHHHHHHHHH
Confidence            346799999999999665543

>TIGR00618 sbcc exonuclease SbcC

Probab=92.63  E-value=0.031  Score=43.79  Aligned_cols=21  Identities=24%  Similarity=0.085  Sum_probs=17.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +-.+|++|||+|||++.-+++
T Consensus        27 gl~~I~G~nGaGKSTildAI~   47 (1042)
T TIGR00618        27 PIFLICGKTGAGKTTLLDAIT   47 (1042)
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            477899999999999875544

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

>TIGR00959 ffh signal recognition particle protein

Probab=92.61  E-value=0.011  Score=42.64  Aligned_cols=32  Identities=19%  Similarity=0.147  Sum_probs=23.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT----VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~   60 (67)
                      ...++++|+|+|||+++..++..    .+.+++++.
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~  135 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVA  135 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEe
Confidence            45778899999999998776654    244565553

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.60  E-value=0.044  Score=39.96  Aligned_cols=38  Identities=16%  Similarity=0.188  Sum_probs=24.5

Q ss_pred             chhhHHHH---HhcCCc-ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRK---MFGNGR-ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~---~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|+.+...   ++..+. .+.-++.+|+|+|||+++..++..
T Consensus        18 Gq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~   59 (472)
T PRK14962         18 GQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKS   59 (472)
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            36665443   334332 233588999999999998665443

>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup

Probab=92.49  E-value=0.16  Score=34.81  Aligned_cols=33  Identities=18%  Similarity=0.113  Sum_probs=21.5

Q ss_pred             chhhHHHHH--------hcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKM--------FGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~--------~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+..        +. +.+...+..++||||||.+...
T Consensus        56 ~q~~vy~~~~~~~v~~~~~-G~n~~i~ayG~tgSGKT~Tm~G   96 (325)
T cd01369          56 TQEDVYNFVAKPIVDDVLN-GYNGTIFAYGQTGSGKTYTMEG   96 (325)
T ss_pred             CHHHHHHHHHHHHHHHHHc-CccceEEEeCCCCCCceEEecC
Confidence            366666553        33 3334455669999999999754

Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-c

>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=92.48  E-value=0.023  Score=36.11  Aligned_cols=25  Identities=16%  Similarity=0.182  Sum_probs=19.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+.++.+|||+|||.++-.++..+.
T Consensus         4 ~~~ll~GpsGvGKT~la~~la~~l~   28 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTELAKALAELLF   28 (171)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4678999999999988866665543

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 ....

>TIGR00235 udk uridine kinase

Probab=92.48  E-value=0.028  Score=36.01  Aligned_cols=23  Identities=22%  Similarity=-0.023  Sum_probs=17.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....|++|+|||||+.+-.+...
T Consensus         7 ~vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         7 IIIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            45567899999999988655443

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis

Probab=92.48  E-value=0.15  Score=34.91  Aligned_cols=33  Identities=9%  Similarity=0.067  Sum_probs=21.3

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..++...       .+.+...+..++||||||.+..
T Consensus        53 ~q~~vy~~~~~p~v~~~l~G~n~~i~ayG~tgSGKT~T~~   92 (321)
T cd01374          53 TNREVYERIAKPVVRSALEGYNGTIFAYGQTSSGKTFTMS   92 (321)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCceeEEeecCCCCCCceecc
Confidence            36666654321       1333445566999999999886

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=92.47  E-value=0.011  Score=42.78  Aligned_cols=32  Identities=16%  Similarity=0.164  Sum_probs=22.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++|+|+|||+++..++..+   +.++++++
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~  135 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVC  135 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEc
Confidence            456788999999999997766543   44555554

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.

>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A

Probab=92.46  E-value=0.037  Score=33.93  Aligned_cols=19  Identities=37%  Similarity=0.441  Sum_probs=0.0

Q ss_pred             eeEEEeCCCCceeEeeeeE
Q psy11637         31 GVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~   49 (67)
                      .++++|.|||||.+.-++.
T Consensus         2 ~viiG~N~sGKS~il~ai~   20 (303)
T PF13304_consen    2 NVIIGPNGSGKSNILEAIY   20 (303)
T ss_dssp             -------------------
T ss_pred             Ccccccccccccccccccc
Confidence            3689999999999886553

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.42  E-value=0.045  Score=37.87  Aligned_cols=23  Identities=17%  Similarity=0.007  Sum_probs=19.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++.+++++||||||....+++..
T Consensus       144 ~siii~G~t~sGKTt~lnall~~  166 (312)
T COG0630         144 KSIIICGGTASGKTTLLNALLDF  166 (312)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            78999999999999888666544

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=92.42  E-value=0.02  Score=41.89  Aligned_cols=20  Identities=25%  Similarity=0.213  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      .|.++.+|+|+|||+++.++
T Consensus       210 ~Nli~lGp~GTGKThla~~l  229 (449)
T TIGR02688       210 YNLIELGPKGTGKSYIYNNL  229 (449)
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            68999999999999888654

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.

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=92.40  E-value=0.013  Score=43.58  Aligned_cols=32  Identities=22%  Similarity=0.145  Sum_probs=21.1

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .++.++.++||||||.+.-.++..   .+.+++|+
T Consensus       176 ~~h~li~G~tGsGKs~~i~~ll~~~~~~g~~~ii~  210 (566)
T TIGR02759       176 TQHILIHGTTGSGKSVAIRKLLRWIRQRGDRAIIY  210 (566)
T ss_pred             ccceEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEE
Confidence            357899999999999766443332   23454444

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).

>PRK13946 shikimate kinase; Provisional

Probab=92.39  E-value=0.0098  Score=37.63  Aligned_cols=26  Identities=38%  Similarity=0.377  Sum_probs=20.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      .+.++.++.|||||.++-.++..++-
T Consensus        11 ~~I~l~G~~GsGKsti~~~LA~~Lg~   36 (184)
T PRK13946         11 RTVVLVGLMGAGKSTVGRRLATMLGL   36 (184)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCC
Confidence            57788899999999999777665543

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=92.38  E-value=0.041  Score=40.35  Aligned_cols=23  Identities=22%  Similarity=0.332  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++.++.+|+|+|||.++-.++..
T Consensus       195 ~~iil~GppGtGKT~lA~~la~~  217 (459)
T PRK11331        195 KNIILQGPPGVGKTFVARRLAYL  217 (459)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999988655443

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.36  E-value=0.013  Score=42.30  Aligned_cols=32  Identities=16%  Similarity=0.129  Sum_probs=22.7

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ++..++++|+|+|||+++..++...   +.++.++
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lI  240 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFI  240 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            3567788999999999987766532   3455444

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=92.35  E-value=0.018  Score=44.94  Aligned_cols=52  Identities=17%  Similarity=0.238  Sum_probs=32.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .+|||=.+.+-.+.-+   +..+.-|.||.|||+++...+..   .+..+.|++++..
T Consensus        74 G~r~ydvQlig~l~L~---~G~IaEm~TGEGKTL~a~l~ayl~aL~G~~VhVvT~Ndy  128 (870)
T CHL00122         74 GLRHFDVQLIGGLVLN---DGKIAEMKTGEGKTLVATLPAYLNALTGKGVHIVTVNDY  128 (870)
T ss_pred             CCCCCchHhhhhHhhc---CCccccccCCCCchHHHHHHHHHHHhcCCceEEEeCCHH
Confidence            4455544444333332   34567799999999988765532   4677888877653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.34  E-value=0.016  Score=43.79  Aligned_cols=30  Identities=17%  Similarity=0.248  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      +..++.+|+|+|||+++-+++...+.+.+.
T Consensus       213 ~giLL~GppGtGKT~laraia~~~~~~~i~  242 (733)
T TIGR01243       213 KGVLLYGPPGTGKTLLAKAVANEAGAYFIS  242 (733)
T ss_pred             ceEEEECCCCCChHHHHHHHHHHhCCeEEE
Confidence            567888999999999886666555544443

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=92.34  E-value=0.047  Score=43.56  Aligned_cols=45  Identities=13%  Similarity=0.008  Sum_probs=31.4

Q ss_pred             cceeeccchhhHHHHHhcC----Ccceee-eEEEeCCCCceeEeeeeEEE
Q psy11637          7 PSAVLRPYQEKSLRKMFGN----GRARSG-VIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~----~~~~~~-~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....-|+-|.+.+..++..    ....+. .|.++||+|||.+.-.++.+
T Consensus       755 D~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrE  804 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQL  804 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            3455688888888776642    222234 48999999999998776544

>PRK13948 shikimate kinase; Provisional

Probab=92.32  E-value=0.011  Score=38.09  Aligned_cols=25  Identities=20%  Similarity=0.115  Sum_probs=20.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+.+++++.|+|||+++-.+...++
T Consensus        11 ~~I~LiG~~GsGKSTvg~~La~~lg   35 (182)
T PRK13948         11 TWVALAGFMGTGKSRIGWELSRALM   35 (182)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHcC
Confidence            6788899999999999977665544

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=92.29  E-value=0.051  Score=41.81  Aligned_cols=30  Identities=17%  Similarity=0.282  Sum_probs=22.0

Q ss_pred             HHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         21 KMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        21 ~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +++......+.++++|+|+|||.++-.++.
T Consensus       200 ~iL~r~~~~n~LLvGppGvGKT~lae~la~  229 (758)
T PRK11034        200 QVLCRRRKNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_pred             HHHhccCCCCeEEECCCCCCHHHHHHHHHH
Confidence            344443346889999999999999866554

>TIGR00767 rho transcription termination factor Rho

Probab=92.29  E-value=0.011  Score=42.81  Aligned_cols=26  Identities=31%  Similarity=0.494  Sum_probs=20.7

Q ss_pred             CcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         26 GRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        26 ~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+.+++|++|+|+|||+++..+...
T Consensus       166 g~Gq~~~IvG~~g~GKTtL~~~i~~~  191 (415)
T TIGR00767       166 GKGQRGLIVAPPKAGKTVLLQKIAQA  191 (415)
T ss_pred             CCCCEEEEECCCCCChhHHHHHHHHh
Confidence            44578999999999999887665554

Members of this family differ in the specificity of RNA binding.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=92.29  E-value=0.015  Score=39.90  Aligned_cols=45  Identities=24%  Similarity=0.273  Sum_probs=30.2

Q ss_pred             eccchhhHHHHHhc----C----CcceeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         11 LRPYQEKSLRKMFG----N----GRARSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        11 lR~yQ~~av~~~~~----~----~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      +-|-|++.+.++++    .    ..+...+++++.|+|||+++-.++..++.+
T Consensus       108 l~~~~~~~~~~~l~~~~~~~~~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~  160 (309)
T PRK08154        108 ASPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARLGVP  160 (309)
T ss_pred             CCHHHHHHHHHHHHHHHhhhhhccCCCEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            34456666655443    1    234678888999999999997776655443

>PRK12608 transcription termination factor Rho; Provisional

Probab=92.28  E-value=0.038  Score=39.65  Aligned_cols=33  Identities=24%  Similarity=0.346  Sum_probs=23.9

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +++.++--+++.+++|.+|.|+|||++...++.
T Consensus       123 vID~l~PiGkGQR~LIvG~pGtGKTTLl~~la~  155 (380)
T PRK12608        123 VVDLVAPIGKGQRGLIVAPPRAGKTVLLQQIAA  155 (380)
T ss_pred             hhhheeecCCCceEEEECCCCCCHHHHHHHHHH
Confidence            444444334557999999999999998866444

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=92.26  E-value=0.021  Score=44.93  Aligned_cols=53  Identities=17%  Similarity=0.216  Sum_probs=35.2

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      ..+|||=.+.+-.+.-+   ...+.-|.||-|||+++...+..   .++.+.|++.+..
T Consensus        82 lG~r~ydVQliGgl~Lh---~G~IAEM~TGEGKTL~atlpaylnAL~GkgVhVVTvNdY  137 (939)
T PRK12902         82 LGMRHFDVQLIGGMVLH---EGQIAEMKTGEGKTLVATLPSYLNALTGKGVHVVTVNDY  137 (939)
T ss_pred             hCCCcchhHHHhhhhhc---CCceeeecCCCChhHHHHHHHHHHhhcCCCeEEEeCCHH
Confidence            34566655555554333   34567899999999998755543   4677888877653

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=92.25  E-value=0.029  Score=37.50  Aligned_cols=23  Identities=22%  Similarity=-0.000  Sum_probs=17.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -.++.+|+|||||+++-.+..+.
T Consensus         4 liil~G~pGSGKSTla~~L~~~~   26 (300)
T PHA02530          4 IILTVGVPGSGKSTWAREFAAKN   26 (300)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHC
Confidence            35677999999999986655443

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=92.22  E-value=0.0093  Score=36.84  Aligned_cols=24  Identities=25%  Similarity=0.329  Sum_probs=18.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +.++++++|+|||+++-.++..++
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~lg   27 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQALG   27 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhC
Confidence            456789999999999976665543

>PRK00625 shikimate kinase; Provisional

Probab=92.18  E-value=0.011  Score=37.71  Aligned_cols=23  Identities=13%  Similarity=-0.016  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.++++.+|+|||+++-.++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l   24 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46788999999999886665543

>PRK14527 adenylate kinase; Provisional

Probab=92.16  E-value=0.033  Score=35.21  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=18.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+|+|||||+.+..++.+
T Consensus         7 ~~i~i~G~pGsGKsT~a~~La~~   29 (191)
T PRK14527          7 KVVIFLGPPGAGKGTQAERLAQE   29 (191)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            46778899999999988665543

>KOG0951|consensus

Probab=92.16  E-value=0.016  Score=47.20  Aligned_cols=35  Identities=20%  Similarity=0.212  Sum_probs=27.9

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE--EeeeeEEEeec
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT--VRKRALVLCNS   62 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~--~~~~~lil~p~   62 (67)
                      .++.++..|+|||||.|+..++.+  -..++++++|.
T Consensus      1159 nd~v~vga~~gsgkt~~ae~a~l~~~~~~~~vyi~p~ 1195 (1674)
T KOG0951|consen 1159 NDNVLVGAPNGSGKTACAELALLRPDTIGRAVYIAPL 1195 (1674)
T ss_pred             cceEEEecCCCCchhHHHHHHhcCCccceEEEEecch
Confidence            378889999999999999766655  24678888875

>cd00106 KISc Kinesin motor domain

Probab=92.16  E-value=0.22  Score=34.00  Aligned_cols=19  Identities=16%  Similarity=0.065  Sum_probs=15.0

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...+..++||||||.+...
T Consensus        80 ~~i~~yG~tgSGKT~tl~G   98 (328)
T cd00106          80 GTIFAYGQTGSGKTYTMFG   98 (328)
T ss_pred             eeEEEecCCCCCCeEEecC
Confidence            4455569999999998766

This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coil

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=92.15  E-value=0.058  Score=32.49  Aligned_cols=20  Identities=30%  Similarity=0.295  Sum_probs=16.1

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ...+|.+++|+||+.++-.+
T Consensus        22 ~pvli~GE~GtGK~~~A~~l   41 (138)
T PF14532_consen   22 SPVLITGEPGTGKSLLARAL   41 (138)
T ss_dssp             S-EEEECCTTSSHHHHHHCC
T ss_pred             CcEEEEcCCCCCHHHHHHHH
Confidence            67899999999999987544

>PRK05541 adenylylsulfate kinase; Provisional

Probab=92.13  E-value=0.029  Score=34.85  Aligned_cols=24  Identities=17%  Similarity=0.072  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+++|||||+++-.+...+
T Consensus         8 ~~I~i~G~~GsGKst~a~~l~~~l   31 (176)
T PRK05541          8 YVIWITGLAGSGKTTIAKALYERL   31 (176)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHH
Confidence            466788999999999986665443

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

Probab=92.13  E-value=0.03  Score=44.02  Aligned_cols=36  Identities=19%  Similarity=0.306  Sum_probs=26.6

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecc
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSG   63 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~   63 (67)
                      .+.|+|---+|||||+++..++..+     ...++||+.+.
T Consensus       273 ~~~G~IWHtqGSGKTlTm~~~A~~l~~~~~~~~v~fvvDR~  313 (962)
T COG0610         273 GKGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVDRK  313 (962)
T ss_pred             CCceEEEeecCCchHHHHHHHHHHHHhccCCCeEEEEechH
Confidence            4679999999999999997665542     34566666653

>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins

Probab=92.07  E-value=0.15  Score=35.23  Aligned_cols=34  Identities=18%  Similarity=0.100  Sum_probs=21.8

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..++...       .|.+...+..++||||||.+...
T Consensus        61 ~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKTyTm~G  101 (333)
T cd01371          61 TQEDVYNETARPLVDSVLEGYNGTIFAYGQTGTGKTFTMEG  101 (333)
T ss_pred             cHHHHHHHHHHHHHHHHhCCCceeEEecCCCCCCCcEeecC
Confidence            47776665332       23234455559999999998765

Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=92.04  E-value=0.013  Score=43.27  Aligned_cols=24  Identities=21%  Similarity=0.234  Sum_probs=18.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-.++.+|+|+|||.+.-.++.++
T Consensus        46 ~iLlLtGP~G~GKtttv~~La~el   69 (519)
T PF03215_consen   46 RILLLTGPSGCGKTTTVKVLAKEL   69 (519)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            346778999999998876555543

>KOG0343|consensus

Probab=92.04  E-value=0.038  Score=42.01  Aligned_cols=48  Identities=15%  Similarity=0.162  Sum_probs=34.0

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----------eeeeEEEeecce
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----------RKRALVLCNSGV   64 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~~lil~p~~~   64 (67)
                      -|++.|--.+.+   +..+-.+-||||||+.++-.+.+.          +-=+|||.||.-
T Consensus        95 iQ~~~Ip~aL~G---~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~~DGlGalIISPTRE  152 (758)
T KOG0343|consen   95 IQRDTIPMALQG---HDVLGAAKTGSGKTLAFLVPVLEALYRLKWSPTDGLGALIISPTRE  152 (758)
T ss_pred             HHHhhcchhccC---cccccccccCCCceeeehHHHHHHHHHcCCCCCCCceeEEecchHH
Confidence            477776666665   577778999999999887554331          235799999863

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=92.04  E-value=0.099  Score=40.62  Aligned_cols=39  Identities=15%  Similarity=0.171  Sum_probs=28.3

Q ss_pred             chhhHHHHHhcC------------CcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         14 YQEKSLRKMFGN------------GRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        14 yQ~~av~~~~~~------------~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .|.+|++.+.+.            ..-++.++.+|||.|||-.+-+++..+
T Consensus       495 GQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~L  545 (786)
T COG0542         495 GQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEAL  545 (786)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHh
Confidence            499999875531            123578889999999999887665543

>PLN02200 adenylate kinase family protein

Probab=92.03  E-value=0.012  Score=39.12  Aligned_cols=24  Identities=17%  Similarity=0.001  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...+|.+|+|||||+++..++.+.
T Consensus        44 ~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         44 FITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh
Confidence            456778999999999987665543

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=92.02  E-value=0.02  Score=41.19  Aligned_cols=29  Identities=24%  Similarity=0.405  Sum_probs=22.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ...++.+|+|+|||.++-+++...+.+++
T Consensus       277 ~giLl~GpPGtGKT~lAkava~~~~~~fi  305 (494)
T COG0464         277 KGVLLYGPPGTGKTLLAKAVALESRSRFI  305 (494)
T ss_pred             CeeEEECCCCCCHHHHHHHHHhhCCCeEE
Confidence            46788899999999999888776554443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.97  E-value=0.053  Score=40.66  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=25.8

Q ss_pred             chhhHHHH---HhcCCccee-eeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRK---MFGNGRARS-GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~---~~~~~~~~~-~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|+.+++.   +++.+.-.+ -++.+|.|+|||.++..++..
T Consensus        17 Gq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~   58 (584)
T PRK14952         17 GQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARS   58 (584)
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            47776654   444433234 478999999999998666543

>TIGR00763 lon ATP-dependent protease La

Probab=91.97  E-value=0.027  Score=43.05  Aligned_cols=28  Identities=21%  Similarity=0.311  Sum_probs=21.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      ...++++|+|+|||.++-+++..++.+.
T Consensus       348 ~~lll~GppG~GKT~lAk~iA~~l~~~~  375 (775)
T TIGR00763       348 PILCLVGPPGVGKTSLGKSIAKALNRKF  375 (775)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhcCCe
Confidence            4578899999999999977776654433

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=91.94  E-value=0.078  Score=33.92  Aligned_cols=20  Identities=40%  Similarity=0.381  Sum_probs=16.6

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +..++++|+|+|||.+.-++
T Consensus        25 ~~~~i~G~NGsGKS~ileAi   44 (220)
T PF02463_consen   25 GLNVIVGPNGSGKSNILEAI   44 (220)
T ss_dssp             SEEEEEESTTSSHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHH
Confidence            57889999999999877544

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>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=91.93  E-value=0.028  Score=33.69  Aligned_cols=21  Identities=19%  Similarity=0.191  Sum_probs=17.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +...+.+|.|+|||+.+..+.
T Consensus        16 e~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          16 VGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             EEEEEEcCCCCCHHHHHHHhh
Confidence            567889999999999776543

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

>CHL00176 ftsH cell division protein; Validated

Probab=91.92  E-value=0.014  Score=43.97  Aligned_cols=30  Identities=20%  Similarity=0.288  Sum_probs=22.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      +..++.+|+|+|||.++-+++.+.+.+.+.
T Consensus       217 ~gVLL~GPpGTGKT~LAralA~e~~~p~i~  246 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAKAIAGEAEVPFFS  246 (638)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCeee
Confidence            467889999999999987776655555443

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=91.91  E-value=0.027  Score=39.61  Aligned_cols=45  Identities=22%  Similarity=0.254  Sum_probs=30.3

Q ss_pred             ceeecc-------chhhHHHH---Hhc----C-CcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637          8 SAVLRP-------YQEKSLRK---MFG----N-GRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus         8 ~~~lR~-------yQ~~av~~---~~~----~-~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...+||       .|++..++   +++    + ..-++.++.+|+|.|||+.+.-++.++
T Consensus        17 e~~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Em   76 (332)
T COG2255          17 ERSLRPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANEL   76 (332)
T ss_pred             hcccCcccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHh
Confidence            456666       27777665   222    2 225789999999999999886555543

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=91.91  E-value=0.018  Score=42.28  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +...+++|||+|||+++..++..
T Consensus       257 ~Vi~LvGpnGvGKTTTiaKLA~~  279 (484)
T PRK06995        257 GVFALMGPTGVGKTTTTAKLAAR  279 (484)
T ss_pred             cEEEEECCCCccHHHHHHHHHHH
Confidence            45678899999999999777643

>PF13173 AAA_14: AAA domain

Probab=91.90  E-value=0.013  Score=34.96  Aligned_cols=31  Identities=16%  Similarity=0.198  Sum_probs=22.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe--eeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR--KRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~--~~~lil   59 (67)
                      +..+|.+|.|+|||+++..++....  ++++++
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi   35 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYI   35 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceee
Confidence            4577889999999999877765543  444443

>cd03279 ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends

Probab=91.90  E-value=0.038  Score=35.61  Aligned_cols=21  Identities=33%  Similarity=0.240  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....+++|+|+|||++.-++.
T Consensus        29 ~~~~i~G~NGsGKSTll~~i~   49 (213)
T cd03279          29 GLFLICGPTGAGKSTILDAIT   49 (213)
T ss_pred             CEEEEECCCCCCHHHHHHHhe
Confidence            467789999999999886654

They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.89  E-value=0.019  Score=42.97  Aligned_cols=22  Identities=27%  Similarity=0.216  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +...+++|+|+|||+++..++.
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6777889999999999866654

>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=91.86  E-value=0.03  Score=30.33  Aligned_cols=20  Identities=30%  Similarity=0.255  Sum_probs=15.7

Q ss_pred             eEEEeCCCCceeEeeeeEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.++.|+|||.++-.+...
T Consensus         3 ~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           3 AITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            46799999999988655544

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.

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=91.86  E-value=0.018  Score=43.70  Aligned_cols=23  Identities=9%  Similarity=0.063  Sum_probs=18.9

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .++.+|.++||+|||.....++.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~  202 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLIT  202 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHH
Confidence            36899999999999998865543

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.

>PLN02199 shikimate kinase

Probab=91.84  E-value=0.021  Score=39.86  Aligned_cols=26  Identities=31%  Similarity=0.301  Sum_probs=20.5

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +.+.++++.+|+|||.++-.++..++
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg  127 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLG  127 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhC
Confidence            36788999999999999876665443

>PRK13721 conjugal transfer ATP-binding protein TraC; Provisional

Probab=91.83  E-value=0.023  Score=43.73  Aligned_cols=24  Identities=17%  Similarity=0.045  Sum_probs=19.5

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+++|.++||||||+....++..
T Consensus       449 N~N~~I~G~sGsGKS~l~k~l~~~  472 (844)
T PRK13721        449 NYNMAVCGTSGAGKTGLIQPLIRS  472 (844)
T ss_pred             cccEEEEcCCCCCHHHHHHHHHHh
Confidence            358999999999999988665543

>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=91.83  E-value=0.067  Score=31.55  Aligned_cols=21  Identities=33%  Similarity=0.290  Sum_probs=16.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|++|.|+|||+..-.+.
T Consensus        12 ~~~~i~G~nGsGKStLl~~l~   32 (137)
T PF00005_consen   12 EIVAIVGPNGSGKSTLLKALA   32 (137)
T ss_dssp             SEEEEEESTTSSHHHHHHHHT
T ss_pred             CEEEEEccCCCccccceeeec
Confidence            577899999999998775443

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 ....

>TIGR00665 DnaB replicative DNA helicase

Probab=91.82  E-value=0.033  Score=39.44  Aligned_cols=44  Identities=11%  Similarity=0.096  Sum_probs=28.5

Q ss_pred             hHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEe
Q psy11637         17 KSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~   60 (67)
                      ..+++++.+ ..+.-.+|.++||+|||..++.++..    .+.+++++.
T Consensus       183 ~~LD~~~~G~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~vl~~S  231 (434)
T TIGR00665       183 TDLDKLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGKPVAFFS  231 (434)
T ss_pred             hhhHhhcCCCCCCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeEEEEe
Confidence            344555432 12345677899999999998877654    245677764

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.

>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=91.81  E-value=0.02  Score=40.43  Aligned_cols=23  Identities=22%  Similarity=0.130  Sum_probs=16.2

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .++.++.+.||||||.+...++.
T Consensus        15 ~~~~li~G~~GsGKT~~i~~ll~   37 (386)
T PF10412_consen   15 NRHILIIGATGSGKTQAIRHLLD   37 (386)
T ss_dssp             GG-EEEEE-TTSSHHHHHHHHHH
T ss_pred             hCcEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999986654443

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.

>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=91.81  E-value=0.072  Score=34.56  Aligned_cols=22  Identities=23%  Similarity=0.289  Sum_probs=15.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...+|++|+|||||..+..+..
T Consensus         4 ~~vlL~Gps~SGKTaLf~~L~~   25 (181)
T PF09439_consen    4 PTVLLVGPSGSGKTALFSQLVN   25 (181)
T ss_dssp             -EEEEE-STTSSHHHHHHHHHH
T ss_pred             ceEEEEcCCCCCHHHHHHHHhc
Confidence            5688999999999987755443

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=91.79  E-value=0.023  Score=39.93  Aligned_cols=31  Identities=16%  Similarity=0.037  Sum_probs=21.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ...++++|+|+|||++...++..+   +.+++++
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li  174 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIA  174 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEe
Confidence            457778999999999876665442   3455554

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.78  E-value=0.062  Score=39.51  Aligned_cols=38  Identities=21%  Similarity=0.212  Sum_probs=25.2

Q ss_pred             chhhHHHHH---hcCCccee-eeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRKM---FGNGRARS-GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~~---~~~~~~~~-~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|+.+++.+   +..+.-.+ -++.+|+|+|||+++..++..
T Consensus        18 Gq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~   59 (504)
T PRK14963         18 GQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMA   59 (504)
T ss_pred             ChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            477766553   34332223 389999999999998666544

>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=91.78  E-value=0.15  Score=34.78  Aligned_cols=21  Identities=24%  Similarity=0.162  Sum_probs=17.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ...-+++|.|+|||+++-.+.
T Consensus        31 ei~~LIGPNGAGKTTlfNlit   51 (250)
T COG0411          31 EIVGLIGPNGAGKTTLFNLIT   51 (250)
T ss_pred             eEEEEECCCCCCceeeeeeec
Confidence            566789999999999885544

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=91.78  E-value=0.029  Score=39.44  Aligned_cols=40  Identities=18%  Similarity=0.202  Sum_probs=30.1

Q ss_pred             eccchhhHHHHHhcC-Cc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         11 LRPYQEKSLRKMFGN-GR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        11 lR~yQ~~av~~~~~~-~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +.|+|++..+++... +. .+.-++++|.|.||+.++..++.
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~~A~   43 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQHLAQ   43 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHHHHH
Confidence            579999999887753 22 35677899999999988865543

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=91.78  E-value=0.05  Score=41.16  Aligned_cols=39  Identities=18%  Similarity=0.206  Sum_probs=26.6

Q ss_pred             chhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         14 YQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        14 yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .|+++++.+... ...++.++.+|+|+|||.++-.+...+
T Consensus        35 gq~~a~~~L~~~~~~~~~~l~~G~~G~GKttla~~l~~~l   74 (637)
T PRK13765         35 GQEHAVEVIKKAAKQRRHVMMIGSPGTGKSMLAKAMAELL   74 (637)
T ss_pred             ChHHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHc
Confidence            377777654431 112578999999999999886655443

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=91.70  E-value=0.036  Score=36.49  Aligned_cols=21  Identities=19%  Similarity=0.170  Sum_probs=17.1

Q ss_pred             eEEEeCCCCceeEeeeeEEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++.+++|||||+++-.+....
T Consensus         3 vl~G~pGSGKST~a~~La~~l   23 (249)
T TIGR03574         3 ILTGLPGVGKSTFSKELAKKL   23 (249)
T ss_pred             EEEcCCCCCHHHHHHHHHHHH
Confidence            678999999999997766543

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=91.67  E-value=0.062  Score=36.05  Aligned_cols=18  Identities=39%  Similarity=0.397  Sum_probs=15.3

Q ss_pred             ceeeeEEEeCCCCceeEe
Q psy11637         28 ARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~   45 (67)
                      ++...|++|.|||||+..
T Consensus        31 Ge~vaI~GpSGSGKSTLL   48 (226)
T COG1136          31 GEFVAIVGPSGSGKSTLL   48 (226)
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            368889999999999765

>KOG0991|consensus

Probab=91.63  E-value=0.022  Score=39.56  Aligned_cols=23  Identities=22%  Similarity=0.173  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      -+.++.+|+|.|||+..+.++.+
T Consensus        49 P~liisGpPG~GKTTsi~~LAr~   71 (333)
T KOG0991|consen   49 PNLIISGPPGTGKTTSILCLARE   71 (333)
T ss_pred             CceEeeCCCCCchhhHHHHHHHH
Confidence            46889999999999988766654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	67
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	2e-25
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	8e-25
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-07
3b6e_A	216	Interferon-induced helicase C domain-containing P;	8e-05
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	5e-04

>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 Length = 237

 Score = 92.8 bits (231), Expect = 2e-25
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 2   TIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN 61
           T        LR YQEK+L +   + R   G IVLP G+GK+ V + A   +    L++  
Sbjct: 85  TPYFDAEISLRDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAINELSTPTLIVVP 141

Query: 62  SGV 64
           +  
Sbjct: 142 TLA 144

>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* Length = 472

 Score = 93.7 bits (233), Expect = 8e-25
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 2   TIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN 61
           T        LR YQEK+L +   + R   G IVLP G+GK+ V + A   +    L++  
Sbjct: 85  TPYFDAEISLRDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAINELSTPTLIVVP 141

Query: 62  S 62
           +
Sbjct: 142 T 142

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 8e-07
 Identities = 12/64 (18%), Positives = 21/64 (32%), Gaps = 6/64 (9%)

Query: 5   LKPSAVLRPYQEKSLRKMFGNGRARSGVIV--LPCGAGKSLVGVTACCTVRKRALVLCNS 62
                V R      LR+     R    V++  +  G+GK+ V +  C       +     
Sbjct: 126 FAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVL-GSGKTWVALDVC---LSYKVQCKMD 181

Query: 63  GVVF 66
             +F
Sbjct: 182 FKIF 185

>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 = 37.1 bits (86), Expect = 8e-05
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 12/61 (19%)

Query: 11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC---------CTVRKRALVLCN 61
          LRPYQ +  +        ++ +I LP G+GK+ V V             +   + +VL N
Sbjct: 34 LRPYQMEVAQPAL---EGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVN 90

Query: 62 S 62
           
Sbjct: 91 K 91

>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 = 35.2 bits (80), Expect = 5e-04
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 9/63 (14%)

Query: 5  LKPSAV-LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC----CTVRKRALVL 59
          L+   +  R YQE     ++   +  + +IVLP G GK+L+ +            + L+L
Sbjct: 3  LRRDLIQPRIYQEV----IYAKCKETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLML 58

Query: 60 CNS 62
            +
Sbjct: 59 APT 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	67
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.39
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.39
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.31
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.28
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.27
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.26
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.26
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.22
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.22
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.21
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.21
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.21
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.2
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.2
3h1t_A	590	Type I site-specific restriction-modification syst	99.19
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.18
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.17
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.17
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.16
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.15
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.15
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.15
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.15
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.15
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.15
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.14
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.12
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.11
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.11
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.1
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.1
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.1
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.09
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.09
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.07
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.07
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.06
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.06
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.04
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.04
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.02
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.98
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	98.95
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	98.93
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.93
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	98.92
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	98.91
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.91
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.89
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	98.88
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.87
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.87
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.85
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.84
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	98.84
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	98.84
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	98.82
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.79
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.79
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.77
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.74
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.72
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.7
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	98.7
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.55
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.53
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.48
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.38
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.36
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.32
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	98.23
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.23
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	98.1
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	98.09
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	98.07
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	98.04
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	98.03
1yks_A	440	Genome polyprotein [contains: flavivirin protease	97.94
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	97.91
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.91
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.86
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.77
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.75
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	97.69
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	97.68
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.47
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	97.24
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.13
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	97.08
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	97.06
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.94
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.75
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.59
3co5_A	143	Putative two-component system transcriptional RES	96.57
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	96.52
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.47
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.44
3bos_A	242	Putative DNA replication factor; P-loop containing	96.42
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.4
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	96.38
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.34
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.3
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.27
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.26
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.24
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	96.22
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	96.21
1p9r_A	418	General secretion pathway protein E; bacterial typ	96.21
1tue_A	212	Replication protein E1; helicase, replication, E1E	96.14
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.05
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.02
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.98
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	95.94
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.91
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	95.9
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	95.84
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	95.83
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.77
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	95.77
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.77
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	95.72
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	95.71
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	95.68
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	95.68
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.63
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	95.62
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	95.62
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.61
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.6
2z43_A	324	DNA repair and recombination protein RADA; archaea	95.59
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.59
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.59
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.59
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.57
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.54
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	95.54
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	95.53
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	95.49
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	95.43
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.43
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.39
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.38
2qgz_A	308	Helicase loader, putative primosome component; str	95.38
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.38
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	95.37
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	95.36
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.36
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.35
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	95.33
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.29
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	95.29
3jux_A	822	Protein translocase subunit SECA; protein transloc	95.28
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.25
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.25
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.21
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	95.19
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.14
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.12
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	95.09
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.07
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.06
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	95.01
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	94.98
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	94.96
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	94.93
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	94.92
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.91
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.9
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	94.86
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	94.86
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	94.85
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	94.84
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.82
2r44_A	331	Uncharacterized protein; putative ATPase, structur	94.78
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.77
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	94.77
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	94.76
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.75
2fna_A	357	Conserved hypothetical protein; structural genomic	94.74
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	94.72
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.69
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	94.69
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.64
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.64
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	94.62
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	94.61
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	94.6
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	94.55
3pvs_A	447	Replication-associated recombination protein A; ma	94.52
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	94.52
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	94.51
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	94.49
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.49
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.49
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	94.44
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.42
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.41
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.41
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	94.4
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.38
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.37
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	94.37
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.35
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	94.34
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	94.33
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.3
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	94.26
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.25
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	94.25
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.22
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.22
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.22
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	94.22
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	94.15
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	94.15
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	94.14
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.13
1via_A	175	Shikimate kinase; structural genomics, transferase	94.1
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	94.1
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.1
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	94.08
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.05
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	94.05
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.02
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	93.99
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	93.99
2ewv_A	372	Twitching motility protein PILT; pilus retraction	93.96
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	93.96
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	93.96
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	93.94
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	93.93
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	93.93
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	93.93
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	93.92
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	93.9
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.86
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.81
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.81
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	93.77
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	93.76
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	93.76
2vli_A	183	Antibiotic resistance protein; transferase, tunica	93.76
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.74
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	93.7
1u94_A	356	RECA protein, recombinase A; homologous recombinat	93.7
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	93.68
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	93.64
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.63
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	93.63
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	93.6
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	93.57
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	93.54
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	93.51
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.48
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	93.47
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.47
3kta_A	182	Chromosome segregation protein SMC; structural mai	93.46
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	93.44
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	93.37
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	93.34
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	93.33
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.31
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	93.31
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.24
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	93.19
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.19
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.18
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.15
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	93.1
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.06
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	93.06
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	93.06
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	93.03
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	93.01
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	92.95
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	92.94
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	92.93
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	92.88
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	92.85
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	92.78
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	92.78
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	92.77
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.75
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	92.74
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.74
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	92.72
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	92.72
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	92.68
2r6a_A	454	DNAB helicase, replicative helicase; replication,	92.66
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	92.6
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	92.55
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	92.5
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	92.5
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.46
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	92.36
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	92.36
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	92.28
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	92.27
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	92.26
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	92.26
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	92.25
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	92.22
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	92.19
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	92.11
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	92.11
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	92.11
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	92.08
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	92.05
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	92.04
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	92.03
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	92.02
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	91.95
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	91.9
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	91.89
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	91.87
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	91.81
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	91.81
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	91.79
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	91.77
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	91.74
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	91.73
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	91.73
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	91.73
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	91.72
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	91.72
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	91.66
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	91.6
3io5_A	333	Recombination and repair protein; storage dimer, i	91.52
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	91.52
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	91.48
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	91.44
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	91.44
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	91.35
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	91.35
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	91.34
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	91.32
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	91.3
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	91.28
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	91.27
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	91.19
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	91.14
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	91.08
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	91.06
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	91.03
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	91.0
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	90.86
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	90.84
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	90.82
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	90.77
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	90.7
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	90.65
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	90.56
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	90.52
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	90.51
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	90.47
1e69_A	322	Chromosome segregation SMC protein; structural mai	90.42
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	90.41
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	90.31
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	90.3
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	90.26
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	90.24
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	90.22
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	90.19
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	90.16
3th5_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	89.62
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	90.13
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	90.09
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	90.07
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	90.01
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	89.97
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	89.93
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	89.89
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	89.86
1g6h_A	257	High-affinity branched-chain amino acid transport	89.77
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	89.75
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	89.69
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	89.67
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	89.64
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	89.63
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	89.63
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	89.63
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	89.63
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.58
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	89.56
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	89.47
1b0u_A	262	Histidine permease; ABC transporter, transport pro	89.43
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	89.35
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	89.31
1ji0_A	240	ABC transporter; ATP binding protein, structural g	89.28
1sgw_A	214	Putative ABC transporter; structural genomics, P p	89.27
2ghi_A	260	Transport protein; multidrug resistance protein, M	89.22
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	89.18
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	89.13
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	89.09
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	89.06
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	89.04
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	89.02
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	89.0
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	88.95
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	88.95
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	88.95
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	88.91
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	88.88
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	88.85
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	88.8
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	88.77
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	88.73
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	88.69
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	88.68
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	88.64
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	88.62
2xxa_A	433	Signal recognition particle protein; protein trans	88.61
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	88.57
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	88.51
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	88.51
3u4q_B	1166	ATP-dependent helicase/deoxyribonuclease subunit;	88.44
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	88.33
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	88.31
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	88.28
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	88.21
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	88.13
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	88.0
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	87.79
2og2_A	359	Putative signal recognition particle receptor; nuc	87.65
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	87.58
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	87.54
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	87.41
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	87.4
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	87.39
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	87.38
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	87.33
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	87.31
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	87.24
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	87.12
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	87.1
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	87.0
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	86.94
3ice_A	422	Transcription termination factor RHO; transcriptio	86.92
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	86.89
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	86.6
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	86.56
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	86.53
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	86.53
3u06_A	412	Protein claret segregational; motor domain, stalk	86.45
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	86.42
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	86.4
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	86.36
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	86.3
2hf9_A	226	Probable hydrogenase nickel incorporation protein	86.3
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	86.29
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	86.19
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	86.17
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	86.13
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	86.09
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	86.0
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	85.96
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	85.92
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	85.74
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	85.66
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	85.66
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	85.65
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	85.63
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	85.6
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	85.47
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	85.4
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	85.29
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	85.23
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	85.1
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	84.94
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	84.78
4h1g_A	715	Maltose binding protein-cakar3 motor domain fusio;	84.77
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	84.68
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	84.54
4aby_A	415	DNA repair protein RECN; hydrolase, double strand	84.54
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	84.53
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	84.48
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	84.43
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	84.33
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	84.29
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	84.21
2o5v_A	359	DNA replication and repair protein RECF; ABC ATPas	84.13
3l0o_A	427	Transcription termination factor RHO; helicase, RH	84.05
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	84.01
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	83.84
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	83.84
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	83.82
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	83.81
2yc2_C	208	IFT27, small RAB-related GTPase; transport protein	83.75
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	83.7
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	83.69
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	83.67
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	83.59
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	83.54
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	83.53
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	83.5
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	83.49
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	83.14
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	83.11
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	83.1
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	82.92

>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=99.39  E-value=1.3e-14  Score=93.98  Aligned_cols=59  Identities=31%  Similarity=0.512  Sum_probs=51.4

Q ss_pred             ccccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          4 DLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         4 ~l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ++.+.+.+||||+++++.+++.   +++++.+|||+|||.+++.++...+.+++|++|+..+
T Consensus        87 ~~~~~~~l~~~Q~~ai~~~~~~---~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~~~L  145 (237)
T 2fz4_A           87 YFDAEISLRDYQEKALERWLVD---KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLAL  145 (237)
T ss_dssp             CCCCCCCCCHHHHHHHHHHTTT---SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHH
T ss_pred             cccCCCCcCHHHHHHHHHHHhC---CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCCHHH
Confidence            4556789999999999999886   4699999999999999988887778999999999643

>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=99.39  E-value=1.1e-14  Score=100.21  Aligned_cols=58  Identities=31%  Similarity=0.536  Sum_probs=50.9

Q ss_pred             cccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      +...+.|||||+++++++++.   +++++.+|||+|||.+++.++...+.++||++|+..+
T Consensus        88 ~~~~~~l~~~Q~~ai~~i~~~---~~~ll~~~TGsGKT~~~l~~i~~~~~~~Lvl~P~~~L  145 (472)
T 2fwr_A           88 FDAEISLRDYQEKALERWLVD---KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLAL  145 (472)
T ss_dssp             CCCCCCBCHHHHHHHHHHTTT---TEEEEECCTTSCHHHHHHHHHHHHCSCEEEEESSHHH
T ss_pred             ccCCCCcCHHHHHHHHHHHhc---CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEECCHHH
Confidence            345678999999999999987   4799999999999999988888888999999999643

>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=99.31  E-value=1.8e-14  Score=89.40  Aligned_cols=56  Identities=30%  Similarity=0.479  Sum_probs=47.5

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE---------eeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV---------RKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~---------~~~~lil~p~~~~   65 (67)
                      ..+.|||||+++++.+++.   ++.++.+|||+|||++++.++...         ..+++|++|+..+
T Consensus        30 ~~~~l~~~Q~~~i~~~~~~---~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~~lil~p~~~L   94 (216)
T 3b6e_A           30 PELQLRPYQMEVAQPALEG---KNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLL   94 (216)
T ss_dssp             CCCCCCHHHHHHHHHHHTT---CCEEEECSCHHHHHHHHHHHHHHHHHHHHHTTCCCCEEEEESSHHH
T ss_pred             CCCCchHHHHHHHHHHhcC---CCEEEEcCCCCCHHHHHHHHHHHHHhhcccccCCCcEEEEECHHHH
Confidence            4678999999999999975   689999999999999998776542         5789999998653

>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=99.28  E-value=6.5e-14  Score=91.20  Aligned_cols=54  Identities=17%  Similarity=0.222  Sum_probs=47.3

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ..|||||+++++.++++   ++.++.+|||+|||.+++..+...+.+++|++|+..+
T Consensus        15 ~~l~~~Q~~~i~~i~~~---~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv~P~~~L   68 (337)
T 2z0m_A           15 KNFTEVQSKTIPLMLQG---KNVVVRAKTGSGKTAAYAIPILELGMKSLVVTPTREL   68 (337)
T ss_dssp             CSCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHTCCEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHhcC---CCEEEEcCCCCcHHHHHHHHHHhhcCCEEEEeCCHHH
Confidence            36999999999999876   6899999999999999887777778899999999654

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.27  E-value=1.1e-13  Score=95.17  Aligned_cols=55  Identities=22%  Similarity=0.320  Sum_probs=46.9

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~~   65 (67)
                      .++|||||.+++..++++   ++.++.+|||+|||++++.++...        +.++||++|+..+
T Consensus         2 ~~~~~~~Q~~~i~~~~~~---~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L   64 (555)
T 3tbk_A            2 PLKPRNYQLELALPAKKG---KNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQIPV   64 (555)
T ss_dssp             CCCCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHH
T ss_pred             CCCCcHHHHHHHHHHhCC---CCEEEEeCCCChHHHHHHHHHHHHHHhcccCCCCEEEEEeCCHHH
Confidence            468999999999999876   689999999999999987766543        6789999999643

>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=99.26  E-value=8.2e-14  Score=93.14  Aligned_cols=56  Identities=27%  Similarity=0.321  Sum_probs=48.1

Q ss_pred             ccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEeeccee
Q psy11637          6 KPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLCNSGVV   65 (67)
Q Consensus         6 ~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~p~~~~   65 (67)
                      +..++|||||+++++.++++    ++++.+|||+|||++++.++...    +.++||++|+..+
T Consensus         5 ~~~~~l~~~Q~~~i~~~~~~----~~ll~~~tG~GKT~~~~~~~~~~~~~~~~~~liv~P~~~L   64 (494)
T 1wp9_A            5 RDLIQPRIYQEVIYAKCKET----NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPL   64 (494)
T ss_dssp             HHHHCCCHHHHHHHHHGGGS----CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHH
T ss_pred             cCCCCccHHHHHHHHHHhhC----CEEEEcCCCCCHHHHHHHHHHHHHhcCCCeEEEEECCHHH
Confidence            35689999999999998875    88999999999999998877654    7899999998643

>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=99.26  E-value=1.3e-13  Score=95.22  Aligned_cols=56  Identities=21%  Similarity=0.410  Sum_probs=44.9

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~~   65 (67)
                      ..++|||||++++..++++   ++.++.+|||+|||++++.++...        +.++||++|+..+
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~---~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~~~~~~~lil~P~~~L   67 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAING---KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPV   67 (556)
T ss_dssp             ----CCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHH
T ss_pred             CCCCCCHHHHHHHHHHHcC---CCEEEEcCCCChHHHHHHHHHHHHHHhCcccCCCeEEEEeCCHHH
Confidence            4578999999999999986   689999999999999987766543        6789999999643

>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=99.22  E-value=2.2e-13  Score=85.64  Aligned_cols=53  Identities=19%  Similarity=0.186  Sum_probs=43.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~------~~~~lil~p~~~~   65 (67)
                      .+||||++++..++++   ++.++.+|||+|||.+++..+...      +.++||++|+..+
T Consensus        36 ~~~~~Q~~~i~~~~~~---~~~li~~~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L   94 (220)
T 1t6n_A           36 HPSEVQHECIPQAILG---MDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   94 (220)
T ss_dssp             CCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCCchhhhhhHHHHHhhhccCCCEEEEEEeCCHHH
Confidence            4999999999999986   589999999999999886555432      3489999999653

>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=99.22  E-value=2.6e-13  Score=84.23  Aligned_cols=53  Identities=21%  Similarity=0.174  Sum_probs=43.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .+||||+++++.++++   ++.++.+|||+|||.+++..+..      .+.+++|++|+..+
T Consensus        25 ~~~~~Q~~~i~~~~~~---~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~Pt~~L   83 (206)
T 1vec_A           25 KPSPIQEESIPIALSG---RDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTREL   83 (206)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHccC---CCEEEECCCCCchHHHHHHHHHHHhcccCCCeeEEEEeCcHHH
Confidence            7999999999999986   68999999999999887644332      13579999999653

>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=99.21  E-value=1.6e-13  Score=89.63  Aligned_cols=54  Identities=20%  Similarity=0.290  Sum_probs=45.3

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~p~~~~   65 (67)
                      +++||||+++++.++++   +++++.+|||+|||.+++.++...    .+++||++|+..+
T Consensus       112 ~~l~~~Q~~ai~~~l~~---~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~~lil~Pt~~L  169 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTAL  169 (282)
T ss_dssp             CCCCHHHHHHHHHHHHH---SEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHH
T ss_pred             cCccHHHHHHHHHHHhc---CCeEEEcCCCCCcHHHHHHHHHHHHHcCCCeEEEEECCHHH
Confidence            58999999999999886   578999999999999997766542    3499999999653

>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=99.21  E-value=2.9e-13  Score=85.57  Aligned_cols=53  Identities=19%  Similarity=0.192  Sum_probs=43.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------------~~~~~lil~p~~~~   65 (67)
                      .+||+|++++..++++   ++.++.+|||+|||.+++..+..            .+.+++|++|+..+
T Consensus        42 ~~~~~Q~~~i~~~~~~---~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~~~lil~Pt~~L  106 (228)
T 3iuy_A           42 KPTPIQSQAWPIILQG---IDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTREL  106 (228)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHC---------CCCSEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCCcEEEEeCCHHH
Confidence            7999999999999876   68999999999999987543221            35679999999754

>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=99.21  E-value=4e-13  Score=84.46  Aligned_cols=53  Identities=15%  Similarity=0.141  Sum_probs=42.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~-----~~~~~lil~p~~~~   65 (67)
                      .+||||++++..++++   ++.++.+|||+|||.+++..+. .     .+.++||++|+..+
T Consensus        36 ~~~~~Q~~~i~~~~~~---~~~lv~~pTGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   94 (224)
T 1qde_A           36 EPSAIQQRAIMPIIEG---HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTREL   94 (224)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHH
T ss_pred             CCcHHHHHHHHHHhcC---CCEEEECCCCCcHHHHHHHHHHHHHhccCCCceEEEEECCHHH
Confidence            6899999999999986   6899999999999988643332 1     24589999999654

>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=99.20  E-value=2.9e-13  Score=83.90  Aligned_cols=54  Identities=22%  Similarity=0.230  Sum_probs=43.5

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~p~~~~   65 (67)
                      ..+||||+++++.++++   ++.++.+|||+|||.+++..+..         .+.+++|++|+..+
T Consensus        22 ~~~~~~Q~~~i~~~~~~---~~~li~~~TGsGKT~~~~~~~~~~l~~~~~~~~~~~~lil~P~~~L   84 (207)
T 2gxq_A           22 TTPTPIQAAALPLALEG---KDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTREL   84 (207)
T ss_dssp             CSCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHCCCCCCTTCCCSEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHcCC---CCEEEECCCCChHHHHHHHHHHHHHhhccccCCCCcEEEEECCHHH
Confidence            37899999999999986   68999999999999986543322         24579999999653

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.20  E-value=4e-13  Score=93.21  Aligned_cols=55  Identities=20%  Similarity=0.284  Sum_probs=46.6

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      .++|||||+++++.+++.   +++++.+|||+|||.+++.++..    .++++||++|++.+
T Consensus       111 ~~~l~~~Q~~ai~~~~~~---~~~ll~~~tGsGKT~~~~~~~~~~~~~~~~~vlvl~P~~~L  169 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTAL  169 (510)
T ss_dssp             EECCCHHHHHHHHHHHHH---SEEEEECCSTTTHHHHHHHHHHHHHHHCSSEEEEEESSHHH
T ss_pred             CCCCCHHHHHHHHHHHhc---CCcEEEeCCCCCHHHHHHHHHHHHHhCCCCeEEEEECcHHH
Confidence            569999999999999975   68999999999999999776654    23499999999653

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.19  E-value=1.2e-12  Score=92.79  Aligned_cols=61  Identities=20%  Similarity=0.348  Sum_probs=41.8

Q ss_pred             ccceeeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEE------------EeeeeEEEeecceee
Q psy11637          6 KPSAVLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCT------------VRKRALVLCNSGVVF   66 (67)
Q Consensus         6 ~~~~~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~------------~~~~~lil~p~~~~v   66 (67)
                      ...+.|||||.++++++++.  ...++.++.+|||+|||.+++.++..            ...++||++|+..++
T Consensus       174 ~~~~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~  248 (590)
T 3h1t_A          174 VSGYSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWSARWNRTGDYRKPRILFLADRNVLV  248 (590)
T ss_dssp             C----CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHHTTCCSSCSSSCCCEEEEEC-----
T ss_pred             cCCCCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHhcccccccccCCCeEEEEeCCHHHH
Confidence            34568999999999998752  11257899999999999998777654            247899999987653

>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=99.18  E-value=4.4e-13  Score=89.09  Aligned_cols=53  Identities=19%  Similarity=0.186  Sum_probs=43.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~------~~~~lil~p~~~~   65 (67)
                      .|||||++++..++++   ++.++.+|||+|||.+++..+...      +.++||++|+..+
T Consensus        30 ~~~~~Q~~~i~~~~~~---~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L   88 (391)
T 1xti_A           30 HPSEVQHECIPQAILG---MDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   88 (391)
T ss_dssp             SCCHHHHHHHHHHTTT---CCEEEECSSCSSHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHhcC---CcEEEECCCCCcHHHHHHHHHHHhhcccCCCeeEEEECCCHHH
Confidence            4999999999999986   689999999999999886544432      4589999999654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.17  E-value=2.5e-13  Score=85.63  Aligned_cols=54  Identities=15%  Similarity=0.079  Sum_probs=44.0

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      ..+||+|+++++.++++   ++.++.+|||+|||.+++..+..      .+.+++|++|+..+
T Consensus        25 ~~~~~~Q~~~i~~~~~~---~~~lv~a~TGsGKT~~~~~~~l~~l~~~~~~~~~lil~Pt~~L   84 (219)
T 1q0u_A           25 YKPTEIQERIIPGALRG---ESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTREL   84 (219)
T ss_dssp             CSCCHHHHHHHHHHHHT---CCEEEECCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHHHhCcCCceEEEEcCcHHH
Confidence            46899999999999986   68999999999999987554432      24589999999754

>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=99.17  E-value=3.3e-13  Score=96.46  Aligned_cols=56  Identities=29%  Similarity=0.444  Sum_probs=46.1

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----e----eeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----R----KRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~----~~~lil~p~~~~   65 (67)
                      ..+.|||||+++++.++++   ++.++.+|||+|||++++.++...     .    +++||++|+..+
T Consensus         4 ~~~~l~~~Q~~~i~~il~g---~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~vlvl~P~~~L   68 (699)
T 4gl2_A            4 AMLQLRPYQMEVAQPALEG---KNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLL   68 (699)
T ss_dssp             ---CCCHHHHHHHHHHHSS---CCEEECCCTTSCHHHHHHHHHHHHHHHHHHHTCCCCBCCEESCSHH
T ss_pred             CCCCccHHHHHHHHHHHhC---CCEEEEcCCCCcHHHHHHHHHHHHHHhccccCCCCeEEEEECCHHH
Confidence            4689999999999999985   689999999999999998777542     2    789999999754

>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=99.16  E-value=7.9e-13  Score=96.91  Aligned_cols=55  Identities=22%  Similarity=0.420  Sum_probs=46.2

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~~   65 (67)
                      ...|||||++++..++++   ++.++.+|||+|||++++.++...        ++++||++|+..+
T Consensus       246 ~~~l~~~Q~~~i~~~l~~---~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~Lvl~Pt~~L  308 (797)
T 4a2q_A          246 TKKARSYQIELAQPAING---KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPV  308 (797)
T ss_dssp             --CCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHHTCCSSCCCCEEEECSSHHH
T ss_pred             CCCCCHHHHHHHHHHHhC---CCEEEEeCCCChHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHH
Confidence            568999999999999876   689999999999999988776553        7799999998643

>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=99.15  E-value=7.9e-13  Score=84.33  Aligned_cols=53  Identities=23%  Similarity=0.286  Sum_probs=42.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~   65 (67)
                      .+||+|++++..++++   ++.++.+|||+|||.+++..+..       .+.+++|++|+..+
T Consensus        51 ~~~~~Q~~~i~~~~~~---~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~lil~Pt~~L  110 (245)
T 3dkp_A           51 MPTPIQMQAIPVMLHG---RELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTREL  110 (245)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHCSCCSSSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCCcHHHHHHHHHHHHHhhcccCCceEEEEeCCHHH
Confidence            5999999999999986   57999999999999987544422       23479999999754

>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=99.15  E-value=7.1e-13  Score=86.95  Aligned_cols=54  Identities=15%  Similarity=0.068  Sum_probs=44.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      .|||+|++++..+++.+  ++.++.+|||+|||.+++..+..     .+.+++|++|+..+
T Consensus        28 ~~~~~Q~~~i~~~~~~~--~~~l~~~~TGsGKT~~~~~~~~~~~~~~~~~~~lil~P~~~L   86 (367)
T 1hv8_A           28 KPTDIQMKVIPLFLNDE--YNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTREL   86 (367)
T ss_dssp             SCCHHHHHHHHHHHHTC--SEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHhCCC--CCEEEECCCCChHHHHHHHHHHHHhcccCCCcEEEEcCCHHH
Confidence            79999999999999764  58889999999999987655443     25689999999653

>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=99.15  E-value=1.1e-12  Score=98.26  Aligned_cols=58  Identities=21%  Similarity=0.394  Sum_probs=46.1

Q ss_pred             cccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeeccee
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGVV   65 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~~   65 (67)
                      +...+.|||||.+++..++++   ++.++.+|||+|||++++.++...        ++++||++|+..+
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g---~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~~~~~~vLvl~Pt~~L  308 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAING---KNALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPV  308 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHTTTTTCCSSCCCCEEEECSSHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHcC---CCEEEEeCCCchHHHHHHHHHHHHHHhccccCCCeEEEEeCCHHH
Confidence            344678999999999999876   689999999999999987776543        6789999998643

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.15  E-value=8.4e-13  Score=84.50  Aligned_cols=53  Identities=19%  Similarity=0.109  Sum_probs=43.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----------~~~~~lil~p~~~~   65 (67)
                      .+||+|++++..++++   ++.++.+|||+|||.+++..+..           .+.++||++|+..+
T Consensus        51 ~~~~~Q~~~i~~~~~g---~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L  114 (242)
T 3fe2_A           51 EPTAIQAQGWPVALSG---LDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTREL  114 (242)
T ss_dssp             SCCHHHHHHHHHHHHT---CCEEEEECTTSCHHHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCcCHHHHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHH
Confidence            4899999999999876   68999999999999997654432           24579999999754

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.15  E-value=8.8e-13  Score=83.73  Aligned_cols=54  Identities=11%  Similarity=0.156  Sum_probs=43.8

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----------~~~~~lil~p~~~~   65 (67)
                      ..+||+|++++..++++   ++.++.+|||+|||.+++..+..          .+.++||++|+..+
T Consensus        46 ~~~~~~Q~~~i~~~~~~---~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~lil~Pt~~L  109 (236)
T 2pl3_A           46 RLVTEIQKQTIGLALQG---KDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTREL  109 (236)
T ss_dssp             CBCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHhCC---CCEEEEeCCCCcHHHHHHHHHHHHHHhhcccccCCceEEEEeCCHHH
Confidence            37899999999999876   68999999999999987654332          24679999999653

>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=99.15  E-value=1.5e-12  Score=93.77  Aligned_cols=53  Identities=25%  Similarity=0.375  Sum_probs=46.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      .|||+|+++++.++++   ++.++++|||+|||++++..+....+++||++|+..+
T Consensus        44 ~~rp~Q~~~i~~il~g---~d~lv~~pTGsGKTl~~~lpal~~~g~~lVisP~~~L   96 (591)
T 2v1x_A           44 KFRPLQLETINVTMAG---KEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISL   96 (591)
T ss_dssp             SCCTTHHHHHHHHHTT---CCEEEECCTTSCTTHHHHHHHHTSSSEEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEECCCChHHHHHHHHHHHcCCcEEEEeCHHHH
Confidence            7899999999999986   6899999999999998876666667899999998654

>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=99.14  E-value=1.1e-12  Score=86.80  Aligned_cols=56  Identities=21%  Similarity=0.200  Sum_probs=45.0

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      ..+||+|++++..++++. +++.++.+|||+|||++++..+..      .+.++||++|+..+
T Consensus        26 ~~~~~~Q~~~i~~~~~~~-~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L   87 (395)
T 3pey_A           26 QKPSKIQERALPLLLHNP-PRNMIAQSQSGTGKTAAFSLTMLTRVNPEDASPQAICLAPSREL   87 (395)
T ss_dssp             CSCCHHHHHHHHHHHCSS-CCCEEEECCTTSCHHHHHHHHHHHHCCTTCCSCCEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHHcCC-CCeEEEECCCCCcHHHHHHHHHHHHhccCCCCccEEEECCCHHH
Confidence            478999999999998862 268999999999999987654432      25689999999754

>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=99.12  E-value=2.5e-12  Score=82.52  Aligned_cols=54  Identities=15%  Similarity=0.239  Sum_probs=43.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---------------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---------------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---------------~~~~~lil~p~~~~   65 (67)
                      ..+||+|++++..++++   ++.++.+|||+|||.+++..+..               .+.++||++|+..+
T Consensus        44 ~~~~~~Q~~~i~~i~~~---~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~~~~lil~Pt~~L  112 (253)
T 1wrb_A           44 QRPTPIQKNAIPAILEH---RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTREL  112 (253)
T ss_dssp             CSCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCCceEEEEECCHHH
Confidence            36899999999999986   68999999999999987654432               12589999999653

>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=99.11  E-value=1.5e-12  Score=87.03  Aligned_cols=53  Identities=19%  Similarity=0.204  Sum_probs=43.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .|||||+++++.++++   ++.++.+|||+|||.+++..+..      .+.+++|++|+..+
T Consensus        43 ~~~~~Q~~~i~~i~~~---~~~li~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  101 (400)
T 1s2m_A           43 KPSPIQEEAIPVAITG---RDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTREL  101 (400)
T ss_dssp             SCCHHHHHHHHHHHHT---CCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhcC---CCEEEECCCCcHHHHHHHHHHHHHHhhccCCccEEEEcCCHHH
Confidence            5999999999999976   57999999999999887654432      24589999999654

>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=99.11  E-value=1.6e-12  Score=84.15  Aligned_cols=53  Identities=19%  Similarity=0.087  Sum_probs=43.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .+||||++++..++++   ++.++.+|||+|||.+++..+..      .+.++||++|+..+
T Consensus        65 ~~~~~Q~~~i~~i~~~---~~~lv~a~TGsGKT~~~~~~il~~l~~~~~~~~~lil~Ptr~L  123 (249)
T 3ber_A           65 KPTKIQIEAIPLALQG---RDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTREL  123 (249)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHHHSCCSSCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEEcCCCCCchhHhHHHHHHHHhcCCCCceEEEEeCCHHH
Confidence            7899999999999986   68999999999999987654432      13579999999754

>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=99.10  E-value=2.4e-12  Score=81.88  Aligned_cols=53  Identities=19%  Similarity=0.154  Sum_probs=42.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeE-EE-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC-CT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~-~~-----~~~~~lil~p~~~~   65 (67)
                      .+||||++++..++++   ++.++.+|||+|||.+++..+ ..     .+.++||++|+..+
T Consensus        46 ~~~~~Q~~~i~~~~~~---~~~l~~a~TGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  104 (230)
T 2oxc_A           46 RPSPVQLKAIPLGRCG---LDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQILILAPTREI  104 (230)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEeCCHHH
Confidence            4999999999998886   689999999999998865433 22     24689999999653

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.10  E-value=1.2e-12  Score=88.73  Aligned_cols=55  Identities=20%  Similarity=0.292  Sum_probs=45.3

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .++++|+|++++..++++   ++.++.+|||+|||.+++..+..   .+.++||++|+..+
T Consensus        19 ~~~~~~~Q~~~i~~i~~~---~~~lv~apTGsGKT~~~l~~~~~~~~~~~~~lil~Pt~~L   76 (414)
T 3oiy_A           19 GKDLTGYQRLWAKRIVQG---KSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTL   76 (414)
T ss_dssp             SSCCCHHHHHHHHHHTTT---CCEECCSCSSSSHHHHHHHHHHHHHTTTCCEEEEESSHHH
T ss_pred             CCCCCHHHHHHHHHHhcC---CCEEEEeCCCCCHHHHHHHHHHHHhcCCCEEEEEECCHHH
Confidence            467899999999999986   58999999999999966555443   36789999999754

>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=99.10  E-value=9e-13  Score=84.29  Aligned_cols=53  Identities=15%  Similarity=0.140  Sum_probs=43.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .+||||++++..++++   ++.++.+|||+|||.+++..+..      .+.++||++|+..+
T Consensus        52 ~~~~~Q~~ai~~i~~~---~~~li~apTGsGKT~~~~l~~l~~l~~~~~~~~~lil~Pt~~L  110 (237)
T 3bor_A           52 KPSAIQQRAIIPCIKG---YDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTREL  110 (237)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEECCCSSHHHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCCcHHHHHHHHHHHHHHhcCCCceEEEEECcHHH
Confidence            4999999999999986   68999999999999887544432      24689999999653

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.09  E-value=2.7e-12  Score=91.70  Aligned_cols=55  Identities=22%  Similarity=0.343  Sum_probs=44.8

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~~   65 (67)
                      -..|||||+++++.++++   ++.++.+|||+|||++++.++...        ++++||++|+..+
T Consensus        11 ~~~lr~~Q~~~i~~~l~g---~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~~~~~~lvl~Pt~~L   73 (696)
T 2ykg_A           11 PFKPRNYQLELALPAMKG---KNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPV   73 (696)
T ss_dssp             --CCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHHHHSCTTCCCCEEEECSSHHH
T ss_pred             CCCccHHHHHHHHHHHcC---CCEEEEcCCCchHHHHHHHHHHHHHHhCccCCCCeEEEEECCHHH
Confidence            468999999999999875   689999999999999987766532        1789999998643

>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=99.09  E-value=2.4e-12  Score=86.06  Aligned_cols=54  Identities=15%  Similarity=0.132  Sum_probs=44.1

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      ..+||||++++..++++   ++.++.+|||+|||++++..+..      .+.+++|++|+..+
T Consensus        61 ~~~~~~Q~~~i~~~~~~---~~~lv~a~TGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  120 (414)
T 3eiq_A           61 EKPSAIQQRAILPCIKG---YDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTREL  120 (414)
T ss_dssp             CSCCHHHHHHHHHHHTT---CCEEECCCSCSSSHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCCHHHHHHhHHHhCC---CCEEEECCCCCcccHHHHHHHHHHHhhcCCceeEEEEeChHHH
Confidence            36899999999999986   57999999999999987554432      35689999999754

>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=99.07  E-value=3.7e-12  Score=85.58  Aligned_cols=53  Identities=15%  Similarity=0.238  Sum_probs=43.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .+||+|++++..++++   ++.++.+|||+|||.+++..+..      .+.++||++|+..+
T Consensus        59 ~~~~~Q~~ai~~i~~~---~~~lv~a~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~Pt~~L  117 (410)
T 2j0s_A           59 KPSAIQQRAIKQIIKG---RDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTREL  117 (410)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CCEEEECCCCCCchHHHHHHHHHHHhhccCCceEEEEcCcHHH
Confidence            4999999999999986   68999999999999887654432      35789999999753

>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=99.07  E-value=2e-12  Score=84.21  Aligned_cols=53  Identities=21%  Similarity=0.285  Sum_probs=43.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----------~~~~~lil~p~~~~   65 (67)
                      .+||+|++++..++++   ++.++.+|||||||.+++..+..          .+.+++|++|+..+
T Consensus        76 ~~~~~Q~~~i~~~~~~---~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~~~~~~~~lil~Pt~~L  138 (262)
T 3ly5_A           76 NMTEIQHKSIRPLLEG---RDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTREL  138 (262)
T ss_dssp             BCCHHHHHHHHHHHHT---CCCEECCCTTSCHHHHHHHHHHHHHHHTTCCGGGCCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CcEEEEccCCCCchHHHHHHHHHHHHhccccccCCceEEEEeCCHHH
Confidence            4899999999999986   68999999999999987654432          25679999999754

>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=99.06  E-value=1.5e-12  Score=86.49  Aligned_cols=54  Identities=15%  Similarity=0.140  Sum_probs=43.7

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      ..|||||++++..++++   ++.++.+|||+|||.+++..+..      .+.++||++|+..+
T Consensus        42 ~~~~~~Q~~~i~~i~~~---~~~lv~~~TGsGKT~~~~~~~~~~l~~~~~~~~~lil~P~~~L  101 (394)
T 1fuu_A           42 EEPSAIQQRAIMPIIEG---HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTREL  101 (394)
T ss_dssp             CSCCHHHHHHHHHHHHT---CCEEECCCSSHHHHHHHHHHHHHHCCTTCCSCCEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHhCC---CCEEEECCCCChHHHHHHHHHHHHhhccCCCCCEEEEcCCHHH
Confidence            37999999999999986   68999999999999886543332      25689999999653

>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=99.06  E-value=2.1e-12  Score=91.50  Aligned_cols=53  Identities=25%  Similarity=0.364  Sum_probs=45.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      .+||+|+++++.++++   ++.++++|||+|||++++..+....++++|++|+..+
T Consensus        25 ~~r~~Q~~~i~~il~g---~d~lv~apTGsGKTl~~~lp~l~~~g~~lvi~P~~aL   77 (523)
T 1oyw_A           25 QFRPGQEEIIDTVLSG---RDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISL   77 (523)
T ss_dssp             SCCTTHHHHHHHHHTT---CCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEECCCCcHHHHHHHHHHHHhCCCEEEECChHHH
Confidence            7899999999999986   6899999999999998876555567889999998654

>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=99.04  E-value=7.1e-12  Score=83.58  Aligned_cols=56  Identities=20%  Similarity=0.147  Sum_probs=44.0

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      ..+||+|++++..++++. +++.++.+|||+|||++++..+..      ...+++|++|+..+
T Consensus        46 ~~~~~~Q~~~i~~~~~~~-~~~~lv~apTGsGKT~~~~~~~~~~~~~~~~~~~~lil~P~~~L  107 (412)
T 3fht_A           46 NRPSKIQENALPLMLAEP-PQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYEL  107 (412)
T ss_dssp             CSCCHHHHHHHHHHHSSS-CCCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCCHHHHHHHHHHhcCC-CCeEEEECCCCchHHHHHHHHHHHHhhhcCCCCCEEEECCCHHH
Confidence            378999999999999852 268999999999999987544332      23489999999754

>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=99.02  E-value=1e-11  Score=85.92  Aligned_cols=56  Identities=27%  Similarity=0.274  Sum_probs=43.7

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecc
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSG   63 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~   63 (67)
                      ...|||||+++++.+... ..++++++..|||+|||+++++++...     .+++||+||+.
T Consensus        35 ~~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~~~~~~~~~LIv~P~~   96 (500)
T 1z63_A           35 KANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLS   96 (500)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECST
T ss_pred             hccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHHhcCCCCCEEEEccHH
Confidence            467999999999765421 112678899999999999998877653     36899999964

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=98.98  E-value=2.5e-11  Score=91.82  Aligned_cols=56  Identities=14%  Similarity=0.119  Sum_probs=46.8

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ..++|+|+|++++..++++   ++.++.+|||||||++++..+..   .+.+++|++|+..+
T Consensus        36 ~~f~l~~~Q~~aI~~il~g---~~vlv~apTGsGKTlv~~~~i~~~~~~g~~vlvl~PtraL   94 (997)
T 4a4z_A           36 WPFELDTFQKEAVYHLEQG---DSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKAL   94 (997)
T ss_dssp             CSSCCCHHHHHHHHHHHTT---CEEEEECCTTSCSHHHHHHHHHHHHHTTCEEEEEESCGGG
T ss_pred             CCCCCCHHHHHHHHHHHcC---CCEEEEECCCCcHHHHHHHHHHHHHhcCCeEEEEeCCHHH
Confidence            4578999999999999886   68999999999999987655543   25689999999765

>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=98.95  E-value=1.9e-11  Score=85.60  Aligned_cols=55  Identities=15%  Similarity=0.256  Sum_probs=43.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~~lil~p~~~~   65 (67)
                      .|||+|++++..++... +++.++.+|||+|||.+++..+...          ..++||++|+..+
T Consensus        94 ~~~~~Q~~~i~~~l~~~-~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Ptr~L  158 (563)
T 3i5x_A           94 GLTPVQQKTIKPILSSE-DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  158 (563)
T ss_dssp             SCCHHHHHHHHHHHSSS-SEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhcCC-CCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCcHHH
Confidence            59999999999999531 2689999999999999876554431          2379999999754

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=98.93  E-value=2e-11  Score=81.81  Aligned_cols=54  Identities=17%  Similarity=0.188  Sum_probs=42.8

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----------------------eeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----------------------RKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----------------------~~~~lil~p~~~   64 (67)
                      ..++|+|++++..++++   ++.++.+|||+|||.+++..+.. .                       ..++||++|+..
T Consensus        36 ~~~~~~Q~~~i~~i~~~---~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lil~Pt~~  112 (417)
T 2i4i_A           36 TRPTPVQKHAIPIIKEK---RDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRE  112 (417)
T ss_dssp             CSCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCBTTBSCSBCCSEEEECSSHH
T ss_pred             CCCCHHHHHHHHHHccC---CCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccccccccccCCccEEEECCcHH
Confidence            37899999999998876   68999999999999877644321 1                       146999999975


Q ss_pred             e
Q psy11637         65 V   65 (67)
Q Consensus        65 ~   65 (67)
                      +
T Consensus       113 L  113 (417)
T 2i4i_A          113 L  113 (417)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.93  E-value=4.1e-11  Score=88.26  Aligned_cols=57  Identities=16%  Similarity=0.205  Sum_probs=45.3

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE------eeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV------RKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~------~~~~lil~p~~~   64 (67)
                      ..+|||||.+++.+++.. ..++++++..+||+|||+++++++...      .+++|||||...
T Consensus       234 ~~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~~~~LIV~P~sl  297 (800)
T 3mwy_W          234 GGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLST  297 (800)
T ss_dssp             SSCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCCSCEEEECCTTT
T ss_pred             CCCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCCCCEEEEECchH
Confidence            568999999999875521 122789999999999999998877543      678999999653

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=98.92  E-value=3.1e-11  Score=85.54  Aligned_cols=55  Identities=15%  Similarity=0.256  Sum_probs=43.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE----------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV----------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~~lil~p~~~~   65 (67)
                      .|||+|++++..++... +++.++.+|||+|||.+++..+...          ..++||++|+..+
T Consensus        43 ~~~~~Q~~~i~~il~~~-~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~Ptr~L  107 (579)
T 3sqw_A           43 GLTPVQQKTIKPILSSE-DHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDL  107 (579)
T ss_dssp             SCCHHHHHHHHHHHCSS-SEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHHccC-CCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcchHHH
Confidence            59999999999999531 2688999999999999876554431          2379999999754

>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=98.91  E-value=3.5e-11  Score=91.87  Aligned_cols=56  Identities=18%  Similarity=0.240  Sum_probs=47.3

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~~~~   65 (67)
                      ..+.|+|+|++++..+.++   ++.++++|||||||+++..++...   +++++|++|+..+
T Consensus       181 ~~f~ltp~Q~~AI~~i~~g---~dvLV~ApTGSGKTlva~l~i~~~l~~g~rvlvl~PtraL  239 (1108)
T 3l9o_A          181 YPFTLDPFQDTAISCIDRG---ESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKAL  239 (1108)
T ss_dssp             CSSCCCHHHHHHHHHHTTT---CCEEEECCSSSHHHHHHHHHHHHHHHTTCEEEEEESSHHH
T ss_pred             CCCCCCHHHHHHHHHHHcC---CCEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEcCcHHH
Confidence            3568999999999998775   689999999999999987666543   7899999999764

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=98.91  E-value=3.7e-11  Score=91.08  Aligned_cols=55  Identities=18%  Similarity=0.256  Sum_probs=46.1

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .+.|+|+|+++++.+.++   ++.++++|||||||+++..++..   .+.+++|++|+.++
T Consensus        84 ~f~L~~~Q~eai~~l~~g---~~vLV~apTGSGKTlva~lai~~~l~~g~rvL~l~PtkaL  141 (1010)
T 2xgj_A           84 PFTLDPFQDTAISCIDRG---ESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKAL  141 (1010)
T ss_dssp             SSCCCHHHHHHHHHHHHT---CEEEEECCTTSCHHHHHHHHHHHHHHTTCEEEEEESSHHH
T ss_pred             CCCCCHHHHHHHHHHHcC---CCEEEECCCCCChHHHHHHHHHHHhccCCeEEEECChHHH
Confidence            568999999999998876   68999999999999998655443   36799999999754

>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=98.89  E-value=4.9e-11  Score=82.26  Aligned_cols=55  Identities=22%  Similarity=0.182  Sum_probs=43.1

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----~~~~lil~p~~~~   65 (67)
                      .++|+|++++..+++.. +++.++.+|||||||.+++..+.. .     ..++||++|+..+
T Consensus       114 ~p~~~Q~~ai~~il~~~-~~~~l~~a~TGsGKT~~~~l~il~~l~~~~~~~~~lil~Pt~~L  174 (479)
T 3fmp_B          114 RPSKIQENALPLMLAEP-PQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYEL  174 (479)
T ss_dssp             SCCHHHHHHHHHHTSBS-CCEEEEECCSSSSHHHHHHHHHHTTCCTTSCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHHcCC-CCcEEEEcCCCCchhHHHHHHHHHHHhhcCCCCcEEEEeChHHH
Confidence            67889999999999752 268999999999999987544432 1     2389999999754

>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=98.88  E-value=4.5e-11  Score=82.31  Aligned_cols=53  Identities=15%  Similarity=0.237  Sum_probs=42.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E----------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V----------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~----------~~~~lil~p~~~~   65 (67)
                      .++|+|++++..++++   ++.++.+|||||||.+++..+.. +          +.++||++||..+
T Consensus        78 ~pt~iQ~~ai~~i~~g---~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~~~~lil~PtreL  141 (434)
T 2db3_A           78 IPTPIQKCSIPVISSG---RDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSPTREL  141 (434)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTCCSEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHhcC---CCEEEECCCCCCchHHHHHHHHHHHHhcccccccCCccEEEEecCHHH
Confidence            5899999999999876   68999999999999987654322 1          3489999999754

>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=98.87  E-value=1.4e-10  Score=88.39  Aligned_cols=58  Identities=21%  Similarity=0.331  Sum_probs=45.2

Q ss_pred             ceeeccchhhHHHHHhcC-----------CcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGN-----------GRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-----------~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~~   65 (67)
                      ...+||||.+|+++++++           ...+++++.+|||||||.+++.++..+     ..++||++|+..+
T Consensus       269 ~~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~~~l~~ll~~~~~~~rvLvlvpr~eL  342 (1038)
T 2w00_A          269 LLVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTSFKAARLATELDFIDKVFFVVDRKDL  342 (1038)
T ss_dssp             EEECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHHHHHHHHHTTCTTCCEEEEEECGGGC
T ss_pred             cccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHHHHHHHHHHhcCCCceEEEEeCcHHH
Confidence            468999999999998752           012578999999999999986555432     2589999998754

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.87  E-value=6.9e-11  Score=83.99  Aligned_cols=57  Identities=16%  Similarity=0.257  Sum_probs=42.4

Q ss_pred             ceeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      .+.+||+|+++++++.+. ..+++.++.+|||+|||..++..+...+.+++|++||..
T Consensus         5 ~~~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~~~~~~~~~~t~~   62 (540)
T 2vl7_A            5 KLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHS   62 (540)
T ss_dssp             ----CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHHTCEEEEEESCHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhCCCcEEEEcCCHH
Confidence            468999999998775532 112689999999999998877666666789999999864

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=98.85  E-value=1.1e-10  Score=87.88  Aligned_cols=55  Identities=16%  Similarity=0.131  Sum_probs=45.9

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeec
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNS   62 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~   62 (67)
                      ..+.|||||.++++++++.. ..++++.++||+|||++++.++...     .+++||+||+
T Consensus       150 ~~~~LrpyQ~eav~~~l~~~-~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~~rvLIVvP~  209 (968)
T 3dmq_A          150 QRTSLIPHQLNIAHDVGRRH-APRVLLADEVGLGKTIEAGMILHQQLLSGAAERVLIIVPE  209 (968)
T ss_dssp             CSSCCCHHHHHHHHHHHHSS-SCEEEECCCTTSCHHHHHHHHHHHHHHTSSCCCEEEECCT
T ss_pred             CCCCCcHHHHHHHHHHHHhc-CCCEEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEeCH
Confidence            46889999999999988753 2578888999999999998877653     3489999998

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.84  E-value=9.9e-11  Score=83.18  Aligned_cols=57  Identities=23%  Similarity=0.300  Sum_probs=45.5

Q ss_pred             eeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      +++||+|.++++++.+. ..+++.++.+|||+|||..++..+...+.+++|++||...
T Consensus         2 ~~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~~~~v~i~~pt~~l   59 (551)
T 3crv_A            2 VKLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVKPKVLFVVRTHNE   59 (551)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHHCSEEEEEESSGGG
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhCCCeEEEEcCCHHH
Confidence            57999999988876542 1126899999999999999876666667899999999753

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=98.84  E-value=7.9e-11  Score=85.08  Aligned_cols=54  Identities=20%  Similarity=0.324  Sum_probs=44.1

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      .|+|+|.++++.++..+  ++.++++|||||||+++...+.+    .++++++++|+.++
T Consensus        30 ~l~~~Q~~~i~~~~~~~--~~~lv~apTGsGKT~~~~l~il~~~~~~~~~il~i~P~r~L   87 (715)
T 2va8_A           30 KLNPPQTEAVKKGLLEG--NRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRAL   87 (715)
T ss_dssp             BCCHHHHHHHHTTTTTT--CCEEEECCTTSCHHHHHHHHHHHHHHHSCSEEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHhcCC--CcEEEEcCCCCcHHHHHHHHHHHHHHHCCCeEEEEeCcHHH
Confidence            89999999999954443  79999999999999999655432    36799999999754

>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=98.84  E-value=3.7e-11  Score=86.85  Aligned_cols=53  Identities=23%  Similarity=0.372  Sum_probs=44.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .|+|+|+++++.++++   ++.++.+|||||||+++...+.+   .++++++++|+.++
T Consensus        25 ~l~~~Q~~~i~~i~~~---~~~lv~apTGsGKT~~~~l~il~~~~~~~~~l~i~P~r~L   80 (702)
T 2p6r_A           25 ELFPPQAEAVEKVFSG---KNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRAL   80 (702)
T ss_dssp             CCCCCCHHHHHHHTTC---SCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CCCHHHHHHHHHHhCC---CcEEEEcCCccHHHHHHHHHHHHHHHhCCcEEEEeCcHHH
Confidence            7999999999997764   68999999999999998655442   26799999999754

>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=98.82  E-value=9.8e-11  Score=84.85  Aligned_cols=53  Identities=19%  Similarity=0.382  Sum_probs=43.3

Q ss_pred             eeccchhhHHHH-HhcCCcceeeeEEEeCCCCceeEeeeeEE-E---EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRK-MFGNGRARSGVIVLPCGAGKSLVGVTACC-T---VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~-~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~---~~~~~lil~p~~~~   65 (67)
                      .|+|+|+++++. +.++   ++.++++|||||||+++...+. .   .+++++|++|+.++
T Consensus        23 ~l~~~Q~~~i~~~~~~~---~~~lv~apTGsGKT~~~~l~il~~~~~~~~~~l~i~P~raL   80 (720)
T 2zj8_A           23 SFYPPQAEALKSGILEG---KNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKAL   80 (720)
T ss_dssp             BCCHHHHHHHTTTGGGT---CEEEEECCGGGCHHHHHHHHHHHHHHHHCSEEEEECSSGGG
T ss_pred             CCCHHHHHHHHHHhcCC---CcEEEEcCCccHHHHHHHHHHHHHHHhCCCEEEEEcCcHHH
Confidence            799999999998 5553   7899999999999999854433 2   36799999999765

>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=98.79  E-value=1.6e-10  Score=88.34  Aligned_cols=59  Identities=19%  Similarity=0.214  Sum_probs=46.2

Q ss_pred             cceeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      ..+++||+|+++++.+++.   +...+.++++|||+|||.+++.++..   .+.+++|++||..+
T Consensus       600 f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g~~vlvlvPt~~L  664 (1151)
T 2eyq_A          600 FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLL  664 (1151)
T ss_dssp             CCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhCCeEEEEechHHH
Confidence            4567899999999998873   32248999999999999988644432   36799999999753

>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=98.79  E-value=1.5e-10  Score=76.94  Aligned_cols=55  Identities=22%  Similarity=0.173  Sum_probs=42.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-EE-----eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-TV-----RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~~-----~~~~lil~p~~~~   65 (67)
                      .++|+|++++..++++. +++.++.+|||||||.+++..+. ..     ..++||++||..+
T Consensus       114 ~pt~iQ~~ai~~il~~~-~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~~~~~lil~PtreL  174 (300)
T 3fmo_B          114 RPSKIQENALPLMLAEP-PQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYEL  174 (300)
T ss_dssp             SCCHHHHHHHHHHTSSS-CCCEEEECCTTSSHHHHHHHHHHHHCCTTSCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHHcCC-CCeEEEECCCCCCccHHHHHHHHHhhhccCCCceEEEEcCcHHH
Confidence            67889999999999752 26899999999999998753332 22     2379999999754

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.77  E-value=2e-10  Score=82.90  Aligned_cols=56  Identities=18%  Similarity=0.192  Sum_probs=47.2

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeecceee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNSGVVF   66 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~~~~v   66 (67)
                      ..|-+.|++|+..++...  .-.+|.+|+|+|||.+...++..+   +.++|+++||+.||
T Consensus       188 ~~LN~~Q~~AV~~al~~~--~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN~Av  246 (646)
T 4b3f_X          188 TCLDTSQKEAVLFALSQK--ELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSNIAV  246 (646)
T ss_dssp             TTCCHHHHHHHHHHHHCS--SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHH
T ss_pred             CCCCHHHHHHHHHHhcCC--CceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCchHHH
Confidence            357889999999998753  478999999999999988777653   67999999999886

>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=98.74  E-value=1.8e-10  Score=85.67  Aligned_cols=58  Identities=12%  Similarity=0.179  Sum_probs=46.9

Q ss_pred             ceeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~~~~   65 (67)
                      .+.|+|+|+++++++++.   +...+.++.+|||||||.+++..+...   +.+++|++||..+
T Consensus       366 pf~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g~qvlvlaPtr~L  429 (780)
T 1gm5_A          366 PFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSIL  429 (780)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHH
T ss_pred             CCCCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEEeCcHHH
Confidence            458999999999998863   223588999999999999997766543   6799999999653

>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=98.72  E-value=4.2e-10  Score=81.37  Aligned_cols=55  Identities=24%  Similarity=0.363  Sum_probs=43.0

Q ss_pred             eeeccchhhHHHHHhcC------CcceeeeEEEeCCCCceeEeeeeEEEE----------eeeeEEEeecc
Q psy11637          9 AVLRPYQEKSLRKMFGN------GRARSGVIVLPCGAGKSLVGVTACCTV----------RKRALVLCNSG   63 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~------~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~~lil~p~~   63 (67)
                      ..|||||+++++.++..      .....+++..+||+|||+++++++...          .+++|||+|+.
T Consensus        54 ~~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~~~~~~p~~~~~LiV~P~s  124 (644)
T 1z3i_X           54 KVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSS  124 (644)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHH
T ss_pred             hcccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHhCccccCCCCcEEEEecHH
Confidence            47999999999987531      123578899999999999998877542          24689999974

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.70  E-value=3.6e-10  Score=86.33  Aligned_cols=55  Identities=20%  Similarity=0.292  Sum_probs=45.5

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .++++|+|++++..++++   ++.++.+|||||||.+++.++..   .+.++||++||..+
T Consensus        76 gf~pt~iQ~~ai~~il~g---~dvlv~ApTGSGKTl~~l~~il~~~~~~~~~Lil~PtreL  133 (1104)
T 4ddu_A           76 GKDLTGYQRLWAKRIVQG---KSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTL  133 (1104)
T ss_dssp             SSCCCHHHHHHHHHHTTT---CCEEECCSTTCCHHHHHHHHHHHHHTTTCCEEEEESSHHH
T ss_pred             CCCCCHHHHHHHHHHHcC---CCEEEEeCCCCcHHHHHHHHHHHHHhcCCeEEEEechHHH
Confidence            457999999999999986   68999999999999966555443   36789999999754

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=98.70  E-value=4.1e-10  Score=81.60  Aligned_cols=56  Identities=16%  Similarity=0.287  Sum_probs=41.6

Q ss_pred             eeeccchhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~   64 (67)
                      +++||+|+++++++.+. ..+++.++.+|||+|||+.++..+..    .+.+++|++||..
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~kvli~t~T~~   62 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNS   62 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHTCEEEEEESSHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcCCeEEEECCCHH
Confidence            57899999999976543 12378999999999999988665443    2679999999864

>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=98.55  E-value=2.7e-09  Score=84.39  Aligned_cols=54  Identities=15%  Similarity=0.305  Sum_probs=44.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      .+.|.|.+++..++..+  ++.++.+|||||||+++..++.+     -++++++++|+.++
T Consensus       926 ~fnpiQ~q~~~~l~~~~--~nvlv~APTGSGKTliaelail~~l~~~~~~kavyi~P~raL  984 (1724)
T 4f92_B          926 FFNPIQTQVFNTVYNSD--DNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEAL  984 (1724)
T ss_dssp             BCCHHHHHHHHHHHSCC--SCEEEECCTTSCCHHHHHHHHHHHHHHCTTCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHhcCC--CcEEEEeCCCCCchHHHHHHHHHHHHhCCCCEEEEEcChHHH
Confidence            47788999999999865  68999999999999999665543     25689999999764

>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=98.53  E-value=3.3e-09  Score=83.95  Aligned_cols=54  Identities=19%  Similarity=0.234  Sum_probs=44.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE--------------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT--------------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~--------------~~~~~lil~p~~~~   65 (67)
                      .|.+.|.+++..+++.+  ++.++++|||||||+++...+.+              .+.++++++|+.++
T Consensus        79 ~ln~iQs~~~~~al~~~--~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kAL  146 (1724)
T 4f92_B           79 TLNRIQSKLYRAALETD--ENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSL  146 (1724)
T ss_dssp             BCCHHHHHTHHHHHTCC--CCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHHcCC--CcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHH
Confidence            57788999999988765  79999999999999998655432              14589999999765

>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=98.48  E-value=3.5e-09  Score=80.40  Aligned_cols=53  Identities=19%  Similarity=0.268  Sum_probs=41.8

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      +.+ |+|++++..++++   ++.++.+|||||||..++.++..   .+.++||++||..+
T Consensus        56 ~~p-~iQ~~ai~~il~g---~dvlv~apTGSGKTl~~lp~l~~~~~~~~~~lil~PtreL  111 (1054)
T 1gku_B           56 EPR-AIQKMWAKRILRK---ESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLL  111 (1054)
T ss_dssp             SCC-HHHHHHHHHHHTT---CCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHH
T ss_pred             CCH-HHHHHHHHHHHhC---CCEEEEcCCCCCHHHHHHHHHHHHhhcCCeEEEEeccHHH
Confidence            447 9999999999976   68999999999999743333332   25789999999754

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.38  E-value=1.4e-08  Score=73.24  Aligned_cols=55  Identities=20%  Similarity=0.220  Sum_probs=45.4

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecceee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVVF   66 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~v   66 (67)
                      ..|.+.|.+|++.++..   ...+|.+|+|+|||.+...++..    .+.++++++||+.|+
T Consensus       179 ~~ln~~Q~~av~~~l~~---~~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~tn~A~  237 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQR---PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAV  237 (624)
T ss_dssp             CCCCHHHHHHHHHHHTC---SEEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESSHHHH
T ss_pred             CCCCHHHHHHHHHHhcC---CCeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCcHHHH
Confidence            46788999999998875   57889999999999988766553    356899999998774

>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=98.36  E-value=1.8e-08  Score=64.30  Aligned_cols=54  Identities=13%  Similarity=0.064  Sum_probs=40.6

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE--------eeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV--------RKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~--------~~~~lil~p~~~   64 (67)
                      ...++++|++++..+.++   +..++.+|||||||+.+..++...        ..++++++|+..
T Consensus        59 ~~p~~~~q~~~i~~i~~g---~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~~~~~~~l~~~p~~~  120 (235)
T 3llm_A           59 LLPVKKFESEILEAISQN---SVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRI  120 (235)
T ss_dssp             TSGGGGGHHHHHHHHHHC---SEEEEECCTTSSHHHHHHHHHHHHHHHTTCGGGCEEEEEESSHH
T ss_pred             cCChHHHHHHHHHHHhcC---CEEEEEeCCCCCcHHhHHHHHhcchhhcCCCCceEEEEeccchH
Confidence            356789999999999876   688999999999997554333221        237888888864

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.32  E-value=2.3e-08  Score=74.43  Aligned_cols=55  Identities=25%  Similarity=0.328  Sum_probs=45.6

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecceee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVVF   66 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~v   66 (67)
                      ..|.+.|++|++.++..   ...+|.+|+|+|||.+...++..    .+.++|+++||+.|+
T Consensus       359 ~~Ln~~Q~~Av~~~l~~---~~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~tn~A~  417 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQR---PLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAV  417 (802)
T ss_dssp             CCCCHHHHHHHHHHTTC---SEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESSHHHH
T ss_pred             ccCCHHHHHHHHHHhcC---CCEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCcHHHH
Confidence            46788999999999875   57899999999999988776653    257999999998774

>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=98.23  E-value=1.4e-08  Score=74.75  Aligned_cols=53  Identities=19%  Similarity=0.066  Sum_probs=39.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      .++++|+++++.+.++   ++.++.+|||||||..+...+.+.+.+++|++|+..+
T Consensus       217 P~~~~q~~i~~~L~~~---~~vlv~ApTGSGKT~a~~l~ll~~g~~vLVl~PTReL  269 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSF---QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAA  269 (666)
T ss_dssp             CSCCCCCSCCCCCSSC---EEEEEECCTTSCTTTHHHHHHHHTTCCEEEEESCHHH
T ss_pred             CcHHHHHHHHHHHHcC---CeEEEEeCCchhHHHHHHHHHHHCCCeEEEEcchHHH
Confidence            4455666666655544   6899999999999987765555556689999999753

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=98.23  E-value=5.3e-08  Score=72.55  Aligned_cols=55  Identities=20%  Similarity=0.220  Sum_probs=45.4

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecceee
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVVF   66 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~v   66 (67)
                      ..|.+.|++|++.++..   ...+|.+|+|+|||.+...++..    .+.++++++||..|+
T Consensus       355 ~~Ln~~Q~~Av~~~l~~---~~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~tn~A~  413 (800)
T 2wjy_A          355 PDLNHSQVYAVKTVLQR---PLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAV  413 (800)
T ss_dssp             CCCCHHHHHHHHHHHTS---SEEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEESSHHHH
T ss_pred             cCCCHHHHHHHHHhccC---CeEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcCcHHHH
Confidence            46788999999998875   57889999999999988766554    357999999998764

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=98.10  E-value=5.3e-08  Score=71.37  Aligned_cols=56  Identities=21%  Similarity=0.232  Sum_probs=37.6

Q ss_pred             eeccchh-----hHHHHHhc---CCcceeeeEEEeCCCCceeEeeeeEE-E---EeeeeEEEeeccee
Q psy11637         10 VLRPYQE-----KSLRKMFG---NGRARSGVIVLPCGAGKSLVGVTACC-T---VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~-----~av~~~~~---~~~~~~~~i~~pTGsGKT~i~~~~~~-~---~~~~~lil~p~~~~   65 (67)
                      .++|-|+     +++..++.   -..+++.++.+|||||||++++..+. .   .+.+++|++||..+
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~~lilaPTr~L  282 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLRTAVLAPTRVV  282 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCcEEEEccHHHH
Confidence            5777788     88877661   01127899999999999999743332 2   24689999999753

>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=98.09  E-value=2.5e-07  Score=67.40  Aligned_cols=63  Identities=17%  Similarity=0.222  Sum_probs=51.5

Q ss_pred             ccccccceeeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          2 TIDLKPSAVLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         2 ~~~l~~~~~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      +|+|...++++.+|.++++++.+.  ...+..++.+.||||||++++.++...++++|||+|+..
T Consensus         4 ~~~~~~~~~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~~~~~~~~~~lvv~~~~~   68 (661)
T 2d7d_A            4 RFELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSNLIKEVNKPTLVIAHNKT   68 (661)
T ss_dssp             CCCCCCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHCCCEEEECSSHH
T ss_pred             cceeecCCCCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHHHHHHhCCCEEEEECCHH
Confidence            578888999999999999987653  111346788999999999999888777889999999853

>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=98.07  E-value=1.1e-07  Score=65.98  Aligned_cols=52  Identities=29%  Similarity=0.296  Sum_probs=36.2

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeE-EE---EeeeeEEEeeccee
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC-CT---VRKRALVLCNSGVV   65 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~-~~---~~~~~lil~p~~~~   65 (67)
                      ..|-|+ ++..+++.+  +..++.+|||||||.+++..+ ..   .+.+++|++||..+
T Consensus         5 ~~~iq~-~i~~~l~~~--~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~lvl~Ptr~L   60 (451)
T 2jlq_A            5 GEPDYE-VDEDIFRKK--RLTIMDLHPGAGKTKRILPSIVREALLRRLRTLILAPTRVV   60 (451)
T ss_dssp             CSCCCC-CCGGGGSTT--CEEEECCCTTSSCCTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CCCcHH-HHHHHHhcC--CeEEEECCCCCCHhhHHHHHHHHHHHhcCCcEEEECCCHHH
Confidence            344554 677777764  466888999999999754333 22   35689999999753

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=98.04  E-value=1.5e-07  Score=65.07  Aligned_cols=37  Identities=30%  Similarity=0.320  Sum_probs=29.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE----EEeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC----TVRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~----~~~~~~lil~p~~~~   65 (67)
                      ++.++.+|||||||.+++..+.    ..+.+++|++||..+
T Consensus         3 ~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~~lvl~Pt~~L   43 (431)
T 2v6i_A            3 ELTVLDLHPGAGKTRRVLPQLVREAVKKRLRTVILAPTRVV   43 (431)
T ss_dssp             CEEEEECCTTSCTTTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEECcHHHH
Confidence            6889999999999999844332    235689999999753

>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=98.03  E-value=1.3e-07  Score=65.93  Aligned_cols=44  Identities=27%  Similarity=0.280  Sum_probs=31.8

Q ss_pred             HHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E---EeeeeEEEeeccee
Q psy11637         20 RKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T---VRKRALVLCNSGVV   65 (67)
Q Consensus        20 ~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~---~~~~~lil~p~~~~   65 (67)
                      .+++..+  ++.++.+|||||||.+++..+. .   .+.++||++|+..+
T Consensus        15 ~~~l~~~--~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~~lvl~Ptr~L   62 (459)
T 2z83_A           15 PNMLRKR--QMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLAPTRVV   62 (459)
T ss_dssp             CGGGSTT--CEEEECCCTTSCTTTTHHHHHHHHHHHTTCCEEEEECSHHH
T ss_pred             HHHHhcC--CcEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEECchHHH
Confidence            3345443  6899999999999999644332 2   35689999999753

>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=97.94  E-value=1.6e-07  Score=65.13  Aligned_cols=37  Identities=32%  Similarity=0.313  Sum_probs=28.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      ++.++.+|||||||.+++..+..    .+.+++|++||..+
T Consensus         9 ~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~~~lil~Ptr~L   49 (440)
T 1yks_A            9 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVV   49 (440)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHHHHhcCCeEEEEcchHHH
Confidence            78999999999999997443322    24589999999754

>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=97.91  E-value=1.9e-07  Score=67.75  Aligned_cols=48  Identities=27%  Similarity=0.224  Sum_probs=33.6

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeee-eEEE---EeeeeEEEeeccee
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVT-ACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~-~~~~---~~~~~lil~p~~~~   65 (67)
                      |+.++..++++   ++.++.+|||||||.+++. ++.+   .+.++||++||..+
T Consensus       176 q~~~i~~l~~g---~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~vLvl~PtreL  227 (618)
T 2whx_A          176 YEVDEDIFRKK---RLTIMDLHPGAGKTKRILPSIVREALKRRLRTLILAPTRVV  227 (618)
T ss_dssp             CCCCGGGGSTT---CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             cccCHHHHhcC---CeEEEEcCCCCCHHHHHHHHHHHHHHhCCCeEEEEcChHHH
Confidence            33344444444   7899999999999998633 3332   25689999999753

>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=97.91  E-value=3.5e-07  Score=65.91  Aligned_cols=55  Identities=20%  Similarity=0.132  Sum_probs=44.6

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .+.|-+.|+++++.++..   +..+|.+|+|+|||+++..++..   .+.++++++||..|
T Consensus       187 ~~~L~~~Q~~Av~~~~~~---~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~A  244 (574)
T 3e1s_A          187 RKGLSEEQASVLDQLAGH---RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKA  244 (574)
T ss_dssp             TTTCCHHHHHHHHHHTTC---SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             cCCCCHHHHHHHHHHHhC---CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHH
Confidence            345778999999999875   68899999999999988766654   36789999998654

>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=97.86  E-value=6.2e-07  Score=65.37  Aligned_cols=57  Identities=18%  Similarity=0.186  Sum_probs=46.2

Q ss_pred             ceeeccchhhHHHHHhcCC-c-ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNG-R-ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~-~-~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~   64 (67)
                      .+++++.|.++++++.+.- . .+..++.+.||||||++++.++...++++|||+|+..
T Consensus         6 ~~~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~~~~~~~~~~lvv~~~~~   64 (664)
T 1c4o_A            6 GPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNKI   64 (664)
T ss_dssp             SCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSHH
T ss_pred             CCCCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHHHHHHhCCCEEEEecCHH
Confidence            4589999999999877531 1 1246788999999999999888877889999999863

>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=97.77  E-value=8.3e-07  Score=64.08  Aligned_cols=50  Identities=20%  Similarity=0.169  Sum_probs=38.9

Q ss_pred             cchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeeccee
Q psy11637         13 PYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVV   65 (67)
Q Consensus        13 ~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~   65 (67)
                      +.|++|+..++.+   +..++.+|+|+|||++...++..       .+.++++++||..|
T Consensus       152 ~~Q~~Ai~~~l~~---~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~~~~~vll~APTg~A  208 (608)
T 1w36_D          152 NWQKVAAAVALTR---RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKA  208 (608)
T ss_dssp             CHHHHHHHHHHTB---SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHH
T ss_pred             HHHHHHHHHHhcC---CCEEEEeCCCCCHHHHHHHHHHHHHHhhhcCCCeEEEEeCChhH
Confidence            5699999998865   68899999999999877554432       23489999998754

>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=97.75  E-value=7.3e-07  Score=61.99  Aligned_cols=56  Identities=11%  Similarity=0.102  Sum_probs=41.6

Q ss_pred             eeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEE---e-eeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTV---R-KRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~---~-~~~lil~p~~~~   65 (67)
                      .|-+.|+++++.++..  ...+..+|.+|+|+|||+++..++..+   + .++++++||..|
T Consensus        25 ~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~T~~A   86 (459)
T 3upu_A           25 DLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAPTHAA   86 (459)
T ss_dssp             CCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEESSHHH
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecCcHHH
Confidence            4666899999986542  111488999999999999887766553   2 378999998654

>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=97.69  E-value=1.5e-06  Score=64.47  Aligned_cols=52  Identities=17%  Similarity=0.077  Sum_probs=36.2

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----E--eeeeEEEeeccee
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----V--RKRALVLCNSGVV   65 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~--~~~~lil~p~~~~   65 (67)
                      -+.|++++..++..+  ++.++++|||||||+..-.++..    .  +.++++++|+..+
T Consensus        95 ~~~q~~~i~~~l~~~--~~vii~gpTGSGKTtllp~ll~~~~~~~~~g~~ilvl~P~r~L  152 (773)
T 2xau_A           95 VHAQRDEFLKLYQNN--QIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVA  152 (773)
T ss_dssp             GGGGHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHHHCGGGGTCEEEEEESCHHH
T ss_pred             hHHHHHHHHHHHhCC--CeEEEECCCCCCHHHHHHHHHHHhccccCCCceEEecCchHHH
Confidence            346888888877654  57899999999999943222221    1  3468999998654

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=97.68  E-value=2.1e-06  Score=63.11  Aligned_cols=36  Identities=11%  Similarity=0.093  Sum_probs=26.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ++.++++|||||||..++..+.. .+..+|++|+..+
T Consensus       156 k~vlv~apTGSGKT~~al~~l~~-~~~gl~l~PtR~L  191 (677)
T 3rc3_A          156 KIIFHSGPTNSGKTYHAIQKYFS-AKSGVYCGPLKLL  191 (677)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH-SSSEEEEESSHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHh-cCCeEEEeCHHHH
Confidence            67899999999999954433322 2455999999754

>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=97.47  E-value=3.9e-06  Score=59.55  Aligned_cols=51  Identities=14%  Similarity=0.128  Sum_probs=38.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE-------eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV-------RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~-------~~~~lil~p~~~~   65 (67)
                      .|-+.|++++..   .  ++..+|.+++|||||.+...-+..+       ..++|++++|+.|
T Consensus         9 ~Ln~~Q~~av~~---~--~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~~~~~iL~ltft~~a   66 (647)
T 3lfu_A            9 SLNDKQREAVAA---P--RSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKA   66 (647)
T ss_dssp             TCCHHHHHHHTC---C--SSCEEEEECTTSCHHHHHHHHHHHHHHTSCCCGGGEEEEESSHHH
T ss_pred             cCCHHHHHHHhC---C--CCCEEEEECCCCCHHHHHHHHHHHHHHhCCCChhhEEEEeccHHH
Confidence            577889999972   1  2578999999999999886544321       2589999998764

>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=97.24  E-value=2e-05  Score=59.58  Aligned_cols=50  Identities=14%  Similarity=0.080  Sum_probs=37.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .+.|-|..++-.++++    + +..|+||+|||.+++..+..   .+..++|++||..
T Consensus        83 ~pt~VQ~~~ip~ll~G----~-Iaea~TGeGKTlaf~LP~~l~aL~g~~vlVltptre  135 (844)
T 1tf5_A           83 FPFKVQLMGGVALHDG----N-IAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEY  135 (844)
T ss_dssp             CCCHHHHHHHHHHHTT----S-EEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSHH
T ss_pred             CCcHHHHHhhHHHhCC----C-EEEccCCcHHHHHHHHHHHHHHHcCCCEEEEeCCHH
Confidence            4445588888877764    3 88999999999998765542   3568999999864

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.13  E-value=0.0001  Score=43.56  Aligned_cols=40  Identities=13%  Similarity=0.111  Sum_probs=26.7

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+.+.+.+.+++..+.....++.+|+|+|||.++..++..
T Consensus        27 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           27 RDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHH
Confidence            3334444444554443467899999999999988666554

>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=97.08  E-value=3.2e-05  Score=58.56  Aligned_cols=50  Identities=14%  Similarity=0.032  Sum_probs=37.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .+.|-|..++-.++.+    + +..|+||+|||.+++..+..   .+..++|++||..
T Consensus        74 ~p~~VQ~~~i~~ll~G----~-Iaem~TGsGKTlaf~LP~l~~~l~g~~vlVltPTre  126 (853)
T 2fsf_A           74 RHFDVQLLGGMVLNER----C-IAEMRTGEGKTLTATLPAYLNALTGKGVHVVTVNDY  126 (853)
T ss_dssp             CCCHHHHHHHHHHHSS----E-EEECCTTSCHHHHHHHHHHHHHTTSSCCEEEESSHH
T ss_pred             CCChHHHhhcccccCC----e-eeeecCCchHHHHHHHHHHHHHHcCCcEEEEcCCHH
Confidence            3444588888777764    3 88899999999988755432   3568999999964

>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=97.06  E-value=3.8e-05  Score=58.52  Aligned_cols=49  Identities=18%  Similarity=0.244  Sum_probs=36.2

Q ss_pred             eccc--hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637         11 LRPY--QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus        11 lR~y--Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      +|||  |..++-.++.+    + +..|+||+|||++++..+..   .+..++|++||..
T Consensus       110 ~rP~~VQ~~~ip~Ll~G----~-Iaem~TGeGKTLa~~LP~~l~aL~g~~v~VvTpTre  163 (922)
T 1nkt_A          110 QRPFDVQVMGAAALHLG----N-VAEMKTGEGKTLTCVLPAYLNALAGNGVHIVTVNDY  163 (922)
T ss_dssp             CCCCHHHHHHHHHHHTT----E-EEECCTTSCHHHHTHHHHHHHHTTTSCEEEEESSHH
T ss_pred             CCCCHHHHHHHHhHhcC----C-EEEecCCCccHHHHHHHHHHHHHhCCCeEEEeCCHH
Confidence            3554  77777766653    3 88999999999998755532   3668999999864

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.94  E-value=0.00012  Score=43.35  Aligned_cols=37  Identities=8%  Similarity=0.128  Sum_probs=24.8

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+.+.+++......+.++.+|+|+|||.++..++..
T Consensus        30 ~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           30 EIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             HHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHH
Confidence            3333444444433467889999999999988666554

>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=96.75  E-value=0.00025  Score=42.75  Aligned_cols=39  Identities=13%  Similarity=0.118  Sum_probs=26.2

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+...+.+.++++.+...+.++.+|+|+|||.++..++.
T Consensus        22 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~   60 (226)
T 2chg_A           22 QDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALAR   60 (226)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            334445555666554334588999999999998765544

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=96.59  E-value=5.2e-05  Score=54.65  Aligned_cols=51  Identities=14%  Similarity=0.188  Sum_probs=37.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~   65 (67)
                      .|-|.|+++++..  .   +..+|.++.|||||.+...-+..       ...++|+++.|+.|
T Consensus         2 ~L~~~Q~~av~~~--~---~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~~~~~IL~lTfT~~A   59 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--T---GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKA   59 (673)
T ss_dssp             CCCHHHHHHHHCC--S---SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHH
T ss_pred             CCCHHHHHHHhCC--C---CCEEEEeCCCCChHHHHHHHHHHHHHhcCCCHHHeEEEeccHHH
Confidence            4778899999852  2   57889999999999888653322       13578999888654

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.57  E-value=0.00071  Score=39.95  Aligned_cols=23  Identities=9%  Similarity=-0.125  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.++.+|+|+|||.++-.+...
T Consensus        28 ~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A           28 SPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             SCEEEEEETTCCHHHHHGGGCCT
T ss_pred             CcEEEECCCCccHHHHHHHHHHh
Confidence            67889999999999988665543

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=96.52  E-value=9.8e-05  Score=56.66  Aligned_cols=50  Identities=18%  Similarity=0.119  Sum_probs=37.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE---EEeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC---TVRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~---~~~~~~lil~p~~~   64 (67)
                      .+.|-|..++-.++.+   +  +..|.||+|||++++..+.   ..+..++|++||..
T Consensus        79 ~Pt~VQ~~~ip~LlqG---~--IaeakTGeGKTLvf~Lp~~L~aL~G~qv~VvTPTre  131 (997)
T 2ipc_A           79 RHFDVQLIGGAVLHEG---K--IAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDY  131 (997)
T ss_dssp             CCCHHHHHHHHHHHTT---S--EEECCSTHHHHHHHHHHHHHHHTTCSCCEEEESSHH
T ss_pred             CCcHHHHhhcccccCC---c--eeeccCCCchHHHHHHHHHHHHHhCCCEEEEeCCHH
Confidence            3445588888877764   3  7889999999998866553   23568999999964

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=96.47  E-value=0.00014  Score=46.71  Aligned_cols=32  Identities=13%  Similarity=0.045  Sum_probs=24.1

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ....++.+|+|+|||.++-+++...+.+.+.+
T Consensus        64 ~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i   95 (272)
T 1d2n_A           64 LVSVLLEGPPHSGKTALAAKIAEESNFPFIKI   95 (272)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHHTCSEEEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHhCCCEEEE
Confidence            46788899999999999877766555554443

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.44  E-value=0.00041  Score=41.93  Aligned_cols=39  Identities=21%  Similarity=0.196  Sum_probs=26.6

Q ss_pred             cchhhHHHHHh---cC---CcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         13 PYQEKSLRKMF---GN---GRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        13 ~yQ~~av~~~~---~~---~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.|+++++...   +.   ..+...++.+|+|+|||+++..++..
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~   61 (180)
T 3ec2_A           17 VSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKA   61 (180)
T ss_dssp             HHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            35777776643   22   12356778899999999988665543

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.42  E-value=0.00062  Score=41.84  Aligned_cols=36  Identities=11%  Similarity=0.183  Sum_probs=24.2

Q ss_pred             hhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         16 EKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        16 ~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +++++.   +.........++.+|+|+|||.++..++..
T Consensus        37 ~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~   75 (242)
T 3bos_A           37 DELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACAR   75 (242)
T ss_dssp             HHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            444443   443323467889999999999988666544

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.40  E-value=0.00016  Score=46.38  Aligned_cols=32  Identities=16%  Similarity=0.274  Sum_probs=23.8

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ....++.+|+|+|||.++-+++...+.+.+.+
T Consensus        51 ~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v   82 (285)
T 3h4m_A           51 PKGILLYGPPGTGKTLLAKAVATETNATFIRV   82 (285)
T ss_dssp             CSEEEEESSSSSSHHHHHHHHHHHTTCEEEEE
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhCCCEEEE
Confidence            35688899999999999877766555554443

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.38  E-value=0.00024  Score=46.50  Aligned_cols=41  Identities=17%  Similarity=0.174  Sum_probs=28.4

Q ss_pred             ccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+.+.+.+.+++.    .+.....+|.+|+|+|||.++-.++...
T Consensus        25 r~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~   69 (386)
T 2qby_A           25 REDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKL   69 (386)
T ss_dssp             CHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            5556666666554    2234678889999999999887666543

>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=96.34  E-value=0.00013  Score=48.88  Aligned_cols=29  Identities=21%  Similarity=0.273  Sum_probs=22.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      .+.++.+|+|+|||.++-+++...+.+.+
T Consensus        52 ~~vll~GppGtGKT~la~~ia~~~~~~~~   80 (363)
T 3hws_A           52 SNILLIGPTGSGKTLLAETLARLLDVPFT   80 (363)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            57889999999999998777665554444

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.30  E-value=0.00074  Score=39.89  Aligned_cols=23  Identities=9%  Similarity=-0.181  Sum_probs=19.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.++.+|+|+|||.++-.+...
T Consensus        25 ~~vll~G~~GtGKt~lA~~i~~~   47 (145)
T 3n70_A           25 IAVWLYGAPGTGRMTGARYLHQF   47 (145)
T ss_dssp             SCEEEESSTTSSHHHHHHHHHHS
T ss_pred             CCEEEECCCCCCHHHHHHHHHHh
Confidence            67899999999999998666544

>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=96.27  E-value=0.00035  Score=42.89  Aligned_cols=44  Identities=18%  Similarity=0.236  Sum_probs=30.5

Q ss_pred             hHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         17 KSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      ..+++++..  ..+...+|.+|+|+|||+.+..++...+++++++.
T Consensus         7 ~~LD~~l~Ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~   52 (220)
T 2cvh_A            7 KSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVD   52 (220)
T ss_dssp             HHHHHHTTSSBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEE
T ss_pred             HHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEE
Confidence            456777753  22357888999999999998766653345666654

>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=96.26  E-value=0.00017  Score=52.72  Aligned_cols=51  Identities=18%  Similarity=0.154  Sum_probs=37.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~   65 (67)
                      .|-|.|++|+..   .+  +..+|.++.|||||.+...-+..       ...++|+++.|+.|
T Consensus        11 ~Ln~~Q~~av~~---~~--g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~~p~~IL~vTFTnkA   68 (724)
T 1pjr_A           11 HLNKEQQEAVRT---TE--GPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKA   68 (724)
T ss_dssp             TSCHHHHHHHHC---CS--SCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHH
T ss_pred             hCCHHHHHHHhC---CC--CCEEEEEcCCCCHHHHHHHHHHHHHHhcCCCHHHeEEEeccHHH
Confidence            578899999975   12  57889999999999987653322       13578999888654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.24  E-value=0.00035  Score=43.46  Aligned_cols=43  Identities=9%  Similarity=0.195  Sum_probs=29.7

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .+++++..+  .+...+|.+|+|+|||..++.++..   .+++++++.
T Consensus        11 ~LD~~l~gGl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~   58 (247)
T 2dr3_A           11 GVDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA   58 (247)
T ss_dssp             THHHHTTTSEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             hHHHHcCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            456666532  2356788999999999998766543   245777664

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=96.22  E-value=0.00047  Score=45.56  Aligned_cols=41  Identities=17%  Similarity=0.108  Sum_probs=26.8

Q ss_pred             ccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+.+.+.+.+++.    .+..+..+|.+|+|+|||.++..++...
T Consensus        25 r~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~   69 (384)
T 2qby_B           25 REDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEI   69 (384)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHH
Confidence            4444444444442    3334578899999999999987666543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=96.21  E-value=0.00025  Score=46.54  Aligned_cols=41  Identities=15%  Similarity=0.230  Sum_probs=28.1

Q ss_pred             ccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+.+.+.+..++.    .+.....+|.+|+|+|||.++-.+....
T Consensus        24 r~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~   68 (387)
T 2v1u_A           24 REAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRL   68 (387)
T ss_dssp             CHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHH
Confidence            4455555655553    2234678888999999999987766554

>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=96.21  E-value=0.0016  Score=45.40  Aligned_cols=39  Identities=15%  Similarity=0.210  Sum_probs=27.3

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +.+.+.+.++.++.. .++..+|.+|||||||++..+++.
T Consensus       151 ~~~~~~~~L~~l~~~-~ggii~I~GpnGSGKTTlL~allg  189 (418)
T 1p9r_A          151 MTAHNHDNFRRLIKR-PHGIILVTGPTGSGKSTTLYAGLQ  189 (418)
T ss_dssp             CCHHHHHHHHHHHTS-SSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh-cCCeEEEECCCCCCHHHHHHHHHh
Confidence            344566677777642 235678899999999998765544

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=96.14  E-value=0.00011  Score=47.82  Aligned_cols=42  Identities=17%  Similarity=0.301  Sum_probs=27.6

Q ss_pred             HHHHhcCC-cceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         19 LRKMFGNG-RARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        19 v~~~~~~~-~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      ++.|++.- +....++.+|+|+|||..+.+++..+.++++-++
T Consensus        48 l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~fa   90 (212)
T 1tue_A           48 LKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFV   90 (212)
T ss_dssp             HHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCC
T ss_pred             HHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeEE
Confidence            44555542 2234777899999999998887766555544333

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.05  E-value=0.00024  Score=48.81  Aligned_cols=27  Identities=19%  Similarity=0.233  Sum_probs=21.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ...+|++|||+|||.++..++.+++..
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~e   67 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLE   67 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCc
Confidence            357788999999999998887766543

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.02  E-value=0.00065  Score=46.03  Aligned_cols=41  Identities=5%  Similarity=-0.210  Sum_probs=29.3

Q ss_pred             ccchhhHHHHHhc----CCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFG----NGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~----~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+-|.+.+..++.    .+...+.+|.+|+|+|||.++-.++..+
T Consensus        25 Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L   69 (318)
T 3te6_A           25 QVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDEL   69 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            5556666665443    3445788899999999999887766554

>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=95.98  E-value=0.00095  Score=40.40  Aligned_cols=39  Identities=15%  Similarity=0.105  Sum_probs=24.7

Q ss_pred             ccchhhHHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         12 RPYQEKSLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+...+.+.+++..+. ....+|.+|+|+|||.++..++.
T Consensus        28 ~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~   67 (250)
T 1njg_A           28 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAK   67 (250)
T ss_dssp             CHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3334445555555432 23578899999999988755543

>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=95.94  E-value=0.0017  Score=42.34  Aligned_cols=35  Identities=17%  Similarity=0.161  Sum_probs=23.6

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+..++..+...+.++.+|+|+|||.++-.++..
T Consensus        47 ~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~   81 (353)
T 1sxj_D           47 TVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKE   81 (353)
T ss_dssp             HHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            33444555443245888999999999988665544

>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=95.91  E-value=0.00035  Score=44.86  Aligned_cols=31  Identities=13%  Similarity=0.224  Sum_probs=23.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .+.++.+|+|+|||.++-.++...+.+.+.+
T Consensus        51 ~~vll~G~~GtGKT~la~~la~~l~~~~~~i   81 (310)
T 1ofh_A           51 KNILMIGPTGVGKTEIARRLAKLANAPFIKV   81 (310)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEEE
Confidence            5788999999999999876665555444433

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=95.90  E-value=0.00032  Score=46.12  Aligned_cols=31  Identities=16%  Similarity=-0.018  Sum_probs=23.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ...++.+|+|+|||.++-+++...+.+++.+
T Consensus        37 ~~lLl~GppGtGKT~la~aiA~~l~~~~i~v   67 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQCELVFRKMGINPIMM   67 (293)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCCEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEE
Confidence            4566779999999999987776665555544

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=95.84  E-value=0.00031  Score=44.30  Aligned_cols=31  Identities=19%  Similarity=0.402  Sum_probs=22.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ...++.+|+|+|||.++-+++...+.+.+.+
T Consensus        40 ~~vll~G~~GtGKT~la~~la~~~~~~~~~~   70 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLAKAVATEAQVPFLAM   70 (262)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEEe
Confidence            4578899999999999877666555444443

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.83  E-value=0.00043  Score=48.78  Aligned_cols=34  Identities=21%  Similarity=0.354  Sum_probs=26.1

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN   61 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p   61 (67)
                      .+..++.+|+|+|||.++-+++.+.+.+++.+..
T Consensus       215 prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~  248 (434)
T 4b4t_M          215 PKGALMYGPPGTGKTLLARACAAQTNATFLKLAA  248 (434)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEG
T ss_pred             CCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEeh
Confidence            4567888999999999998877776666555543

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.77  E-value=0.00057  Score=44.85  Aligned_cols=29  Identities=14%  Similarity=0.146  Sum_probs=22.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      .+.++.+|+|+|||.++-.+....+.+.+
T Consensus        56 ~~vll~G~~GtGKT~la~~ia~~~~~~~~   84 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLANIISYEMSANIK   84 (338)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHTTCCEE
T ss_pred             CeEEEECcCCCCHHHHHHHHHHHhCCCeE
Confidence            57889999999999998777655544433

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=95.77  E-value=0.002  Score=44.94  Aligned_cols=32  Identities=13%  Similarity=0.176  Sum_probs=23.1

Q ss_pred             HHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         20 RKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        20 ~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++......+.++.+|+|+|||.++-.++..
T Consensus       193 ~~~l~r~~~~~~LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          193 IEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             HHHHHCSSSCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             HHHHhccCCCCeEEECCCCCCHHHHHHHHHHH
Confidence            33444433468899999999999988666544

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.77  E-value=0.0024  Score=41.17  Aligned_cols=24  Identities=17%  Similarity=0.099  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.++.+|+|+|||.++-.++...
T Consensus        68 ~~vll~G~~GtGKT~la~~la~~l   91 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVALKMAGLL   91 (309)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHH
Confidence            468899999999999986655443

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.72  E-value=0.00071  Score=47.68  Aligned_cols=31  Identities=19%  Similarity=0.206  Sum_probs=23.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      +..++.+|+|+|||.++-.++...+.+++.+
T Consensus        78 ~~lLL~GppGtGKTtla~~la~~l~~~~i~i  108 (516)
T 1sxj_A           78 RAAMLYGPPGIGKTTAAHLVAQELGYDILEQ  108 (516)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHTTCEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCCEEEE
Confidence            5688889999999999877766655555444

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.71  E-value=0.00052  Score=48.42  Aligned_cols=34  Identities=18%  Similarity=0.277  Sum_probs=26.0

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN   61 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p   61 (67)
                      .+..++.+|+|+|||.++-+++.+.+.+++.+..
T Consensus       215 prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~  248 (437)
T 4b4t_L          215 PKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPA  248 (437)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEG
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEeh
Confidence            3567888999999999998887776666555543

>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=95.68  E-value=0.00098  Score=41.40  Aligned_cols=34  Identities=21%  Similarity=0.232  Sum_probs=25.3

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..+++++..+  .+....|.+|+|+|||.++..++.
T Consensus        11 ~~LD~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           11 KELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             hHHHHhhcCCCcCCeEEEEECCCCCcHHHHHHHHHH
Confidence            4567777542  235788899999999999876655

>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=95.68  E-value=0.0016  Score=41.97  Aligned_cols=37  Identities=19%  Similarity=0.267  Sum_probs=24.4

Q ss_pred             hhhHHH---HHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLR---KMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~---~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |++.++   ++++.+...+.++.+|+|+|||.++-.++..
T Consensus        30 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~   69 (327)
T 1iqp_A           30 QEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARE   69 (327)
T ss_dssp             CHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            444444   4554433235888999999999988665543

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=95.63  E-value=0.0028  Score=42.13  Aligned_cols=41  Identities=17%  Similarity=0.213  Sum_probs=30.2

Q ss_pred             eccchhhHHHHHhc---CCc-ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         11 LRPYQEKSLRKMFG---NGR-ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        11 lR~yQ~~av~~~~~---~~~-~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.|+|+++++.+.+   .+. .+.-++.+|+|+|||.++..++..
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~   47 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRY   47 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHH
Confidence            57999999877553   332 345788999999999988666543

>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=95.62  E-value=0.00078  Score=43.70  Aligned_cols=29  Identities=14%  Similarity=0.124  Sum_probs=22.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ...++.+|+|+|||.++-.+....+.+.+
T Consensus        39 ~~vll~G~~GtGKT~la~~i~~~~~~~~~   67 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLAHVIAHELGVNLR   67 (324)
T ss_dssp             CCCEEECCTTCCCHHHHHHHHHHHTCCEE
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            57889999999999998776655444443

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.62  E-value=0.00058  Score=48.00  Aligned_cols=34  Identities=15%  Similarity=0.250  Sum_probs=25.6

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN   61 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p   61 (67)
                      .+..++.+|+|+|||.++-+++...+.+++.+..
T Consensus       206 prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~  239 (428)
T 4b4t_K          206 PRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNG  239 (428)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEG
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            3557888999999999998887766666555443

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=95.61  E-value=0.00068  Score=52.32  Aligned_cols=54  Identities=19%  Similarity=0.182  Sum_probs=38.3

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeee-eEE---E-----EeeeeEEEeeccee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVT-ACC---T-----VRKRALVLCNSGVV   65 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~-~~~---~-----~~~~~lil~p~~~~   65 (67)
                      ....|-|-|++++..-   +  ++.+|.+..|||||.+... ++.   .     -..++|+++.|+.|
T Consensus         7 ~~~~~t~eQ~~~i~~~---~--~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~~~~~~il~~Tft~~a   69 (1232)
T 3u4q_A            7 ADSTWTDDQWNAIVST---G--QDILVAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNAS   69 (1232)
T ss_dssp             ---CCCHHHHHHHHCC---S--SCEEEEECTTCCHHHHHHHHHHHHHSCSSSCCCGGGEEEECSSHHH
T ss_pred             CCCCCCHHHHHHHhCC---C--CCEEEEecCCCcHHHHHHHHHHHHHhcCCCCCCccceEEEeccHHH
Confidence            3567888899998753   2  6889999999999998653 222   2     12578999998765

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=95.60  E-value=0.0018  Score=41.49  Aligned_cols=37  Identities=14%  Similarity=0.231  Sum_probs=24.3

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+.++.   +++.+...+.++.+|+|+|||.++..++..
T Consensus        22 ~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~   61 (319)
T 2chq_A           22 QDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARD   61 (319)
T ss_dssp             CHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHH
Confidence            5555544   444433235889999999999888655443

>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=95.59  E-value=0.0013  Score=43.73  Aligned_cols=45  Identities=16%  Similarity=0.225  Sum_probs=31.6

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEE---------eeeeEEEee
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTV---------RKRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---------~~~~lil~p   61 (67)
                      ..+++++..+  .+...+|.+|+|+|||.+++.++...         +++++++.-
T Consensus        94 ~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~  149 (324)
T 2z43_A           94 QALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDT  149 (324)
T ss_dssp             HHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEES
T ss_pred             hhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEEC
Confidence            4567777532  23567889999999999998776542         457777753

>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=95.59  E-value=0.00043  Score=41.44  Aligned_cols=26  Identities=19%  Similarity=0.040  Sum_probs=19.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      ...++++++|||||+++-.+...++.
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~~   29 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLPE   29 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCC
Confidence            35678899999999998766655443

>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=95.59  E-value=0.0018  Score=42.58  Aligned_cols=41  Identities=20%  Similarity=0.173  Sum_probs=26.7

Q ss_pred             ccchhhHHHHHhcC----Ccce--eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         12 RPYQEKSLRKMFGN----GRAR--SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        12 R~yQ~~av~~~~~~----~~~~--~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+.+.+.+.+++..    ..+.  ..+|.+|+|+|||.++-.+....
T Consensus        22 r~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~   68 (389)
T 1fnn_A           22 REQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY   68 (389)
T ss_dssp             CHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHH
Confidence            44455555555532    2224  68899999999999886665543

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.59  E-value=0.00061  Score=42.35  Aligned_cols=44  Identities=9%  Similarity=0.197  Sum_probs=30.6

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~   60 (67)
                      ..+|+.+.+|  .+...+|.+++|+|||..++.++..    .+++++++.
T Consensus        17 ~~LD~~l~GGl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s   66 (251)
T 2zts_A           17 PGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVT   66 (251)
T ss_dssp             TTTGGGTTTSEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             HHHHHhhcCCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeec
Confidence            3456777643  2456888899999999998876543    245677664

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.57  E-value=0.0026  Score=40.85  Aligned_cols=37  Identities=16%  Similarity=0.098  Sum_probs=24.7

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+.+.++++.+...+.++.+|+|+|||.++..++..
T Consensus        29 ~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~   65 (323)
T 1sxj_B           29 TIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHE   65 (323)
T ss_dssp             HHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHH
Confidence            3444455665543234889999999999887665544

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.54  E-value=0.00039  Score=41.97  Aligned_cols=24  Identities=25%  Similarity=0.221  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|||||+++-.++..+
T Consensus         6 ~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            6 TNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            467789999999999987665543

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=95.54  E-value=0.00039  Score=44.95  Aligned_cols=22  Identities=18%  Similarity=0.226  Sum_probs=17.5

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|.+|+|||||+++..++...
T Consensus         4 i~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            4 HLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHhcC
Confidence            4678999999999987765543

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=95.53  E-value=0.0005  Score=43.68  Aligned_cols=29  Identities=21%  Similarity=0.332  Sum_probs=21.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ...++.+|+|+|||+++-+++...+.+.+
T Consensus        46 ~~vll~G~~GtGKT~la~~la~~~~~~~~   74 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLLAKAIAGEAKVPFF   74 (257)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHTCCEE
T ss_pred             CeEEEECcCCCCHHHHHHHHHHHcCCCEE
Confidence            45788999999999988666554444443

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.49  E-value=0.00066  Score=47.63  Aligned_cols=34  Identities=15%  Similarity=0.274  Sum_probs=25.7

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN   61 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p   61 (67)
                      .+..++.+|+|+|||.++-+++.+.+.+++.+..
T Consensus       182 prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~  215 (405)
T 4b4t_J          182 PKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSG  215 (405)
T ss_dssp             CCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEG
T ss_pred             CCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEh
Confidence            3567888999999999998877766655555443

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=95.43  E-value=0.00062  Score=44.72  Aligned_cols=29  Identities=17%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      ...++.+|+|+|||+++-+++...+.+.+
T Consensus        50 ~~vLL~Gp~GtGKT~la~ala~~~~~~~i   78 (301)
T 3cf0_A           50 KGVLFYGPPGCGKTLLAKAIANECQANFI   78 (301)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHTTCEEE
T ss_pred             ceEEEECCCCcCHHHHHHHHHHHhCCCEE
Confidence            56788999999999998766655444433

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=95.43  E-value=0.00061  Score=45.04  Aligned_cols=31  Identities=16%  Similarity=0.222  Sum_probs=23.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ...++.+|+|+|||.++-+++...+.+.+.+
T Consensus        52 ~~vLl~GppGtGKT~la~aia~~~~~~~~~v   82 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLAKAVATEANSTFFSV   82 (322)
T ss_dssp             CEEEEECSSSSCHHHHHHHHHHHHTCEEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHCCCEEEE
Confidence            4678899999999999877766555444433

>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=95.39  E-value=0.0035  Score=39.90  Aligned_cols=23  Identities=22%  Similarity=0.304  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+|+|+|||.++-.+...
T Consensus        30 ~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A           30 KPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHT
T ss_pred             CCEEEECCCCCcHHHHHHHHHHh
Confidence            67889999999999988665544

>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=95.38  E-value=0.0016  Score=38.00  Aligned_cols=19  Identities=26%  Similarity=0.067  Sum_probs=15.9

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      ..++.+|+|||||+++-.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3568899999999998766

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.38  E-value=0.00073  Score=44.95  Aligned_cols=23  Identities=17%  Similarity=0.112  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.++.+|+|+|||.++.+++..
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH
Confidence            67888999999999998766553

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.38  E-value=0.0024  Score=38.95  Aligned_cols=23  Identities=13%  Similarity=0.111  Sum_probs=18.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+|+|+|||+++.+++..
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~   77 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANE   77 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            56888899999999988666554

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=95.37  E-value=0.0064  Score=38.47  Aligned_cols=35  Identities=17%  Similarity=0.200  Sum_probs=24.4

Q ss_pred             eeeccc-hhhHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637          9 AVLRPY-QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus         9 ~~lR~y-Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      +.++.| |..+++.+-..   ....|.+|.|+|||+..-
T Consensus         5 i~pk~~g~~~~l~~i~~G---e~~~liG~nGsGKSTLl~   40 (208)
T 3b85_A            5 IRPKTLGQKHYVDAIDTN---TIVFGLGPAGSGKTYLAM   40 (208)
T ss_dssp             CCCCSHHHHHHHHHHHHC---SEEEEECCTTSSTTHHHH
T ss_pred             cccCCHhHHHHHHhccCC---CEEEEECCCCCCHHHHHH
Confidence            334444 66677776433   567789999999998763

>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=95.36  E-value=0.0011  Score=44.64  Aligned_cols=32  Identities=19%  Similarity=0.339  Sum_probs=23.5

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ....++.+|+|+|||.++-+++...+.+++.+
T Consensus       117 ~~~vLl~GppGtGKT~la~aia~~~~~~~~~i  148 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIGKCIASQSGATFFSI  148 (357)
T ss_dssp             CSEEEEESSTTSSHHHHHHHHHHHTTCEEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHcCCeEEEE
Confidence            35688899999999999877665555454443

>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=95.36  E-value=0.00096  Score=43.75  Aligned_cols=31  Identities=19%  Similarity=0.090  Sum_probs=22.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ...++.+|+|+|||+++-.++...   +.+++++
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i   71 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYS   71 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            568888999999999987666544   3444443

>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=95.35  E-value=0.0027  Score=38.22  Aligned_cols=23  Identities=17%  Similarity=0.089  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....+++|+|||||+++-.++..
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhc
Confidence            56778999999999988655443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=95.33  E-value=0.0012  Score=44.75  Aligned_cols=31  Identities=16%  Similarity=0.293  Sum_probs=23.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .+.+|.+|+|+|||.++-+++...+.+++.+
T Consensus       149 ~~vLL~GppGtGKT~la~aia~~~~~~~~~v  179 (389)
T 3vfd_A          149 RGLLLFGPPGNGKTMLAKAVAAESNATFFNI  179 (389)
T ss_dssp             SEEEEESSTTSCHHHHHHHHHHHTTCEEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHhhcCcEEEe
Confidence            5788999999999999877766555555444

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.29  E-value=0.0038  Score=45.66  Aligned_cols=37  Identities=14%  Similarity=0.272  Sum_probs=25.5

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+.+++   ++......+.++.+|+|+|||.++-.++..
T Consensus       185 ~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          185 RSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             CHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             chHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHHHHHHHH
Confidence            4444444   444433468999999999999988666544

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=95.29  E-value=0.00066  Score=43.80  Aligned_cols=28  Identities=18%  Similarity=0.274  Sum_probs=20.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      ...++.+|+|+|||+++-+++...+.+.
T Consensus        55 ~~vll~Gp~GtGKT~la~~la~~~~~~~   82 (297)
T 3b9p_A           55 KGLLLFGPPGNGKTLLARAVATECSATF   82 (297)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHHHTTCEE
T ss_pred             CeEEEECcCCCCHHHHHHHHHHHhCCCe
Confidence            5788899999999998866655444333

>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=95.28  E-value=0.00094  Score=50.52  Aligned_cols=52  Identities=15%  Similarity=0.250  Sum_probs=35.5

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .+|||-.+.+-.+.-+   ..-+.-|.||+|||+++...+..   .++.+.|++|+..
T Consensus        73 g~r~~dvQligg~~L~---~G~iaEM~TGEGKTLva~lp~~lnAL~G~~vhVvT~ndy  127 (822)
T 3jux_A           73 GMRPFDVQVMGGIALH---EGKVAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDY  127 (822)
T ss_dssp             SCCCCHHHHHHHHHHH---TTCEEECCTTSCHHHHTHHHHHHHHTTSSCEEEEESSHH
T ss_pred             CCCCcHHHHHHHHHHh---CCChhhccCCCCccHHHHHHHHHHHhcCCceEEEeccHH
Confidence            4567755555553322   12377899999999998766542   3677999998864

>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=95.25  E-value=0.00073  Score=46.15  Aligned_cols=25  Identities=12%  Similarity=0.178  Sum_probs=19.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      -.+|++|||+|||.++..++...+.
T Consensus        12 ~i~i~GptgsGKt~la~~La~~~~~   36 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKILPV   36 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSCE
T ss_pred             EEEEECCCccCHHHHHHHHHHhCCC
Confidence            4677899999999999887766543

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.25  E-value=0.0041  Score=38.50  Aligned_cols=22  Identities=18%  Similarity=0.123  Sum_probs=16.7

Q ss_pred             ceeeeEEEeCCCCceeEeeeeE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +....|.+|+|||||+++-.+.
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~   43 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLA   43 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3566788999999998874443

>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=95.21  E-value=0.0032  Score=41.35  Aligned_cols=36  Identities=14%  Similarity=0.025  Sum_probs=23.6

Q ss_pred             hhhHHHH---Hh-cCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRK---MF-GNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~---~~-~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+++++.   ++ +.+...+.++.+|+|+|||+++-.++.
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           19 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             CHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHH
T ss_pred             CHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            5555544   44 333323488899999999998865544

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=95.19  E-value=0.00099  Score=41.32  Aligned_cols=34  Identities=21%  Similarity=0.155  Sum_probs=25.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~   62 (67)
                      .-.++.+|+|+|||+.++.++.+.   +.+++++.|.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~   40 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPK   40 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeec
Confidence            356788999999999987766543   4567777654

>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=95.14  E-value=0.00072  Score=46.29  Aligned_cols=24  Identities=25%  Similarity=0.227  Sum_probs=19.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      -.+|++|||+|||.++..++...+
T Consensus         5 ~i~i~GptgsGKt~la~~La~~~~   28 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVMLAKRLN   28 (322)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             EEEEECCCcCCHHHHHHHHHHhCc
Confidence            456789999999999987776544

>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=95.12  E-value=0.00087  Score=44.96  Aligned_cols=29  Identities=21%  Similarity=0.293  Sum_probs=21.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      .+.++.+|+|+|||.++-.++...+.+.+
T Consensus        73 ~~ill~Gp~GtGKT~la~~la~~l~~~~~  101 (376)
T 1um8_A           73 SNILLIGPTGSGKTLMAQTLAKHLDIPIA  101 (376)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            46889999999999998766655544433

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=95.09  E-value=0.00087  Score=45.65  Aligned_cols=24  Identities=17%  Similarity=0.225  Sum_probs=19.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ..+|++|||+|||.++..++...+
T Consensus         7 ~i~i~GptGsGKTtla~~La~~l~   30 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADALP   30 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcC
Confidence            567889999999999877766544

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=95.07  E-value=0.0053  Score=44.71  Aligned_cols=34  Identities=15%  Similarity=0.210  Sum_probs=23.7

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.+++......+.++.+|+|+|||.++-.++..
T Consensus       197 ~l~~~l~~~~~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          197 RAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             HHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCCeEEEcCCCCCHHHHHHHHHHH
Confidence            3344444444468899999999999988655543

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.06  E-value=0.0028  Score=38.51  Aligned_cols=21  Identities=19%  Similarity=0.260  Sum_probs=16.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +..+|++|+|+|||+++-.+.
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~   26 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLI   26 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            467788999999999875544

>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=95.01  E-value=0.0029  Score=42.51  Aligned_cols=45  Identities=18%  Similarity=0.284  Sum_probs=31.5

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---------EeeeeEEEee
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---------VRKRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---------~~~~~lil~p   61 (67)
                      ..+++++..+  .+...+|.+|+|+|||..++.++..         .+++++++.-
T Consensus       109 ~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~  164 (343)
T 1v5w_A          109 QEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDT  164 (343)
T ss_dssp             HHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEES
T ss_pred             hhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEEC
Confidence            3467777532  2456788899999999999876653         2567777753

>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=94.98  E-value=0.00099  Score=44.92  Aligned_cols=30  Identities=17%  Similarity=0.210  Sum_probs=22.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      +..++.+|+|+|||.++-+++...+.+.+.
T Consensus        85 ~~iLL~GppGtGKT~la~ala~~~~~~~~~  114 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLAKAVATEANSTFFS  114 (355)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHhCCCEEE
Confidence            457888999999999987666555444433

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=94.96  E-value=0.0021  Score=47.77  Aligned_cols=38  Identities=13%  Similarity=0.255  Sum_probs=25.9

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |.+.+++   ++..+...+.++++|+|+|||.++-.++...
T Consensus       175 r~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la~~la~~l  215 (854)
T 1qvr_A          175 RDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRI  215 (854)
T ss_dssp             CHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHHHHHHHH
Confidence            4444444   4434434678999999999999887666543

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.93  E-value=0.0012  Score=46.81  Aligned_cols=33  Identities=15%  Similarity=0.223  Sum_probs=25.0

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      .+..++.+|+|+|||.++-+++.+.+.+++.+.
T Consensus       216 prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~  248 (437)
T 4b4t_I          216 PKGVILYGAPGTGKTLLAKAVANQTSATFLRIV  248 (437)
T ss_dssp             CSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEE
T ss_pred             CCCCceECCCCchHHHHHHHHHHHhCCCEEEEE
Confidence            356788899999999999877776655555443

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.92  E-value=0.001  Score=47.55  Aligned_cols=33  Identities=15%  Similarity=0.214  Sum_probs=24.9

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      .+..++.+|+|+|||.++-+++.+.+.+++.+.
T Consensus       243 prGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs  275 (467)
T 4b4t_H          243 PKGILLYGPPGTGKTLCARAVANRTDATFIRVI  275 (467)
T ss_dssp             CSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEE
T ss_pred             CCceEeeCCCCCcHHHHHHHHHhccCCCeEEEE
Confidence            356778899999999999877776665555444

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.91  E-value=0.00077  Score=41.53  Aligned_cols=23  Identities=22%  Similarity=0.150  Sum_probs=18.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++++|+|||||+++-.++..
T Consensus        26 ~~i~l~G~~GsGKsTl~~~La~~   48 (199)
T 3vaa_A           26 VRIFLTGYMGAGKTTLGKAFARK   48 (199)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            57788999999999998666543

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.90  E-value=0.0028  Score=37.55  Aligned_cols=21  Identities=19%  Similarity=-0.018  Sum_probs=16.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..++.+|+|||||+++-.+..
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHh
Confidence            457889999999998866554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=94.86  E-value=0.0013  Score=43.75  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=19.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +..++.+|+|+|||.++-+++...
T Consensus        46 ~~iLL~GppGtGKT~la~ala~~~   69 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLAKAVATEA   69 (322)
T ss_dssp             SEEEEESSSSSCHHHHHHHHHHHT
T ss_pred             ceEEEECCCCccHHHHHHHHHHHc
Confidence            567888999999999987776655

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=94.86  E-value=0.0017  Score=46.09  Aligned_cols=35  Identities=14%  Similarity=0.090  Sum_probs=27.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      +-.++.++.|+|||......+..  ++.+|++||..+
T Consensus       162 ~v~~I~G~aGsGKTt~I~~~~~~--~~~lVlTpT~~a  196 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEILSRVNF--EEDLILVPGRQA  196 (446)
T ss_dssp             EEEEEEECTTSCHHHHHHHHCCT--TTCEEEESCHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHhcc--CCeEEEeCCHHH
Confidence            45778999999999988665542  678999999754

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=94.85  E-value=0.0025  Score=45.11  Aligned_cols=31  Identities=19%  Similarity=0.295  Sum_probs=23.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ...++.+|+|+|||+++-++....+.+++.+
T Consensus       239 ~~vLL~GppGtGKT~lAraia~~~~~~fv~v  269 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIARAVANETGAFFFLI  269 (489)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHCSSEEEEE
T ss_pred             CcEEEECcCCCCHHHHHHHHHHHhCCCEEEE
Confidence            5688899999999999877766555554443

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=94.84  E-value=0.0028  Score=45.41  Aligned_cols=53  Identities=28%  Similarity=0.279  Sum_probs=39.2

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeecc
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSG   63 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~   63 (67)
                      .+.|.|||++.++.+...   +..++..|-|+|||.++...+..     -+.++++++|+.
T Consensus       161 ~~~l~p~Q~~i~~~l~~~---r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~~~~i~~va~t~  218 (592)
T 3cpe_A          161 KVQLRDYQRDMLKIMSSK---RMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKG  218 (592)
T ss_dssp             BCCCCHHHHHHHHHHHHC---SEEEEEECSSSCHHHHHHHHHHHHHHTSSSCEEEEEESSH
T ss_pred             cCcCCHHHHHHHHhhccc---cEEEEEEcCccChHHHHHHHHHHHHHhCCCCeEEEEECCH
Confidence            467899999999887332   57889999999999887543322     134788888874

>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=94.82  E-value=0.0028  Score=42.19  Aligned_cols=34  Identities=12%  Similarity=0.060  Sum_probs=24.0

Q ss_pred             hHHHHHhcCC-cce-eeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNG-RAR-SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~-~~~-~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+++.|++.. ..+ ..++.+|+|+|||..+.+++.
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            3456677753 223 477779999999999876664

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=94.78  E-value=0.00072  Score=44.42  Aligned_cols=37  Identities=16%  Similarity=0.025  Sum_probs=24.3

Q ss_pred             hhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+++++.+... ..+++.++.+|+|+|||.++-.+...
T Consensus        32 ~~~~~~~l~~~l~~~~~vll~G~pGtGKT~la~~la~~   69 (331)
T 2r44_A           32 QKYMINRLLIGICTGGHILLEGVPGLAKTLSVNTLAKT   69 (331)
T ss_dssp             CHHHHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCeEEEECCCCCcHHHHHHHHHHH
Confidence            55665553321 01268999999999999887655443

>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=94.77  E-value=0.014  Score=35.65  Aligned_cols=33  Identities=30%  Similarity=0.424  Sum_probs=24.1

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ..+++.+..+  .+....|.+|+|+|||+.+..++
T Consensus        12 ~~LD~~l~ggi~~G~~~~l~G~nGsGKSTll~~l~   46 (231)
T 4a74_A           12 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA   46 (231)
T ss_dssp             HHHHHHTTSSEESSEEEEEEESTTSSHHHHHHHHH
T ss_pred             hhHHhHhcCCCCCCcEEEEECCCCCCHHHHHHHHH
Confidence            4667777532  24678889999999999886554

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=94.77  E-value=0.0038  Score=38.35  Aligned_cols=22  Identities=23%  Similarity=0.286  Sum_probs=17.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+|.|||||+++-.+..
T Consensus        30 ~~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           30 RHVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5677889999999998755443

>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=94.76  E-value=0.0031  Score=43.71  Aligned_cols=25  Identities=20%  Similarity=0.365  Sum_probs=20.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ++.++.+|+|+|||.++-+++...+
T Consensus        64 ~~iLl~GppGtGKT~la~ala~~l~   88 (456)
T 2c9o_A           64 RAVLLAGPPGTGKTALALAIAQELG   88 (456)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CeEEEECCCcCCHHHHHHHHHHHhC
Confidence            5788899999999999876665544

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.75  E-value=0.0029  Score=38.68  Aligned_cols=44  Identities=11%  Similarity=0.147  Sum_probs=29.3

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      +.+++++..+  .+...+|.+|+|+|||+.+..++..   .+++++++.
T Consensus        10 ~~Ld~~~~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           10 LDFDKLIQGGIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             HHHHGGGTTSEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             hHHHHHhcCCCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            4567766421  2356788999999999988766543   245666654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=94.74  E-value=0.0027  Score=41.01  Aligned_cols=47  Identities=13%  Similarity=0.020  Sum_probs=33.1

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      +--|+.+.+.+.+ ++.   ...+|.+|.|.|||.....+......+.+++
T Consensus        15 ~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~   61 (357)
T 2fna_A           15 FFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELNLPYIYL   61 (357)
T ss_dssp             SCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             hcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcCCCEEEE
Confidence            4447777777777 765   4788899999999998876655443344443

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=94.72  E-value=0.011  Score=38.06  Aligned_cols=40  Identities=15%  Similarity=-0.004  Sum_probs=29.9

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +--|+.+.+.+.++++.+  +..+|.+|.|.|||.....+..
T Consensus        14 ~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~   53 (350)
T 2qen_A           14 IFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLN   53 (350)
T ss_dssp             SCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHH
T ss_pred             cCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHH
Confidence            444777777787777643  5788999999999988765543

>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=94.69  E-value=0.004  Score=38.69  Aligned_cols=22  Identities=27%  Similarity=0.197  Sum_probs=17.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...++++|+|+|||+++-.++.
T Consensus         9 ~~i~l~GpsGsGKsTl~~~L~~   30 (208)
T 3tau_A            9 LLIVLSGPSGVGKGTVREAVFK   30 (208)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHHHh
Confidence            4577889999999998865543

>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=94.69  E-value=0.0024  Score=41.67  Aligned_cols=45  Identities=16%  Similarity=0.304  Sum_probs=27.3

Q ss_pred             hhHHHHHhcCCcceee-eEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         16 EKSLRKMFGNGRARSG-VIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~-~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      .+.+.++++.+...+. ++.+|+|+|||.++..++...+.+++.+-
T Consensus        35 ~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~   80 (324)
T 3u61_B           35 KETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVN   80 (324)
T ss_dssp             HHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEE
T ss_pred             HHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEc
Confidence            3444456655432344 44577999999998777665555544443

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.64  E-value=0.0042  Score=37.71  Aligned_cols=20  Identities=30%  Similarity=0.330  Sum_probs=15.8

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|.+|+|||||+++-.+
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L   27 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRAL   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECcCCCCHHHHHHHH
Confidence            45678899999999887444

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.64  E-value=0.011  Score=42.13  Aligned_cols=22  Identities=18%  Similarity=0.104  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...+|++|||||||++.-+++.
T Consensus       261 ~~i~I~GptGSGKTTlL~aL~~  282 (511)
T 2oap_1          261 FSAIVVGETASGKTTTLNAIMM  282 (511)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGG
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            5688999999999988755443

>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=94.62  E-value=0.0041  Score=40.94  Aligned_cols=34  Identities=21%  Similarity=0.378  Sum_probs=25.2

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..+++++..+  .+...+|.+|+|+|||..++.++.
T Consensus        85 ~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~  120 (322)
T 2i1q_A           85 SELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCV  120 (322)
T ss_dssp             HHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHH
T ss_pred             hhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4567777532  245688889999999999987664

>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=94.61  E-value=0.0034  Score=36.89  Aligned_cols=22  Identities=18%  Similarity=-0.075  Sum_probs=17.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+|.+|.|||||+++-.+...
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3567899999999988665543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=94.60  E-value=0.0069  Score=36.26  Aligned_cols=23  Identities=22%  Similarity=-0.023  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....+.+|+|+|||+.+-.++..
T Consensus        37 ~~~~l~G~~G~GKTtL~~~i~~~   59 (149)
T 2kjq_A           37 QFIYVWGEEGAGKSHLLQAWVAQ   59 (149)
T ss_dssp             SEEEEESSSTTTTCHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            57788999999999987655443

>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=94.55  E-value=0.0062  Score=39.72  Aligned_cols=22  Identities=18%  Similarity=0.107  Sum_probs=18.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+.++.+|+|+|||.++-.+..
T Consensus        46 ~~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           46 GGVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             CCEEEECCGGGCTTHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHH
Confidence            5788999999999998865544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.52  E-value=0.0018  Score=45.27  Aligned_cols=33  Identities=18%  Similarity=0.246  Sum_probs=22.6

Q ss_pred             HHhcCCcceeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         21 KMFGNGRARSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        21 ~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +.++.+...+.++.+|+|+|||+++-.+....+
T Consensus        43 ~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~~   75 (447)
T 3pvs_A           43 RAIEAGHLHSMILWGPPGTGKTTLAEVIARYAN   75 (447)
T ss_dssp             HHHHHTCCCEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             HHHHcCCCcEEEEECCCCCcHHHHHHHHHHHhC
Confidence            344433334688999999999998866654433

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=94.52  E-value=0.0092  Score=39.30  Aligned_cols=25  Identities=20%  Similarity=0.280  Sum_probs=20.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +..++.+|+|+|||.++-.++..+.
T Consensus        71 ~~vLl~GppGtGKT~la~~la~~l~   95 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIAMGMAQALG   95 (368)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhc
Confidence            5788999999999999877665543

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=94.51  E-value=0.003  Score=39.80  Aligned_cols=31  Identities=16%  Similarity=0.078  Sum_probs=25.3

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEeeeeEEEeec
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVRKRALVLCNS   62 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~   62 (67)
                      .+|.+++|||||..+..++.. +.+.++++..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~   32 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATS   32 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecC
Confidence            368899999999999887776 6778887753

>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=94.49  E-value=0.0071  Score=39.94  Aligned_cols=36  Identities=19%  Similarity=0.248  Sum_probs=24.1

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+++++.   +++.+.-.+.++.+|+|+|||+++..++.
T Consensus        30 ~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~   68 (340)
T 1sxj_C           30 QNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAR   68 (340)
T ss_dssp             CHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHH
Confidence            6666654   44444222378899999999988865543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.49  E-value=0.0045  Score=36.69  Aligned_cols=22  Identities=41%  Similarity=0.516  Sum_probs=17.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+|+|||||+++-.+..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3567889999999998755443

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.49  E-value=0.0081  Score=39.14  Aligned_cols=31  Identities=16%  Similarity=0.204  Sum_probs=21.0

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +++.+- -..++...|++|||||||++.-.++
T Consensus        16 vl~~i~-i~~g~~v~i~Gp~GsGKSTll~~l~   46 (261)
T 2eyu_A           16 KVLELC-HRKMGLILVTGPTGSGKSTTIASMI   46 (261)
T ss_dssp             HHHHGG-GCSSEEEEEECSTTCSHHHHHHHHH
T ss_pred             HHHHHh-hCCCCEEEEECCCCccHHHHHHHHH
Confidence            444433 2223678899999999998875544

>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=94.44  E-value=0.0015  Score=41.11  Aligned_cols=34  Identities=24%  Similarity=0.149  Sum_probs=26.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~   62 (67)
                      .-.++.+|+|+|||+.++.++.+.   +.+++++.|.
T Consensus         9 ~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~   45 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPE   45 (191)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEec
Confidence            467778999999999888777664   5678887654

>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=94.42  E-value=0.0017  Score=45.63  Aligned_cols=25  Identities=24%  Similarity=0.214  Sum_probs=19.8

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      ..+|++|||+|||.++..++...+.
T Consensus         4 ~i~i~GptgsGKttla~~La~~~~~   28 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKFNG   28 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHTE
T ss_pred             EEEEECcchhhHHHHHHHHHHHCCC
Confidence            4578899999999998877765543

>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=94.41  E-value=0.0028  Score=44.00  Aligned_cols=24  Identities=21%  Similarity=0.036  Sum_probs=19.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|+|||+++-++....
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l  154 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYV  154 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            568889999999999887665543

>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=94.41  E-value=0.013  Score=40.00  Aligned_cols=32  Identities=16%  Similarity=0.121  Sum_probs=21.5

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .++++.... ++..+|.+|||||||++.-.++.
T Consensus       114 ~l~~l~~~~-~g~i~I~GptGSGKTTlL~~l~g  145 (356)
T 3jvv_A          114 VFKRVSDVP-RGLVLVTGPTGSGKSTTLAAMLD  145 (356)
T ss_dssp             HHHHHHHCS-SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             HHHHHHhCC-CCEEEEECCCCCCHHHHHHHHHh
Confidence            344444322 25788899999999988765544

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=94.40  E-value=0.0059  Score=40.07  Aligned_cols=34  Identities=18%  Similarity=0.174  Sum_probs=21.5

Q ss_pred             hHHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +.+.++++.+. .+..++.+|+|+|||.++..++.
T Consensus        26 ~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~   60 (373)
T 1jr3_A           26 TALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAK   60 (373)
T ss_dssp             HHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            33444444332 23468899999999988765543

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.38  E-value=0.0061  Score=37.71  Aligned_cols=20  Identities=40%  Similarity=0.411  Sum_probs=16.2

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +...|++|+|+|||++.-.+
T Consensus         5 ~~i~lvGpsGaGKSTLl~~L   24 (198)
T 1lvg_A            5 RPVVLSGPSGAGKSTLLKKL   24 (198)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            46778999999999887544

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.37  E-value=0.0016  Score=39.32  Aligned_cols=24  Identities=17%  Similarity=-0.017  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+++|||||+++-.+....
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            467788999999999986665443

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=94.37  E-value=0.0041  Score=43.14  Aligned_cols=53  Identities=28%  Similarity=0.279  Sum_probs=39.8

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeecc
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSG   63 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~   63 (67)
                      .+.|.|||++.++.+...   +..++..+-+.|||.+++..+..     -+.++++++|+.
T Consensus       161 p~~L~p~Qk~il~~l~~~---R~~vi~~sRq~GKT~l~a~~~l~~a~~~~g~~v~~vA~t~  218 (385)
T 2o0j_A          161 KVQLRDYQRDMLKIMSSK---RMTVCNLSRQLGKTTVVAIFLAHFVCFNKDKAVGILAHKG  218 (385)
T ss_dssp             ECCCCHHHHHHHHHHHHS---SEEEEEECSSSCHHHHHHHHHHHHHHSSSSCEEEEEESSH
T ss_pred             CCCCCHHHHHHHHhhccC---cEEEEEEcCcCChhHHHHHHHHHHHHhCCCCeEEEEeCCH
Confidence            468899999999876433   56889999999999887654332     245788888874

>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=94.35  E-value=0.0038  Score=42.36  Aligned_cols=45  Identities=29%  Similarity=0.295  Sum_probs=32.0

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...+++++. .+  .+...+|.+|+|+|||..++.++...   +++++++.
T Consensus        46 ~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~   96 (349)
T 2zr9_A           46 SISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFID   96 (349)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            346778887 32  24568888999999999988776543   45666664

>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=94.34  E-value=0.0021  Score=41.58  Aligned_cols=23  Identities=22%  Similarity=0.147  Sum_probs=18.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...+|.+|||+|||.+++.++.+
T Consensus        35 ~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           35 LGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            45678899999999888777654

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=94.33  E-value=0.0085  Score=39.55  Aligned_cols=22  Identities=27%  Similarity=0.276  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+.+|.+|+|+|||.++-.+..
T Consensus        26 ~~vLi~Ge~GtGKt~lAr~i~~   47 (304)
T 1ojl_A           26 ATVLIHGDSGTGKELVARALHA   47 (304)
T ss_dssp             SCEEEESCTTSCHHHHHHHHHH
T ss_pred             CcEEEECCCCchHHHHHHHHHH
Confidence            6789999999999998865544

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.30  E-value=0.0015  Score=44.85  Aligned_cols=24  Identities=25%  Similarity=0.286  Sum_probs=18.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ..+|.+|||||||.++..++...+
T Consensus         9 lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             eEEEECCCcCcHHHHHHHHHHHcC
Confidence            456889999999999877665543

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=94.26  E-value=0.005  Score=43.86  Aligned_cols=38  Identities=18%  Similarity=0.162  Sum_probs=25.6

Q ss_pred             hhhHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         15 QEKSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        15 Q~~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+++++.++.. ..+++.++.+|+|+|||.++-++....
T Consensus        27 q~~~i~~l~~al~~~~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           27 RSHAIRLCLLAALSGESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             CHHHHHHHHHHHHHTCEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             HHHHHHHHHHHHhcCCeeEeecCchHHHHHHHHHHHHHH
Confidence            55555554321 112689999999999999886665543

>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=94.25  E-value=0.0057  Score=36.96  Aligned_cols=20  Identities=30%  Similarity=0.293  Sum_probs=16.1

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ..++.+|+|+|||+++-.+.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~   23 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLA   23 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHh
Confidence            45688999999999876554

>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=94.25  E-value=0.0022  Score=41.39  Aligned_cols=34  Identities=21%  Similarity=0.087  Sum_probs=26.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~   62 (67)
                      .-.++.+|+|+|||+.++.++.+.   +.+++++.|.
T Consensus        13 ~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~   49 (223)
T 2b8t_A           13 WIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPK   49 (223)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEec
Confidence            567778999999999988777664   4578877654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.22  E-value=0.0055  Score=37.13  Aligned_cols=21  Identities=29%  Similarity=0.227  Sum_probs=16.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.+|+|||||+++-.+.
T Consensus         7 ~~i~l~G~~GsGKSTl~~~L~   27 (207)
T 2j41_A            7 LLIVLSGPSGVGKGTVRKRIF   27 (207)
T ss_dssp             CEEEEECSTTSCHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            466788999999998875443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.22  E-value=0.0074  Score=36.43  Aligned_cols=23  Identities=13%  Similarity=-0.003  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus        14 ~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           14 IVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH
Confidence            56778899999999988666544

>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=94.22  E-value=0.0026  Score=44.13  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=19.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +..++.+|+|+|||.++-+++...
T Consensus       168 ~~vLL~GppGtGKT~lA~aia~~~  191 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLAKAVATEA  191 (444)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHc
Confidence            567889999999999987766655

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=94.15  E-value=0.0015  Score=40.26  Aligned_cols=22  Identities=23%  Similarity=0.042  Sum_probs=17.2

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|.+|+|||||+++-.+....
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4678999999999986665443

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=94.15  E-value=0.002  Score=40.29  Aligned_cols=24  Identities=25%  Similarity=0.239  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|||||+++-.+....
T Consensus         8 ~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            8 LRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            457788999999999986665443

>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=94.14  E-value=0.0016  Score=40.19  Aligned_cols=22  Identities=27%  Similarity=0.149  Sum_probs=17.2

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|.+|+|||||+++-.++...
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5678999999999986665443

>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=94.13  E-value=0.0078  Score=36.06  Aligned_cols=23  Identities=9%  Similarity=0.010  Sum_probs=17.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus         6 ~~I~l~G~~GsGKST~~~~L~~~   28 (193)
T 2rhm_A            6 ALIIVTGHPATGKTTLSQALATG   28 (193)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            45678899999999988665443

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.10  E-value=0.0015  Score=39.23  Aligned_cols=22  Identities=23%  Similarity=0.163  Sum_probs=17.5

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+|.+|+|||||+++-.++..
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            4678899999999998666544

>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=94.10  E-value=0.002  Score=40.75  Aligned_cols=22  Identities=23%  Similarity=0.315  Sum_probs=17.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.+|+|+|||+++-.++..
T Consensus        51 g~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3688899999999887655443

>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=94.08  E-value=0.005  Score=42.24  Aligned_cols=46  Identities=20%  Similarity=0.171  Sum_probs=33.1

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      ...+++++. .+  .+...+|.+|+|+|||+.++.++...   +++++++..
T Consensus        46 ~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~   97 (356)
T 3hr8_A           46 SLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDA   97 (356)
T ss_dssp             CHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEec
Confidence            456788887 43  24567888999999999988776653   456777654

>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=94.05  E-value=0.0067  Score=36.19  Aligned_cols=24  Identities=17%  Similarity=0.091  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|||||+++-.+...+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l   27 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNL   27 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            356788999999999886665543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=94.05  E-value=0.007  Score=36.24  Aligned_cols=22  Identities=23%  Similarity=0.273  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...++.+++|||||+++-.+..
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4567889999999998866654

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.02  E-value=0.0086  Score=37.44  Aligned_cols=21  Identities=29%  Similarity=0.300  Sum_probs=12.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.+|+|+|||+++-.+.
T Consensus        28 ~ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           28 VILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             CEEEEECSCC----CHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHH
Confidence            456788999999999876555

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=93.99  E-value=0.0073  Score=35.98  Aligned_cols=24  Identities=25%  Similarity=0.178  Sum_probs=18.6

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ..++.+++|||||+++-.+...++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            356889999999999877665543

>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=93.99  E-value=0.0062  Score=41.17  Aligned_cols=35  Identities=29%  Similarity=0.395  Sum_probs=25.3

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.++..+  .+....|.+|+|+|||..+..++..
T Consensus       118 ~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~  154 (349)
T 1pzn_A          118 KSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVM  154 (349)
T ss_dssp             HHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4567777542  2466788999999999988766543

>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=93.96  E-value=0.0091  Score=40.72  Aligned_cols=22  Identities=23%  Similarity=0.161  Sum_probs=18.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +..+|++|||||||++.-.++.
T Consensus       137 ~~i~ivG~~GsGKTTll~~l~~  158 (372)
T 2ewv_A          137 GLILVTGPTGSGKSTTIASMID  158 (372)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            6788999999999998865544

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=93.96  E-value=0.0069  Score=44.91  Aligned_cols=52  Identities=17%  Similarity=0.193  Sum_probs=39.0

Q ss_pred             chhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecceee
Q psy11637         14 YQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVVF   66 (67)
Q Consensus        14 yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~v   66 (67)
                      -|+++++++++... +..+|.++-|.|||...-.++.....+.+|.+|+..++
T Consensus       179 dQ~~al~~~~~~~~-~~~vlta~RGRGKSa~lG~~~a~~~~~~~vtAP~~~a~  230 (671)
T 2zpa_A          179 EQQQLLKQLMTMPP-GVAAVTAARGRGKSALAGQLISRIAGRAIVTAPAKAST  230 (671)
T ss_dssp             HHHHHHHHHTTCCS-EEEEEEECTTSSHHHHHHHHHHHSSSCEEEECSSCCSC
T ss_pred             HHHHHHHHHHHhhh-CeEEEecCCCCCHHHHHHHHHHHHHhCcEEECCCHHHH
Confidence            59999999887532 56789999999999666445544455678889987664

>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=93.96  E-value=0.0013  Score=39.59  Aligned_cols=22  Identities=32%  Similarity=0.356  Sum_probs=17.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..+|.+++|||||+++-.+...
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~   25 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKA   25 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4578899999999998666544

>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=93.94  E-value=0.0018  Score=38.94  Aligned_cols=23  Identities=17%  Similarity=0.226  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus        12 ~~i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A           12 PNILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEeCCCCCHHHHHHHHHHH
Confidence            46778999999999988665543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=93.93  E-value=0.0072  Score=38.85  Aligned_cols=23  Identities=30%  Similarity=0.348  Sum_probs=18.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+|+|+|||.++-.+...
T Consensus        48 ~~~ll~G~~GtGKt~la~~la~~   70 (311)
T 4fcw_A           48 GSFLFLGPTGVGKTELAKTLAAT   70 (311)
T ss_dssp             EEEEEESCSSSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHHH
Confidence            46789999999999988666554

>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=93.93  E-value=0.002  Score=38.51  Aligned_cols=22  Identities=14%  Similarity=0.037  Sum_probs=17.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.+++|||||+++-.+...
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~~   29 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5678899999999988665544

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=93.93  E-value=0.007  Score=37.27  Aligned_cols=22  Identities=23%  Similarity=0.227  Sum_probs=17.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...++++|+|||||+++-.+..
T Consensus        13 ~~i~l~G~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           13 PPLVVCGPSGVGKGTLIKKVLS   34 (204)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4567889999999998865544

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=93.92  E-value=0.0015  Score=38.84  Aligned_cols=24  Identities=21%  Similarity=0.184  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.+|.++.|||||+++-.+..++
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            467788999999999987665543

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=93.90  E-value=0.0074  Score=39.67  Aligned_cols=24  Identities=13%  Similarity=0.029  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++++|+|||||+++-.+....
T Consensus        34 ~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            456778999999999987665443

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.86  E-value=0.0094  Score=42.76  Aligned_cols=34  Identities=24%  Similarity=0.344  Sum_probs=24.4

Q ss_pred             hhhHHHHHh---cCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRKMF---GNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~~~---~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+++++.+.   ..+  ...++.+|+|+|||+++-.++.
T Consensus        46 ~~~~l~~l~~~i~~g--~~vll~Gp~GtGKTtlar~ia~   82 (604)
T 3k1j_A           46 QEHAVEVIKTAANQK--RHVLLIGEPGTGKSMLGQAMAE   82 (604)
T ss_dssp             CHHHHHHHHHHHHTT--CCEEEECCTTSSHHHHHHHHHH
T ss_pred             chhhHhhccccccCC--CEEEEEeCCCCCHHHHHHHHhc
Confidence            666665533   333  6889999999999999865543

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.81  E-value=0.021  Score=38.63  Aligned_cols=22  Identities=23%  Similarity=0.166  Sum_probs=17.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...+|++|||||||++.-.++.
T Consensus       176 ~~i~ivG~sGsGKSTll~~l~~  197 (361)
T 2gza_A          176 RVIVVAGETGSGKTTLMKALMQ  197 (361)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHh
Confidence            6888999999999987755443

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.81  E-value=0.014  Score=35.20  Aligned_cols=18  Identities=28%  Similarity=0.318  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....+++|+|||||+.+-
T Consensus        10 ei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A           10 SLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHH
Confidence            567789999999998764

>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=93.77  E-value=0.0084  Score=36.78  Aligned_cols=23  Identities=17%  Similarity=0.024  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....|++|.|||||+++-.+...
T Consensus        26 ~~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           26 CVIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            56778899999999988655543

>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=93.76  E-value=0.007  Score=37.31  Aligned_cols=20  Identities=30%  Similarity=0.257  Sum_probs=16.1

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ...|.+|+|||||+++-.+.
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~   26 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMA   26 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            46688999999999885544

>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=93.76  E-value=0.008  Score=35.80  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=16.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....+.+|.|||||+++-.+.
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~   29 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVA   29 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHH
Confidence            467788999999999875443

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=93.76  E-value=0.0017  Score=38.79  Aligned_cols=27  Identities=22%  Similarity=0.069  Sum_probs=16.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ...++.+++|||||+++-.+...++.+
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l~~~   32 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERLPGS   32 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHSTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCC
Confidence            356778999999999987766554443

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.74  E-value=0.0088  Score=35.99  Aligned_cols=24  Identities=17%  Similarity=0.011  Sum_probs=18.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+++|||||+++-.+...+
T Consensus        13 ~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           13 KIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            457788999999999986655443

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=93.70  E-value=0.009  Score=35.63  Aligned_cols=23  Identities=17%  Similarity=0.003  Sum_probs=17.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~   26 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEK   26 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999998655443

>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=93.70  E-value=0.005  Score=42.03  Aligned_cols=45  Identities=22%  Similarity=0.232  Sum_probs=32.0

Q ss_pred             hHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         17 KSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      ..++.++. .+  .+...+|.+|+|+|||.+++.++...   +.+++++.-
T Consensus        49 ~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~   99 (356)
T 1u94_A           49 LSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   99 (356)
T ss_dssp             HHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             HHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            45777776 32  23567888999999999998777543   456777653

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=93.68  E-value=0.011  Score=36.17  Aligned_cols=20  Identities=15%  Similarity=-0.041  Sum_probs=15.7

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|.+|+|||||+++-.+
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l   26 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQAL   26 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            45668899999999887443

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=93.64  E-value=0.0018  Score=41.45  Aligned_cols=25  Identities=16%  Similarity=0.069  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ...++.+|+|||||+++-.+....+
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4567889999999999876655443

>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=93.63  E-value=0.0017  Score=38.47  Aligned_cols=22  Identities=23%  Similarity=0.209  Sum_probs=17.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.+++|||||+++-.+...
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~   25 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARA   25 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999998665544

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=93.63  E-value=0.0066  Score=40.29  Aligned_cols=44  Identities=14%  Similarity=0.080  Sum_probs=30.1

Q ss_pred             hHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         17 KSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ..+++++.. ..+.-.+|.+++|+|||..++.++...   +.+++++.
T Consensus        56 ~~LD~~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~s  103 (315)
T 3bh0_A           56 TELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  103 (315)
T ss_dssp             HHHHHHHSSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             HHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEE
Confidence            445666632 123568888999999999988776542   35777765

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=93.60  E-value=0.0072  Score=36.93  Aligned_cols=22  Identities=36%  Similarity=0.330  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...+|.++.|||||+++-.+..
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~   40 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAE   40 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3577889999999998865543

>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=93.57  E-value=0.0087  Score=36.33  Aligned_cols=23  Identities=17%  Similarity=0.125  Sum_probs=18.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus        11 ~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           11 INILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            46788999999999988655443

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=93.54  E-value=0.0031  Score=40.62  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=17.6

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..++.+|+|+|||+++-.++...
T Consensus        75 gvll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           75 GVLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCcChHHHHHHHHHHHc
Confidence            36888999999999876555433

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=93.51  E-value=0.013  Score=38.87  Aligned_cols=43  Identities=14%  Similarity=0.188  Sum_probs=29.6

Q ss_pred             eeccchhhHHHHHh-c----C--CcceeeeE--EEeCCCCceeEeeeeEEEE
Q psy11637         10 VLRPYQEKSLRKMF-G----N--GRARSGVI--VLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        10 ~lR~yQ~~av~~~~-~----~--~~~~~~~i--~~pTGsGKT~i~~~~~~~~   52 (67)
                      .=|+.+.+.+.+++ .    .  ......+|  .+|+|+|||.++..+....
T Consensus        25 ~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~   76 (412)
T 1w5s_A           25 RVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRV   76 (412)
T ss_dssp             SSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHH
Confidence            33667777777776 3    2  22356777  7999999999887665543

>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=93.48  E-value=0.013  Score=35.07  Aligned_cols=19  Identities=26%  Similarity=0.226  Sum_probs=15.7

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      +-.+|++|+|+|||.+.-+
T Consensus        24 g~~~I~G~NGsGKStil~A   42 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDA   42 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            5678999999999987644

>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=93.47  E-value=0.0029  Score=39.33  Aligned_cols=24  Identities=25%  Similarity=0.171  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+++|||||+++-.++..+
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            456788999999999986665543

>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=93.46  E-value=0.015  Score=34.80  Aligned_cols=20  Identities=35%  Similarity=0.335  Sum_probs=16.0

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +..+|++|+|+|||.+.-++
T Consensus        27 g~~~i~G~NGsGKStll~ai   46 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAI   46 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHH
Confidence            46778999999999876443

>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=93.44  E-value=0.0045  Score=39.26  Aligned_cols=24  Identities=25%  Similarity=0.421  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|+|||.++-+++...
T Consensus        45 ~~vll~G~~GtGKT~la~~la~~~   68 (268)
T 2r62_A           45 KGVLLVGPPGTGKTLLAKAVAGEA   68 (268)
T ss_dssp             SCCCCBCSSCSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHHHHh
Confidence            457888999999999986665543

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=93.37  E-value=0.0047  Score=40.31  Aligned_cols=22  Identities=23%  Similarity=0.368  Sum_probs=17.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++.+|+|+|||+++-+++..
T Consensus        46 GvlL~Gp~GtGKTtLakala~~   67 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLLAKAVANE   67 (274)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHH
Confidence            3778899999999887655443

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=93.34  E-value=0.011  Score=36.73  Aligned_cols=24  Identities=13%  Similarity=-0.126  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|||||+++-.++..+
T Consensus         6 ~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            6 LKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            456788999999999986665443

>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=93.33  E-value=0.0092  Score=39.64  Aligned_cols=22  Identities=18%  Similarity=0.243  Sum_probs=17.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...++.+|+|+|||+++-.++.
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~   73 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIAS   73 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHH
Confidence            4678999999999988755443

>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=93.31  E-value=0.0022  Score=39.28  Aligned_cols=24  Identities=25%  Similarity=0.278  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+++|||||+++-.+....
T Consensus        21 ~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            356778999999999986665543

>3auy_A DNA double-strand break repair RAD50 ATPase; DNA repair, ABC transporter ATPase domain-like; HET: DNA ADP; 2.70A {Methanocaldococcus jannaschii} PDB: 3aux_A* 3av0_B*

Probab=93.31  E-value=0.017  Score=38.95  Aligned_cols=20  Identities=25%  Similarity=0.147  Sum_probs=16.4

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +-.+|.+|||+|||.+.-++
T Consensus        26 gl~vi~G~NGaGKT~ileAI   45 (371)
T 3auy_A           26 GIVAIIGENGSGKSSIFEAV   45 (371)
T ss_dssp             EEEEEEECTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            57889999999999876443

>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=93.24  E-value=0.022  Score=38.80  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=15.8

Q ss_pred             ceeeeEEEeCCCCceeEe
Q psy11637         28 ARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~   45 (67)
                      ..+.+|.+|||||||...
T Consensus        53 ~~h~~i~G~tGsGKs~~~   70 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLL   70 (437)
T ss_dssp             GGCEEEEECTTSSHHHHH
T ss_pred             cceEEEECCCCCCHHHHH
Confidence            468999999999999865

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=93.19  E-value=0.0041  Score=38.75  Aligned_cols=25  Identities=12%  Similarity=-0.007  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      ...++.+++|||||+++-.+...++
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~   30 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYG   30 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            3567789999999999876655443

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.19  E-value=0.0097  Score=41.57  Aligned_cols=43  Identities=14%  Similarity=0.081  Sum_probs=30.0

Q ss_pred             HHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         18 SLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        18 av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      .+++++.+ ..+.-.+|.+++|+|||..++.++...   +.+++++.
T Consensus       186 ~LD~~lgGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fS  232 (444)
T 3bgw_A          186 ELDRMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHS  232 (444)
T ss_dssp             HHHHHHSSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEEC
T ss_pred             HHHhhcCCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEE
Confidence            45666642 123567888999999999998776653   56777764

>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=93.18  E-value=0.021  Score=38.35  Aligned_cols=22  Identities=14%  Similarity=0.111  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +...|++|||||||+..-.++.
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g  193 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIME  193 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGG
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            6788999999999987754443

>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=93.15  E-value=0.0085  Score=41.06  Aligned_cols=46  Identities=22%  Similarity=0.268  Sum_probs=32.3

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      ...++..+. .+  .+...+|.+|+|+|||..++.++...   +++++|+.-
T Consensus        59 ~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~  110 (366)
T 1xp8_A           59 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDA  110 (366)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEEC
Confidence            345677776 32  23567888999999999998776643   457777653

>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=93.10  E-value=0.015  Score=35.40  Aligned_cols=20  Identities=25%  Similarity=0.061  Sum_probs=15.6

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ...|.+++|||||+++-.+.
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~   22 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFR   22 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHH
Confidence            34688999999999875543

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.06  E-value=0.011  Score=40.80  Aligned_cols=44  Identities=18%  Similarity=0.257  Sum_probs=30.2

Q ss_pred             hHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         17 KSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      ..+++++.+ ..+.-.+|.+++|+|||..++.++...    +.+++++.
T Consensus       188 ~~LD~~lgGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~s  236 (444)
T 2q6t_A          188 KELDQLIGTLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYS  236 (444)
T ss_dssp             HHHHHHHCCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             HhhhhhcCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEE
Confidence            345666632 123567888999999999988776542    45777764

>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=93.06  E-value=0.0099  Score=36.33  Aligned_cols=19  Identities=16%  Similarity=0.074  Sum_probs=15.1

Q ss_pred             eeEEEeCCCCceeEeeeeE
Q psy11637         31 GVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~   49 (67)
                      ..|.+|.|||||+++-.+.
T Consensus         5 i~l~G~~GsGKST~~~~La   23 (206)
T 1jjv_A            5 VGLTGGIGSGKTTIANLFT   23 (206)
T ss_dssp             EEEECSTTSCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4578999999999885553

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=93.06  E-value=0.026  Score=40.72  Aligned_cols=23  Identities=17%  Similarity=-0.024  Sum_probs=18.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.++.+|+|+|||.++-.+....
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVA  351 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTC
T ss_pred             ceEEECCCchHHHHHHHHHHHhC
Confidence            78999999999999886655443

>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=93.03  E-value=0.015  Score=35.97  Aligned_cols=22  Identities=14%  Similarity=-0.094  Sum_probs=17.3

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .++.+|+|||||+++-.+....
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5688999999999886665543

>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=93.01  E-value=0.0028  Score=39.80  Aligned_cols=24  Identities=33%  Similarity=0.297  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-.+|++|.|+|||++.-.++...
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            346788999999999876665443

>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=92.95  E-value=0.0053  Score=43.56  Aligned_cols=31  Identities=19%  Similarity=0.291  Sum_probs=22.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      +..++.+|+|+|||+++-+++...+.+.+.+
T Consensus        50 ~gvLL~GppGtGKT~Laraia~~~~~~f~~i   80 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLARAVAGEANVPFFHI   80 (476)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCeeeC
Confidence            4578889999999998866655544444433

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=92.94  E-value=0.011  Score=35.52  Aligned_cols=23  Identities=26%  Similarity=0.234  Sum_probs=17.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEEe
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      .+|.+++|||||+++-.+...++
T Consensus         3 I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            3 IAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEECCCccCHHHHHHHHHHhcC
Confidence            46789999999998876665443

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=92.93  E-value=0.0032  Score=38.41  Aligned_cols=23  Identities=17%  Similarity=-0.015  Sum_probs=17.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35677899999999988655543

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=92.88  E-value=0.018  Score=39.08  Aligned_cols=19  Identities=37%  Similarity=0.288  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      +-.+|++|+|+|||.+.-+
T Consensus        24 g~~~i~G~NGaGKTTll~a   42 (365)
T 3qf7_A           24 GITVVEGPNGAGKSSLFEA   42 (365)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHH
Confidence            4667899999999988643

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=92.85  E-value=0.015  Score=35.11  Aligned_cols=22  Identities=27%  Similarity=0.054  Sum_probs=17.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+++|||||+++-.+..
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3466889999999998865544

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=92.78  E-value=0.015  Score=35.12  Aligned_cols=24  Identities=17%  Similarity=-0.162  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.++.|||||+++-.+...+
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHH
Confidence            456788999999999987666543

>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=92.78  E-value=0.005  Score=43.52  Aligned_cols=30  Identities=13%  Similarity=0.212  Sum_probs=22.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      ++.++.+|+|+|||.++-.++..++.+.+.
T Consensus        51 ~~iLl~GppGtGKT~lar~lA~~l~~~~~~   80 (444)
T 1g41_A           51 KNILMIGPTGVGKTEIARRLAKLANAPFIK   80 (444)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCCEEE
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHcCCCcee
Confidence            578889999999999987766655444433

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=92.77  E-value=0.04  Score=33.85  Aligned_cols=22  Identities=14%  Similarity=-0.144  Sum_probs=17.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+|.|||||+++-.+..
T Consensus        23 ~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A           23 LVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4566789999999998865543

>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=92.75  E-value=0.013  Score=37.91  Aligned_cols=44  Identities=11%  Similarity=-0.006  Sum_probs=28.7

Q ss_pred             hHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         17 KSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      .+++.+... ..+...+|.+|+|+|||+.+..++...    +.+++++.
T Consensus        23 ~~Ld~i~~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           23 TGINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             TTHHHHHCSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             HHHHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            456666532 223678889999999999887665432    23666653

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=92.74  E-value=0.038  Score=36.40  Aligned_cols=22  Identities=18%  Similarity=-0.032  Sum_probs=16.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+|.|||||+++-.+..
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4566789999999998754443

>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=92.74  E-value=0.0039  Score=39.27  Aligned_cols=24  Identities=25%  Similarity=0.261  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+++|||||+++-.++..+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            467788999999999987665544

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=92.72  E-value=0.016  Score=36.28  Aligned_cols=19  Identities=32%  Similarity=0.286  Sum_probs=15.5

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ....|++|+|+|||++.-.
T Consensus        24 ~~~~lvGpsGsGKSTLl~~   42 (218)
T 1z6g_A           24 YPLVICGPSGVGKGTLIKK   42 (218)
T ss_dssp             CCEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5677899999999987643

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=92.72  E-value=0.0022  Score=44.09  Aligned_cols=32  Identities=6%  Similarity=-0.073  Sum_probs=22.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      ...+|.+|+|+|||..+..++...+.+++++.
T Consensus       124 sviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs  155 (331)
T 2vhj_A          124 GMVIVTGKGNSGKTPLVHALGEALGGKDKYAT  155 (331)
T ss_dssp             EEEEEECSCSSSHHHHHHHHHHHHHTTSCCEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEE
Confidence            44588899999999998877654344544443

>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=92.68  E-value=0.015  Score=36.66  Aligned_cols=21  Identities=33%  Similarity=0.373  Sum_probs=16.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.+|+|||||+++-.++
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La   48 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIA   48 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            467788999999999875544

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=92.66  E-value=0.011  Score=40.94  Aligned_cols=44  Identities=14%  Similarity=0.223  Sum_probs=30.2

Q ss_pred             hHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         17 KSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      ..+++++.. ..+.-.+|.+++|+|||..++.++...    +.+++++.
T Consensus       191 ~~LD~~~gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          191 TELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             HHHHHHHSSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             HHHHhhcCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            345666532 123567888999999999998776642    34777765

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=92.60  E-value=0.0049  Score=38.56  Aligned_cols=23  Identities=22%  Similarity=-0.032  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....|.++.|||||+++-.+...
T Consensus        13 ~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           13 MVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            44557799999999998665543

>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=92.55  E-value=0.0051  Score=39.27  Aligned_cols=23  Identities=13%  Similarity=0.089  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+|+|||||+++-.+..+
T Consensus        30 ~~I~l~G~~GsGKsT~a~~L~~~   52 (243)
T 3tlx_A           30 GRYIFLGAPGSGKGTQSLNLKKS   52 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            56788899999999998766544

>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=92.50  E-value=0.02  Score=34.99  Aligned_cols=22  Identities=14%  Similarity=-0.153  Sum_probs=16.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+|+|||||+++-.+..
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4566889999999998855543

>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=92.50  E-value=0.021  Score=36.16  Aligned_cols=22  Identities=18%  Similarity=0.292  Sum_probs=17.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +..+|++|+|+|||++.-.++.
T Consensus        20 ~~ivl~GPSGaGKsTL~~~L~~   41 (197)
T 3ney_A           20 KTLVLIGASGVGRSHIKNALLS   41 (197)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECcCCCCHHHHHHHHHh
Confidence            5677889999999998765543

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=92.46  E-value=0.014  Score=36.91  Aligned_cols=21  Identities=29%  Similarity=0.213  Sum_probs=16.4

Q ss_pred             eeEEEeCCCCceeEeeeeEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .++.+|+||||++.+..++.+
T Consensus         3 Iil~GpPGsGKgTqa~~La~~   23 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKE   23 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467799999999988665543

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=92.36  E-value=0.016  Score=39.50  Aligned_cols=44  Identities=11%  Similarity=0.074  Sum_probs=30.7

Q ss_pred             hHHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      ..+++++.. ..+.-.+|.+++|+|||..++.++..   .+.+++|+.
T Consensus        34 ~~LD~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fS   81 (338)
T 4a1f_A           34 VQLDNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFS   81 (338)
T ss_dssp             HHHHHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             hHHHHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            456666653 12356788899999999998877654   356777764

>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=92.36  E-value=0.0075  Score=45.39  Aligned_cols=32  Identities=19%  Similarity=0.289  Sum_probs=23.7

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .+..++.+|+|+|||.++-+++.+.+.+++.+
T Consensus       238 p~GILL~GPPGTGKT~LAraiA~elg~~~~~v  269 (806)
T 3cf2_A          238 PRGILLYGPPGTGKTLIARAVANETGAFFFLI  269 (806)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHTTTTCEEEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCeEEEE
Confidence            35678889999999999877766655544433

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=92.28  E-value=0.021  Score=34.65  Aligned_cols=23  Identities=17%  Similarity=-0.162  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.++.|||||+++-.+...
T Consensus        11 ~~I~l~G~~GsGKST~~~~L~~~   33 (212)
T 2wwf_A           11 KFIVFEGLDRSGKSTQSKLLVEY   33 (212)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHH
Confidence            45678899999999998766554

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=92.27  E-value=0.019  Score=36.78  Aligned_cols=21  Identities=24%  Similarity=0.208  Sum_probs=17.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|++|.|||||+++-.++
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La   48 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALA   48 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            467789999999999885554

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=92.26  E-value=0.015  Score=34.75  Aligned_cols=22  Identities=14%  Similarity=-0.076  Sum_probs=17.2

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .++.++.|||||+++-.+...+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            4578999999999987665543

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=92.26  E-value=0.016  Score=34.02  Aligned_cols=21  Identities=24%  Similarity=0.112  Sum_probs=16.6

Q ss_pred             eeEEEeCCCCceeEeeeeEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .++.+++|||||+++-.+...
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~   23 (168)
T 2pt5_A            3 IYLIGFMCSGKSTVGSLLSRS   23 (168)
T ss_dssp             EEEESCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467899999999988665543

>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=92.25  E-value=0.0099  Score=38.31  Aligned_cols=22  Identities=36%  Similarity=0.650  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...+|.+|+|+|||+.+..++.
T Consensus        31 ~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           31 TVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            5788899999999998876553

>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=92.22  E-value=0.019  Score=34.70  Aligned_cols=24  Identities=13%  Similarity=-0.082  Sum_probs=19.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.++.|||||+++-.+....
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHH
Confidence            456788999999999987766655

>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=92.19  E-value=0.03  Score=34.47  Aligned_cols=19  Identities=37%  Similarity=0.314  Sum_probs=15.6

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ....|++|+|+|||++.-.
T Consensus        21 ei~~l~GpnGsGKSTLl~~   39 (207)
T 1znw_A           21 RVVVLSGPSAVGKSTVVRC   39 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5677899999999987643

>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=92.11  E-value=0.017  Score=37.05  Aligned_cols=23  Identities=17%  Similarity=0.008  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~   27 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKI   27 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHH
Confidence            35677899999999998766654

>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=92.11  E-value=0.006  Score=42.92  Aligned_cols=32  Identities=13%  Similarity=-0.002  Sum_probs=23.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++|+|+|||+++..++..+   +++++++.
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            456777999999999987666543   45666554

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=92.11  E-value=0.042  Score=37.77  Aligned_cols=34  Identities=18%  Similarity=0.133  Sum_probs=21.4

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+...+       .|.+...+..+.||||||+++..
T Consensus        84 sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM~G  124 (359)
T 3nwn_A           84 SQDLVYETVAKDVVSQALDGYNGTIMCYGQTGAGKTYTMMG  124 (359)
T ss_dssp             CHHHHHHHHTHHHHHHHHTTCCEEEEEEESTTSSHHHHHTB
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCEEEEEeCCCCCCccEEeCC
Confidence            36666554321       23334455569999999998764

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=92.08  E-value=0.022  Score=36.42  Aligned_cols=23  Identities=13%  Similarity=0.016  Sum_probs=17.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +..+|.+|+||||++.+..++.+
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            45677899999999988655543

>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=92.05  E-value=0.024  Score=34.44  Aligned_cols=23  Identities=22%  Similarity=-0.096  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.++.|||||+++-.+...
T Consensus        10 ~~I~l~G~~GsGKsT~~~~L~~~   32 (215)
T 1nn5_A           10 ALIVLEGVDRAGKSTQSRKLVEA   32 (215)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            45678899999999998766554

>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=92.04  E-value=0.053  Score=37.22  Aligned_cols=34  Identities=18%  Similarity=0.062  Sum_probs=21.6

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .|.+...+..+.||||||+++..
T Consensus        68 ~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM~G  108 (359)
T 1x88_A           68 KQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTMEG  108 (359)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHHTB
T ss_pred             chhHHHHHHHHHhHHHHhCCCceEEEEeCCCCCCCceEEec
Confidence            47766655321       23333455569999999998764

>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=92.03  E-value=0.041  Score=37.32  Aligned_cols=34  Identities=15%  Similarity=0.005  Sum_probs=21.7

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+...+       .|.+...+..+.||||||+++..
T Consensus        57 sQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G   97 (325)
T 1bg2_A           57 SQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG   97 (325)
T ss_dssp             CHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             CHHHHHHHHhhhhHHHHhCCCeEEEEEECCCCCCCceEecc
Confidence            47766655321       23334455569999999998864

>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=92.02  E-value=0.026  Score=35.83  Aligned_cols=20  Identities=30%  Similarity=0.326  Sum_probs=15.9

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|++|.|+|||++.-.+
T Consensus        17 ~ii~l~GpsGsGKSTLlk~L   36 (219)
T 1s96_A           17 TLYIVSAPSGAGKSSLIQAL   36 (219)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            56778899999999876443

>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=91.95  E-value=0.0084  Score=42.38  Aligned_cols=32  Identities=19%  Similarity=0.146  Sum_probs=23.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++++|+|||+++..++..+   +.+++++.
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~  135 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVC  135 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            456778999999999997776543   45666554

>3qkt_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATP binding, DNA bindi MRE11, replication; HET: DNA ANP; 1.90A {Pyrococcus furiosus} PDB: 3qku_A* 1ii8_A 3qks_B* 3qkr_B* 1ii8_B

Probab=91.90  E-value=0.028  Score=37.47  Aligned_cols=33  Identities=21%  Similarity=0.269  Sum_probs=21.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      .+|+|...-++  +..   +-.+|++|+|+|||.+.-+
T Consensus        10 nF~~~~~~~i~--f~~---~~~~i~G~NGsGKS~lleA   42 (339)
T 3qkt_A           10 NFRSHSDTVVE--FKE---GINLIIGQNGSGKSSLLDA   42 (339)
T ss_dssp             EETTEEEEEEE--CCS---EEEEEECCTTSSHHHHHHH
T ss_pred             cccCccCeEEc--CCC---CeEEEECCCCCCHHHHHHH
Confidence            56777543221  222   5678999999999988754

>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=91.89  E-value=0.035  Score=34.05  Aligned_cols=16  Identities=25%  Similarity=0.208  Sum_probs=13.3

Q ss_pred             eeeEEEeCCCCceeEe
Q psy11637         30 SGVIVLPCGAGKSLVG   45 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~   45 (67)
                      +..|.+|+|+|||+..
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            3468999999999875

>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=91.87  E-value=0.047  Score=37.39  Aligned_cols=33  Identities=9%  Similarity=0.038  Sum_probs=21.3

Q ss_pred             chhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.        +++ |.+...+..+.||||||.++..
T Consensus        57 tQ~~Vy~~~~~plv~~~l~-G~n~tifAYGqTGSGKTyTM~G   97 (349)
T 1t5c_A           57 TTKNVYEEIAAPIIDSAIQ-GYNGTIFAYGQTASGKTYTMMG   97 (349)
T ss_dssp             CHHHHHHHTTHHHHHHHHT-TCCEEEEEEESTTSSHHHHHTB
T ss_pred             CHHHHHHHHHHHHHHHHHc-CCccceeeecCCCCCCCeEEec
Confidence            47666654        333 3334455569999999998753

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=91.81  E-value=0.02  Score=36.92  Aligned_cols=21  Identities=19%  Similarity=-0.018  Sum_probs=16.8

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..++.+++|||||+++-.+..
T Consensus         4 ~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            4 IILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            457889999999998865554

>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=91.81  E-value=0.048  Score=37.74  Aligned_cols=33  Identities=15%  Similarity=0.016  Sum_probs=21.5

Q ss_pred             chhhHHHHH--------hcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKM--------FGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~--------~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..++.        ++ |.+...+..+.||||||+++..
T Consensus        81 ~Q~~Vy~~~~~plv~~~l~-G~n~tifAYGqTGSGKTyTM~G  121 (372)
T 3b6u_A           81 KQFELYDETFRPLVDSVLQ-GFNGTIFAYGQTGTGKTYTMEG  121 (372)
T ss_dssp             CHHHHHHHTHHHHHHHHHT-TCCEEEEEEESTTSSHHHHHTB
T ss_pred             chHHHHHHHHHHHHHHHhC-CCeeeEEeecCCCCCCCEeEec
Confidence            477766553        33 3334455569999999988754

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=91.79  E-value=0.0087  Score=43.59  Aligned_cols=27  Identities=26%  Similarity=0.225  Sum_probs=20.5

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      +.++.+|+|+|||.++-.+....+.+.
T Consensus       490 ~~ll~G~~GtGKT~la~~la~~l~~~~  516 (758)
T 1r6b_X          490 SFLFAGPTGVGKTEVTVQLSKALGIEL  516 (758)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHhcCCE
Confidence            678999999999999866655544443

>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=91.77  E-value=0.029  Score=46.90  Aligned_cols=25  Identities=20%  Similarity=0.450  Sum_probs=19.4

Q ss_pred             HHHHhcCCcceeeeEEEeCCCCceeEe
Q psy11637         19 LRKMFGNGRARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        19 v~~~~~~~~~~~~~i~~pTGsGKT~i~   45 (67)
                      ++.+++.+  +..++++|||+|||.++
T Consensus      1260 l~~~l~~~--~~vLL~GPpGtGKT~la 1284 (2695)
T 4akg_A         1260 FYDLLNSK--RGIILCGPPGSGKTMIM 1284 (2695)
T ss_dssp             HHHHHHHT--CEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCC--CeEEEECCCCCCHHHHH
Confidence            34455544  68999999999999887

>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=91.73  E-value=0.036  Score=37.34  Aligned_cols=31  Identities=23%  Similarity=0.276  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .+.+|.+|||+|||+....++..   .+.+++++
T Consensus        36 ~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~   69 (392)
T 4ag6_A           36 SNWTILAKPGAGKSFTAKMLLLREYMQGSRVIII   69 (392)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             CceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEE
Confidence            68899999999999877554433   24455544

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=91.73  E-value=0.023  Score=35.57  Aligned_cols=22  Identities=27%  Similarity=0.215  Sum_probs=17.2

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .++.+|+|||||+++-.+....
T Consensus         3 I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4678999999999886665443

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=91.73  E-value=0.0088  Score=40.05  Aligned_cols=32  Identities=16%  Similarity=0.038  Sum_probs=22.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++|+|+|||+++..++...   +++++++.
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~  139 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAA  139 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEc
Confidence            456788999999999887665542   45565543

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=91.72  E-value=0.046  Score=38.06  Aligned_cols=34  Identities=24%  Similarity=0.221  Sum_probs=21.7

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .|.+...+..+.||||||+++..
T Consensus        78 tQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTM~G  118 (388)
T 3bfn_A           78 TQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTMLG  118 (388)
T ss_dssp             CHHHHHHHHTGGGHHHHTTTCCEEEEEESCTTSSHHHHHTB
T ss_pred             CHhHHHHHHHHHHHHHhhcCceeeEeeecCCCCCCCeEeec
Confidence            47777765322       23223445569999999988753

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=91.72  E-value=0.03  Score=34.88  Aligned_cols=20  Identities=25%  Similarity=0.202  Sum_probs=16.4

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +-.+|++|+|+|||.+.-++
T Consensus        24 ~~~~I~G~NgsGKStil~ai   43 (203)
T 3qks_A           24 GINLIIGQNGSGKSSLLDAI   43 (203)
T ss_dssp             EEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHHHH
Confidence            57789999999999886443

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=91.66  E-value=0.042  Score=37.70  Aligned_cols=34  Identities=24%  Similarity=0.130  Sum_probs=21.7

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .|.+...+..+.||||||+++..
T Consensus        60 ~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G  100 (355)
T 1goj_A           60 KQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMMG  100 (355)
T ss_dssp             CHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             ccHHHHHHHHHHHHHHHhCCCcceEEEECCCCCCcceEeec
Confidence            47776664221       23334455569999999998754

>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=91.60  E-value=0.026  Score=33.78  Aligned_cols=23  Identities=22%  Similarity=0.082  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....+.++.|||||+++-.+...
T Consensus         6 ~~i~l~G~~GsGKST~~~~L~~~   28 (179)
T 2pez_A            6 CTVWLTGLSGAGKTTVSMALEEY   28 (179)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            45668899999999988655443

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=91.52  E-value=0.016  Score=39.82  Aligned_cols=45  Identities=16%  Similarity=0.148  Sum_probs=30.9

Q ss_pred             hHHHHHhc----CC-cceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEee
Q psy11637         17 KSLRKMFG----NG-RARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~----~~-~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p   61 (67)
                      ..+++.+.    .+ ..+...|.+|+|+|||.+++.++...     +++++++..
T Consensus        12 ~~LD~~LGg~~~GGl~~GiteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~   66 (333)
T 3io5_A           12 PMMNIALSGEITGGMQSGLLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDS   66 (333)
T ss_dssp             HHHHHHHHSSTTCCBCSEEEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEES
T ss_pred             HHHHHHhCCCCCCCCcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEec
Confidence            45677776    43 12367788999999999988776542     456777643

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=91.52  E-value=0.034  Score=38.23  Aligned_cols=17  Identities=18%  Similarity=0.145  Sum_probs=13.7

Q ss_pred             eeEEEeCCCCceeEeee
Q psy11637         31 GVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~   47 (67)
                      .+..+.||||||+++..
T Consensus        88 ifAYGqTGSGKTyTM~G  104 (360)
T 1ry6_A           88 CFAYGQTGSGKTYTMLG  104 (360)
T ss_dssp             EEEECCTTSSHHHHHHB
T ss_pred             EEeeCCCCCCCCEEEec
Confidence            45669999999988754

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=91.48  E-value=0.019  Score=36.36  Aligned_cols=22  Identities=18%  Similarity=-0.153  Sum_probs=16.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...-|.+|.|||||+++-.+..
T Consensus        26 ~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           26 FLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4566789999999998854443

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=91.44  E-value=0.0087  Score=42.65  Aligned_cols=30  Identities=20%  Similarity=0.292  Sum_probs=21.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      ...++.+|+|+|||+++-+++...+.+.+.
T Consensus        65 ~GvLL~GppGtGKTtLaraIa~~~~~~~i~   94 (499)
T 2dhr_A           65 KGVLLVGPPGVGKTHLARAVAGEARVPFIT   94 (499)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHTTCCEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEE
Confidence            347889999999999886665544434333

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=91.44  E-value=0.052  Score=37.40  Aligned_cols=35  Identities=17%  Similarity=0.022  Sum_probs=22.0

Q ss_pred             cchhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         13 PYQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        13 ~yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      .-|++..+....       .|.+...+..+.||||||+++..
T Consensus        63 ~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G  104 (365)
T 2y65_A           63 ASQEKVYNEAAKSIVTDVLAGYNGTIFAYGQTSSGKTHTMEG  104 (365)
T ss_dssp             CCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             CCHHHHHHHhhhhHHHHHhCCCceEEEeecCCCCCCceEEec
Confidence            347776655321       23334455569999999998753

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=91.35  E-value=0.0095  Score=40.01  Aligned_cols=31  Identities=16%  Similarity=0.095  Sum_probs=22.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      +...+++|+|+|||+++..++..   .+++++++
T Consensus       106 ~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVlli  139 (320)
T 1zu4_A          106 NIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIA  139 (320)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            45667799999999998766543   25666665

>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=91.35  E-value=0.017  Score=41.10  Aligned_cols=23  Identities=17%  Similarity=0.180  Sum_probs=18.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+|+|+|||+++-.+...
T Consensus       109 ~~vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A          109 PILCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             CEEEEESSSSSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            56888999999999988655443

>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=91.34  E-value=0.0079  Score=38.90  Aligned_cols=34  Identities=21%  Similarity=0.088  Sum_probs=25.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~   62 (67)
                      .--++.+|.|+|||+.++..+.+.   +.+++++.|.
T Consensus        29 ~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k~~   65 (214)
T 2j9r_A           29 WIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFKPC   65 (214)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEec
Confidence            345567999999999888777653   5678887764

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=91.32  E-value=0.076  Score=35.99  Aligned_cols=32  Identities=19%  Similarity=0.166  Sum_probs=24.6

Q ss_pred             hhHHHHHhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         16 EKSLRKMFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      ..+++.++.-+++....|.+|.|+|||++.-.
T Consensus        59 ~~ald~ll~i~~Gq~~gIiG~nGaGKTTLl~~   90 (347)
T 2obl_A           59 VRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGM   90 (347)
T ss_dssp             CHHHHHHSCEETTCEEEEEECTTSSHHHHHHH
T ss_pred             CEEEEeeeeecCCCEEEEECCCCCCHHHHHHH
Confidence            56888887544447888999999999988533

>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=91.30  E-value=0.058  Score=36.95  Aligned_cols=19  Identities=21%  Similarity=0.086  Sum_probs=14.4

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...+..+.||||||.++..
T Consensus        94 ~tifAYGqTGSGKTyTm~G  112 (354)
T 3gbj_A           94 ACIFAYGQTGSGKSYTMMG  112 (354)
T ss_dssp             EEEEEEECTTSSHHHHHTB
T ss_pred             eEEEeeCCCCCCCceEEec
Confidence            3445569999999998753

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=91.28  E-value=0.01  Score=39.40  Aligned_cols=32  Identities=22%  Similarity=0.203  Sum_probs=23.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .-.+..+..|.|||+++.+++..   .+.+++++-
T Consensus        15 ~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   49 (324)
T 3zq6_A           15 TFVFIGGKGGVGKTTISAATALWMARSGKKTLVIS   49 (324)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEeCCCCchHHHHHHHHHHHHHHCCCcEEEEe
Confidence            34666799999999999877654   356777653

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=91.27  E-value=0.048  Score=37.39  Aligned_cols=33  Identities=15%  Similarity=0.055  Sum_probs=21.3

Q ss_pred             chhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.        +++ |.+...+..+.||||||+++..
T Consensus        69 ~Q~~Vy~~~~~plv~~~l~-G~n~tifAYGqTGSGKTyTm~G  109 (350)
T 2vvg_A           69 CNYGIFQASFKPLIDAVLE-GFNSTIFAYGQTGAGKTWTMGG  109 (350)
T ss_dssp             CHHHHHHHTTHHHHHHHHT-TCCEEEEEECSTTSSHHHHHTB
T ss_pred             chhHHHHHHHHHHHHHHhC-CCceeEEeecCCCCCCCEEeec
Confidence            47666654        333 3334455569999999988753

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=91.19  E-value=0.015  Score=35.36  Aligned_cols=20  Identities=25%  Similarity=-0.011  Sum_probs=15.8

Q ss_pred             eeEEEeCCCCceeEeeeeEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+|.+|.|||||+++-.+..
T Consensus         3 I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            46789999999998865543

>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=91.14  E-value=0.054  Score=36.89  Aligned_cols=34  Identities=18%  Similarity=0.071  Sum_probs=21.3

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .+.+...+..+.||||||+++..
T Consensus        63 ~Q~~vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G  103 (344)
T 4a14_A           63 GQEAVYQACVQPLLEAFFEGFNATVFAYGQTGSGKTYTMGE  103 (344)
T ss_dssp             CHHHHHHHHTHHHHHHHHTTCCEEEEEESSTTSSHHHHHCC
T ss_pred             chhHHHHHHHHHHHHHHHhhcCeeEEEecccCCCceEeecc
Confidence            47776655321       23323455569999999998753

>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=91.08  E-value=0.047  Score=34.86  Aligned_cols=17  Identities=35%  Similarity=0.350  Sum_probs=14.8

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      +...|++|.|||||+..
T Consensus        32 e~~~iiG~nGsGKSTLl   48 (235)
T 3tif_A           32 EFVSIMGPSGSGKSTML   48 (235)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCcHHHHH
Confidence            67789999999999876

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=91.06  E-value=0.059  Score=37.69  Aligned_cols=43  Identities=21%  Similarity=0.208  Sum_probs=30.6

Q ss_pred             eeeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637          9 AVLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.=|+...+.+.+++..  +..+...|++|.|.|||.++..+...
T Consensus       126 ~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             CCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             ecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            44477777777777753  22356778899999999998766543

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=91.03  E-value=0.012  Score=41.22  Aligned_cols=32  Identities=13%  Similarity=0.147  Sum_probs=23.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++++|+|||+++..++...   +.+++++.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~  134 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIA  134 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            356788999999999997776543   45666553

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=91.00  E-value=0.063  Score=33.98  Aligned_cols=17  Identities=29%  Similarity=0.241  Sum_probs=14.6

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      +...|++|.|+|||+..
T Consensus        31 e~~~iiG~nGsGKSTLl   47 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLL   47 (224)
T ss_dssp             CEEEEEECTTSCHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            56778999999999875

>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=90.86  E-value=0.053  Score=33.39  Aligned_cols=23  Identities=17%  Similarity=0.014  Sum_probs=18.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++.+++|||||+++-.+...
T Consensus        26 ~~i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           26 LTIWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            56778899999999988665443

>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=90.84  E-value=0.037  Score=36.62  Aligned_cols=32  Identities=19%  Similarity=0.189  Sum_probs=22.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      +..++++|+|+|||+++..++...    +.+++++.
T Consensus       106 ~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~  141 (296)
T 2px0_A          106 KYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFIT  141 (296)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            467788999999999987665432    34665543

>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=90.82  E-value=0.033  Score=38.62  Aligned_cols=33  Identities=24%  Similarity=0.288  Sum_probs=23.8

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ..+++++..+  .+....|.+|+|+|||..+..++
T Consensus       165 ~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la  199 (400)
T 3lda_A          165 KNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLA  199 (400)
T ss_dssp             HHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHH
T ss_pred             hhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHH
Confidence            3466777543  24678889999999999887543

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=90.77  E-value=0.028  Score=35.35  Aligned_cols=19  Identities=32%  Similarity=0.293  Sum_probs=15.6

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      ..++.+++|||||..+...
T Consensus         7 i~l~tG~pGsGKT~~a~~~   25 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSM   25 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHH
Confidence            4578899999999987653

>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=90.70  E-value=0.07  Score=37.42  Aligned_cols=33  Identities=21%  Similarity=0.166  Sum_probs=21.2

Q ss_pred             chhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.        +++ |.+...+..+.||||||+++..
T Consensus       134 tQ~~Vy~~~~~plV~~~l~-G~N~tifAYGQTGSGKTyTM~G  174 (410)
T 1v8k_A          134 SNEVVYRFTARPLVQTIFE-GGKATCFAYGQTGSGKTHTMGG  174 (410)
T ss_dssp             CHHHHHHHTTHHHHHHHHT-TCEEEEEEEESTTSSHHHHHHC
T ss_pred             ChhhhhHHHHHHHHHHHhc-CCceeEEeecCCCCCCCeEeec
Confidence            47666654        333 3323455569999999998765

>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=90.65  E-value=0.057  Score=36.99  Aligned_cols=33  Identities=18%  Similarity=0.200  Sum_probs=21.0

Q ss_pred             chhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.        +++ |.+...+..+.||||||+++..
T Consensus        85 ~Q~~Vy~~~~~plv~~~l~-G~n~tifAYGqTGSGKTyTm~G  125 (355)
T 3lre_A           85 TQSEVFEHTTKPILRSFLN-GYNCTVLAYGATGAGKTHTMLG  125 (355)
T ss_dssp             CHHHHHHTTHHHHHHHHTT-TCCEEEEEECCTTSSHHHHHTB
T ss_pred             ChHHHHHHHHHHHHHHHhC-CCceEEEEeCCCCCCceeeecc
Confidence            37666654        233 3334455569999999998754

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=90.56  E-value=0.03  Score=34.49  Aligned_cols=21  Identities=24%  Similarity=0.126  Sum_probs=16.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.++.|||||+++-.+.
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~   25 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFA   25 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            346678999999999876554

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=90.52  E-value=0.0098  Score=38.85  Aligned_cols=30  Identities=17%  Similarity=0.139  Sum_probs=22.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~li   58 (67)
                      -+.++.+++|.|||++++.++..+   +.++++
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v   39 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMA   39 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEE
Confidence            457788999999999988776553   345543

>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=90.51  E-value=0.016  Score=40.46  Aligned_cols=43  Identities=7%  Similarity=-0.119  Sum_probs=29.3

Q ss_pred             HHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         18 SLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        18 av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      .+++++.. ..+.-.+|.+++|+|||..++.++...    +.+++++.
T Consensus       231 ~LD~~lgGl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s  278 (503)
T 1q57_A          231 GINDKTLGARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAM  278 (503)
T ss_dssp             THHHHHCCCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEE
T ss_pred             hhhHhhcccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEe
Confidence            34555532 123567888999999999998776542    45777765

>1e69_A Chromosome segregation SMC protein; structural maintenance of chromosomes, coiled coil; 3.1A {Thermotoga maritima} SCOP: c.37.1.12

Probab=90.42  E-value=0.054  Score=35.78  Aligned_cols=20  Identities=40%  Similarity=0.396  Sum_probs=16.2

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +..+|++|+|+|||.+.-++
T Consensus        25 g~~~i~G~NGsGKS~ll~ai   44 (322)
T 1e69_A           25 RVTAIVGPNGSGKSNIIDAI   44 (322)
T ss_dssp             SEEEEECCTTTCSTHHHHHH
T ss_pred             CcEEEECCCCCcHHHHHHHH
Confidence            47789999999999877443

>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=90.41  E-value=0.053  Score=37.09  Aligned_cols=32  Identities=19%  Similarity=0.185  Sum_probs=20.5

Q ss_pred             chhhHHHHH--------hcCCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLRKM--------FGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~~~--------~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..+..        ++ |.+...+..+.||||||.++.
T Consensus        74 sQ~~Vy~~~~~plv~~~l~-G~N~tifAYGQTGSGKTyTM~  113 (344)
T 3dc4_A           74 SQDEMYQALILPLVDKLLE-GFQCTALAYGQTGTGKSYSMG  113 (344)
T ss_dssp             CHHHHHHHHTHHHHHHHHH-TCCEEEEEESSTTSSHHHHHT
T ss_pred             CHHHHHHhhccchhhHhhC-CCceEEEEecCCCCCCCeEEc
Confidence            476666553        33 322345556999999999863

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=90.31  E-value=0.035  Score=36.07  Aligned_cols=22  Identities=36%  Similarity=0.362  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|++++|+|||+++-.++.
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6788999999999998865554

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=90.30  E-value=0.031  Score=33.77  Aligned_cols=21  Identities=29%  Similarity=0.218  Sum_probs=16.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...|.++.|||||+++-.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356789999999998865544

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=90.26  E-value=0.032  Score=35.44  Aligned_cols=23  Identities=17%  Similarity=-0.054  Sum_probs=17.6

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...|.++.|||||+++-.+...+
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45677999999999986665543

>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=90.24  E-value=0.069  Score=34.13  Aligned_cols=18  Identities=28%  Similarity=0.237  Sum_probs=15.4

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        29 e~~~i~G~nGsGKSTLl~   46 (243)
T 1mv5_A           29 SIIAFAGPSGGGKSTIFS   46 (243)
T ss_dssp             EEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            677899999999998763

>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=90.22  E-value=0.064  Score=37.33  Aligned_cols=33  Identities=21%  Similarity=0.166  Sum_probs=20.7

Q ss_pred             chhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.        +++ +.....+..+.||||||+++..
T Consensus       114 sQ~~Vy~~~~~plv~~~l~-G~N~tifAYGQTGSGKTyTM~G  154 (387)
T 2heh_A          114 SNEVVYRFTARPLVQTIFE-GGKATCFAYGQTGSGKTHTMGG  154 (387)
T ss_dssp             CHHHHHHHTTHHHHHHHHT-TCEEEEEEESCTTSSHHHHHC-
T ss_pred             CceeehhhhHHHHHHHHhc-CCceEEEEecCCCCCCCeEecc
Confidence            47666654        333 3223445559999999998765

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=90.19  E-value=0.03  Score=47.53  Aligned_cols=28  Identities=21%  Similarity=0.355  Sum_probs=20.3

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      .++.++..+  +..++++|||+|||.+...
T Consensus      1296 ll~~ll~~~--~pvLL~GptGtGKT~li~~ 1323 (3245)
T 3vkg_A         1296 VLHAWLSEH--RPLILCGPPGSGKTMTLTS 1323 (3245)
T ss_dssp             HHHHHHHTT--CCCEEESSTTSSHHHHHHH
T ss_pred             HHHHHHHCC--CcEEEECCCCCCHHHHHHH
Confidence            344455554  6899999999999966533

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=90.16  E-value=0.13  Score=35.83  Aligned_cols=19  Identities=26%  Similarity=0.137  Sum_probs=15.2

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      ...+++|+|+|||+..-.+
T Consensus        71 ~valvG~nGaGKSTLln~L   89 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTL   89 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHH
Confidence            6678899999999876433

>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTPase, GTP binding, protein binding, signali protein; HET: GNP; 2.30A {Homo sapiens}

Probab=89.62  E-value=0.055  Score=32.57  Aligned_cols=42  Identities=21%  Similarity=0.156  Sum_probs=27.5

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...|+|-+...-+.++.. +.-+.++++++|+|||.+...+..
T Consensus        11 ~~~~~~~~~~m~~~~~~~-~~~ki~v~G~~~~GKSsli~~l~~   52 (204)
T 3th5_A           11 SSGLVPRGSHMENLYFQG-QAIKCVVVGDGAVGKTCLLISYTT   52 (204)
Confidence            455666555544444432 235678899999999988865543

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=90.13  E-value=0.062  Score=37.06  Aligned_cols=34  Identities=21%  Similarity=0.101  Sum_probs=21.5

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .+.+...+..+.||||||+++..
T Consensus        80 ~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G  120 (373)
T 2wbe_C           80 KQCDVYSVVVSPLIEEVLNGYNCTVFAYGQTGTGKTHTMVG  120 (373)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHTB
T ss_pred             chhHHHHHHHHHHHHHHhCCceEEEEeecCCCCCcceeccc
Confidence            47776655321       13324455569999999998754

>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=90.09  E-value=0.065  Score=34.23  Aligned_cols=18  Identities=28%  Similarity=0.176  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        32 e~~~i~G~nGsGKSTLl~   49 (237)
T 2cbz_A           32 ALVAVVGQVGCGKSSLLS   49 (237)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            677899999999998763

>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=90.07  E-value=0.015  Score=41.35  Aligned_cols=35  Identities=6%  Similarity=-0.042  Sum_probs=30.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecc
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSG   63 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~   63 (67)
                      .+..+.+-+|||||+++..++...++++|||+|+.
T Consensus        15 ~~~~l~g~~gs~ka~~~a~l~~~~~~p~lvv~~~~   49 (483)
T 3hjh_A           15 EQRLLGELTGAACATLVAEIAERHAGPVVLIAPDM   49 (483)
T ss_dssp             CEEEEECCCTTHHHHHHHHHHHHSSSCEEEEESSH
T ss_pred             CeEEEeCCCchHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            46788999999999999988888889999999974

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=90.01  E-value=0.045  Score=35.69  Aligned_cols=21  Identities=24%  Similarity=0.022  Sum_probs=16.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.++.|||||+++-.+.
T Consensus        76 ~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            346678999999999885554

>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=89.97  E-value=0.07  Score=35.09  Aligned_cols=18  Identities=28%  Similarity=0.167  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|||||+..-
T Consensus        35 e~~~iiGpnGsGKSTLl~   52 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQ   52 (275)
T ss_dssp             SEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998764

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=89.93  E-value=0.047  Score=36.43  Aligned_cols=21  Identities=14%  Similarity=-0.114  Sum_probs=16.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.+|+|||||+++-.+.
T Consensus        91 ~ivgI~G~sGsGKSTL~~~L~  111 (312)
T 3aez_A           91 FIIGVAGSVAVGKSTTARVLQ  111 (312)
T ss_dssp             EEEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCchHHHHHHHHH
Confidence            456678999999999875443

>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=89.89  E-value=0.095  Score=36.15  Aligned_cols=32  Identities=16%  Similarity=0.127  Sum_probs=20.2

Q ss_pred             chhhHHHH-------HhcCCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLRK-------MFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~~-------~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..+.       +++ |.+...+..+.||||||+++.
T Consensus        60 ~Q~~Vy~~~~~lv~~~l~-G~n~tifAYGqTGSGKTyTM~   98 (369)
T 3cob_A           60 TQDDVFEDTKYLVQSAVD-GYNVCIFAYGQTGSGKTFTIY   98 (369)
T ss_dssp             CHHHHHHTTTHHHHHHHT-TCEEEEEEEECTTSSHHHHHT
T ss_pred             CcceehhhhhhhhHhhhc-CCceEEEEECCCCCCCeEeec
Confidence            46666554       333 322344455999999998874

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=89.86  E-value=0.045  Score=40.03  Aligned_cols=22  Identities=23%  Similarity=0.297  Sum_probs=18.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.++.+|||+|||.++-++...
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~  544 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAES  544 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5889999999999998666554

>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=89.77  E-value=0.071  Score=34.38  Aligned_cols=18  Identities=33%  Similarity=0.397  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        34 e~~~liG~nGsGKSTLlk   51 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLIN   51 (257)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998763

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=89.75  E-value=0.036  Score=36.64  Aligned_cols=24  Identities=21%  Similarity=0.210  Sum_probs=17.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ....|.+|+|||||+++-.+....
T Consensus        32 ~ii~I~G~sGsGKSTla~~L~~~l   55 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFTSIQIYNHL   55 (290)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            345677999999999886554443

>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=89.69  E-value=0.076  Score=34.60  Aligned_cols=18  Identities=39%  Similarity=0.361  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      +...|++|.|+|||+..-
T Consensus        38 e~~~liG~nGsGKSTLl~   55 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLR   55 (266)
T ss_dssp             CEEEEECCTTSCHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHH
Confidence            567789999999998763

>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=89.67  E-value=0.071  Score=36.67  Aligned_cols=33  Identities=27%  Similarity=0.228  Sum_probs=21.1

Q ss_pred             chhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.        +++ |.+...+..+.||||||+++..
T Consensus        69 sQ~~Vy~~~~~plv~~~l~-G~N~tifAYGqTGSGKTyTm~G  109 (366)
T 2zfi_A           69 SQKQVYRDIGEEMLQHAFE-GYNVCIFAYGQTGAGKSYTMMG  109 (366)
T ss_dssp             CHHHHHHHTHHHHHHHHHT-TCCEEEEEECSTTSSHHHHHTB
T ss_pred             cHHHHHHHHHHHHHHHHhc-CCeeEEEEeCCCCCCCceEeeC
Confidence            36666554        333 3334455569999999988754

>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=89.64  E-value=0.013  Score=44.17  Aligned_cols=29  Identities=17%  Similarity=0.288  Sum_probs=22.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRAL   57 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~l   57 (67)
                      +..++.+|+|+|||.++-+++.+.+.+.+
T Consensus       512 ~gvLl~GPPGtGKT~lAkaiA~e~~~~f~  540 (806)
T 3cf2_A          512 KGVLFYGPPGCGKTLLAKAIANECQANFI  540 (806)
T ss_dssp             SCCEEESSTTSSHHHHHHHHHHTTTCEEE
T ss_pred             ceEEEecCCCCCchHHHHHHHHHhCCceE
Confidence            45788899999999998777666554443

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=89.63  E-value=0.081  Score=35.13  Aligned_cols=31  Identities=19%  Similarity=0.102  Sum_probs=21.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ....+++|+|+|||++...++...   ++++++.
T Consensus       101 ~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V~l~  134 (302)
T 3b9q_A          101 AVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLMA  134 (302)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEE
Confidence            456788999999999886554432   3455444

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=89.63  E-value=0.17  Score=35.33  Aligned_cols=31  Identities=19%  Similarity=0.294  Sum_probs=24.3

Q ss_pred             hhHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         16 EKSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      ..+++.++.-.++....|.+|.|+|||++.-
T Consensus       145 ~~vld~vl~i~~Gq~~~IvG~sGsGKSTLl~  175 (438)
T 2dpy_A          145 VRAINALLTVGRGQRMGLFAGSGVGKSVLLG  175 (438)
T ss_dssp             CHHHHHHSCCBTTCEEEEEECTTSSHHHHHH
T ss_pred             ceEEeeeEEecCCCEEEEECCCCCCHHHHHH
Confidence            5688888664445788899999999998753

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=89.63  E-value=0.26  Score=28.66  Aligned_cols=30  Identities=23%  Similarity=0.263  Sum_probs=20.3

Q ss_pred             HHHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         20 RKMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        20 ~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +.++......+.++++++|+|||.+...+.
T Consensus        10 ~~~~~~~~~~~i~v~G~~~~GKssli~~l~   39 (183)
T 1moz_A           10 DKLWGSNKELRILILGLDGAGKTTILYRLQ   39 (183)
T ss_dssp             GGGTTCSSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             HHhcCCCCccEEEEECCCCCCHHHHHHHHh
Confidence            344441223678899999999998765444

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=89.63  E-value=0.041  Score=35.62  Aligned_cols=22  Identities=27%  Similarity=0.190  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.+|+|||||+++-.+..
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3577889999999998865543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.58  E-value=0.033  Score=45.72  Aligned_cols=45  Identities=22%  Similarity=0.217  Sum_probs=32.6

Q ss_pred             hHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         17 KSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        17 ~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      ..++..+. .+  .+.+.++.+|+|+|||.++.+++..   .+.+++|+..
T Consensus      1413 ~~LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~ 1463 (2050)
T 3cmu_A         1413 LSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA 1463 (2050)
T ss_dssp             HHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECT
T ss_pred             HHHHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEc
Confidence            34677776 32  2468889999999999999877654   3567777653

>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=89.56  E-value=0.08  Score=33.58  Aligned_cols=18  Identities=22%  Similarity=0.206  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        35 e~~~i~G~nGsGKSTLl~   52 (229)
T 2pze_A           35 QLLAVAGSTGAGKTSLLM   52 (229)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998763

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=89.47  E-value=0.089  Score=35.93  Aligned_cols=17  Identities=18%  Similarity=0.120  Sum_probs=13.1

Q ss_pred             eeeEEEeCCCCceeEee
Q psy11637         30 SGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~   46 (67)
                      ..+..+.||||||+++.
T Consensus        88 tifAYGqTGSGKTyTm~  104 (349)
T 3t0q_A           88 CIFAYGQTGSGKTYTML  104 (349)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             eEEEeCCCCCCCceEeC
Confidence            34455999999998874

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=89.43  E-value=0.083  Score=34.25  Aligned_cols=18  Identities=28%  Similarity=0.159  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        33 e~~~liG~nGsGKSTLlk   50 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLR   50 (262)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998763

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=89.35  E-value=0.09  Score=35.91  Aligned_cols=32  Identities=13%  Similarity=0.174  Sum_probs=20.0

Q ss_pred             chhhHHHHH-------hcCCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLRKM-------FGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~~~-------~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..+.+       ++ |.+...+..+.||||||+++.
T Consensus        65 ~Q~~Vy~~v~~lv~~~l~-G~n~tifAYGqTGSGKTyTM~  103 (347)
T 1f9v_A           65 TNVDVFKEVGQLVQSSLD-GYNVCIFAYGQTGSGKTFTML  103 (347)
T ss_dssp             CHHHHHHHHHHHHGGGGG-TCCEEEEEECCTTSSHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhcC-CceeEEEEECCCCCCCcEecc
Confidence            466666542       22 322344556999999998774

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=89.31  E-value=0.014  Score=43.30  Aligned_cols=24  Identities=29%  Similarity=0.358  Sum_probs=19.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+.++.+|+|+|||.++-.+....
T Consensus       589 ~~vLl~Gp~GtGKT~lA~~la~~~  612 (854)
T 1qvr_A          589 GSFLFLGPTGVGKTELAKTLAATL  612 (854)
T ss_dssp             EEEEEBSCSSSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            467889999999999886665543

>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=89.28  E-value=0.082  Score=33.77  Aligned_cols=18  Identities=22%  Similarity=0.187  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        33 e~~~l~G~nGsGKSTLl~   50 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLS   50 (240)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998763

>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=89.27  E-value=0.083  Score=33.48  Aligned_cols=18  Identities=22%  Similarity=0.108  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      +...|.+|.|+|||+..-
T Consensus        36 e~~~iiG~NGsGKSTLlk   53 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLK   53 (214)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998764

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=89.22  E-value=0.083  Score=34.22  Aligned_cols=18  Identities=28%  Similarity=0.370  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        47 e~~~i~G~nGsGKSTLl~   64 (260)
T 2ghi_A           47 TTCALVGHTGSGKSTIAK   64 (260)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            677899999999998763

>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=89.18  E-value=0.084  Score=33.96  Aligned_cols=18  Identities=33%  Similarity=0.209  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        36 e~~~i~G~nGsGKSTLl~   53 (247)
T 2ff7_A           36 EVIGIVGRSGSGKSTLTK   53 (247)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            577799999999998763

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=89.13  E-value=0.021  Score=37.87  Aligned_cols=31  Identities=13%  Similarity=-0.004  Sum_probs=21.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ..++++++|+|||+++..++...   +++++++.
T Consensus       100 vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~  133 (297)
T 1j8m_F          100 VIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVG  133 (297)
T ss_dssp             EEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            45677999999999887666443   45666543

>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=89.09  E-value=0.03  Score=37.14  Aligned_cols=33  Identities=18%  Similarity=0.058  Sum_probs=22.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE-EeeeeEEEeec
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT-VRKRALVLCNS   62 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~-~~~~~lil~p~   62 (67)
                      ..+|.++.|||||+..-.+... .+.++.|+.|.
T Consensus         6 v~~i~G~~GaGKTTll~~l~~~~~~~~~aVi~~d   39 (318)
T 1nij_A            6 VTLLTGFLGAGKTTLLRHILNEQHGYKIAVIENE   39 (318)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHSCCCCCEEEECSS
T ss_pred             EEEEEecCCCCHHHHHHHHHhhcCCCcEEEEEec
Confidence            4678899999999887544432 34566666654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=89.06  E-value=0.1  Score=34.05  Aligned_cols=17  Identities=29%  Similarity=0.245  Sum_probs=14.1

Q ss_pred             eeeEEEeCCCCceeEee
Q psy11637         30 SGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~   46 (67)
                      +..+++|+|+|||+..-
T Consensus         4 ~v~lvG~nGaGKSTLln   20 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVN   20 (270)
T ss_dssp             EEEEEESSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            56789999999998763

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=89.04  E-value=0.051  Score=35.77  Aligned_cols=22  Identities=27%  Similarity=0.045  Sum_probs=14.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...|.+|.|||||+++-.+...
T Consensus         7 iIgItG~sGSGKSTva~~L~~~   28 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQI   28 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3557799999999998666553

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=89.02  E-value=0.1  Score=35.85  Aligned_cols=28  Identities=18%  Similarity=0.147  Sum_probs=20.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      ...++.+|+|+|||+.+-.++...++.+
T Consensus       170 ~~i~l~G~~GsGKSTl~~~l~~~~~g~~  197 (377)
T 1svm_A          170 RYWLFKGPIDSGKTTLAAALLELCGGKA  197 (377)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHCCEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhcCCcE
Confidence            5677899999999998866554444443

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=89.00  E-value=0.1  Score=36.35  Aligned_cols=18  Identities=17%  Similarity=0.132  Sum_probs=13.7

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ...+..+.||||||+++.
T Consensus       142 ~tifAYGqTGSGKTyTM~  159 (403)
T 4etp_A          142 VAIFAYGQTGSGKTFTML  159 (403)
T ss_dssp             EEEEEESCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCCceEeC
Confidence            344556999999998874

>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=88.95  E-value=0.086  Score=35.37  Aligned_cols=31  Identities=16%  Similarity=0.127  Sum_probs=20.8

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      +....|++|+|+|||++.-.++....+.++.
T Consensus       126 Ge~vaIvGpsGsGKSTLl~lL~gl~~G~I~~  156 (305)
T 2v9p_A          126 KNCLAFIGPPNTGKSMLCNSLIHFLGGSVLS  156 (305)
T ss_dssp             CSEEEEECSSSSSHHHHHHHHHHHHTCEEEC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhhhcCceEEE
Confidence            3677899999999998875444322444433

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=88.95  E-value=0.091  Score=34.94  Aligned_cols=22  Identities=23%  Similarity=0.119  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....+++|+|+|||++...++.
T Consensus       103 ~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          103 RVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHH
Confidence            4667889999999998765543

>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=88.95  E-value=0.095  Score=33.89  Aligned_cols=17  Identities=41%  Similarity=0.333  Sum_probs=14.7

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|.+|.|+|||+..
T Consensus        27 e~~~liG~NGsGKSTLl   43 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLL   43 (249)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCcHHHHH
Confidence            56778999999999876

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=88.91  E-value=0.094  Score=37.00  Aligned_cols=33  Identities=24%  Similarity=0.224  Sum_probs=21.1

Q ss_pred             chhhHHHHH--------hcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKM--------FGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~--------~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+..        ++ |.+...+..+.||||||+++..
T Consensus       116 sQ~~Vy~~~~~plv~~~l~-GyN~tIfAYGQTGSGKTyTM~G  156 (443)
T 2owm_A          116 TQEHVYDSLGEEFLDHNFE-GYHTCIFAYGQTGSGKSYTMMG  156 (443)
T ss_dssp             CHHHHHHHHHHHHHHHHHT-TCCEEEEEESSTTSSHHHHHTC
T ss_pred             CHHHHHHhhhhhHHHHhhc-CCceEEEEeCCCCCCCCEEeec
Confidence            376666543        33 3334455569999999998753

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=88.88  E-value=0.096  Score=33.83  Aligned_cols=18  Identities=22%  Similarity=0.084  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        32 e~~~l~G~nGsGKSTLl~   49 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLD   49 (253)
T ss_dssp             CEEEEECCSSSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998763

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=88.85  E-value=0.082  Score=32.82  Aligned_cols=18  Identities=28%  Similarity=0.301  Sum_probs=14.4

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....+++|+|+|||+..-
T Consensus         2 ~~i~i~G~nG~GKTTll~   19 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIH   19 (189)
T ss_dssp             CCEEEESCCSSCHHHHHH
T ss_pred             CEEEEECCCCChHHHHHH
Confidence            356689999999998763

>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=88.80  E-value=0.098  Score=31.63  Aligned_cols=18  Identities=22%  Similarity=0.067  Sum_probs=14.8

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....+.+|.|+|||+..-
T Consensus        34 e~v~L~G~nGaGKTTLlr   51 (158)
T 1htw_A           34 IMVYLNGDLGAGKTTLTR   51 (158)
T ss_dssp             EEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998653

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=88.77  E-value=0.099  Score=36.13  Aligned_cols=21  Identities=29%  Similarity=0.434  Sum_probs=16.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      .+.++.+|+|+|||+++-.++
T Consensus        25 ~~i~l~G~~G~GKTTl~~~la   45 (359)
T 2ga8_A           25 VCVILVGSPGSGKSTIAEELC   45 (359)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHH
Confidence            347888999999999885444

>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=88.73  E-value=0.1  Score=33.91  Aligned_cols=18  Identities=28%  Similarity=0.187  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        42 ei~~l~G~NGsGKSTLlk   59 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLR   59 (256)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            577789999999998763

>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=88.69  E-value=0.1  Score=34.06  Aligned_cols=18  Identities=33%  Similarity=0.392  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      +...|.+|.|+|||+..-
T Consensus        51 ei~~liG~NGsGKSTLlk   68 (263)
T 2olj_A           51 EVVVVIGPSGSGKSTFLR   68 (263)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEEcCCCCcHHHHHH
Confidence            567789999999998763

>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=88.68  E-value=0.1  Score=33.94  Aligned_cols=17  Identities=35%  Similarity=0.505  Sum_probs=14.9

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|.+|.|+|||+..
T Consensus        47 e~~~l~G~NGsGKSTLl   63 (267)
T 2zu0_C           47 EVHAIMGPNGSGKSTLS   63 (267)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            57779999999999876

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=88.64  E-value=0.1  Score=34.27  Aligned_cols=18  Identities=22%  Similarity=0.119  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        48 e~~~liG~NGsGKSTLlk   65 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLN   65 (279)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHH
Confidence            567789999999998763

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=88.62  E-value=0.097  Score=33.96  Aligned_cols=18  Identities=22%  Similarity=0.180  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        34 e~~~liG~nGsGKSTLl~   51 (266)
T 2yz2_A           34 ECLLVAGNTGSGKSTLLQ   51 (266)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHH
Confidence            567789999999998763

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=88.61  E-value=0.025  Score=39.54  Aligned_cols=32  Identities=22%  Similarity=0.143  Sum_probs=23.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE----eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV----RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~----~~~~lil~   60 (67)
                      +..++++++|+|||+++..++..+    +.+++++.
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd  136 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVS  136 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEe
Confidence            456677999999999998776542    55666553

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=88.57  E-value=0.052  Score=37.34  Aligned_cols=22  Identities=32%  Similarity=0.036  Sum_probs=17.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .-.++++++|||||+++-.+..
T Consensus       259 ~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          259 EVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             CEEEEESCTTSSHHHHHHHHTG
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4567789999999998866543

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=88.51  E-value=0.051  Score=36.71  Aligned_cols=20  Identities=20%  Similarity=-0.060  Sum_probs=15.2

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ..-|.+|+|||||+++-.+.
T Consensus        94 iigI~GpsGSGKSTl~~~L~  113 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLK  113 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            35567999999999875443

>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=88.51  E-value=0.099  Score=33.56  Aligned_cols=18  Identities=39%  Similarity=0.562  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        30 e~~~l~G~nGsGKSTLlk   47 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGK   47 (250)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            567789999999998763

>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=88.44  E-value=0.025  Score=43.24  Aligned_cols=34  Identities=18%  Similarity=0.212  Sum_probs=25.7

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE------eeeeEEEeecce
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV------RKRALVLCNSGV   64 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~------~~~~lil~p~~~   64 (67)
                      .+|.+..|||||.+.+.=+..+      ..+++++||...
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            4788999999999887544321      368999998764

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=88.33  E-value=0.12  Score=35.71  Aligned_cols=33  Identities=15%  Similarity=0.165  Sum_probs=21.0

Q ss_pred             chhhHHHHH-------hcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKM-------FGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~-------~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+.+       ++ +.+...+..+.||||||+++..
T Consensus        96 ~Q~~Vy~~v~~lv~~~l~-G~N~tifAYGqTGSGKTyTM~G  135 (376)
T 2rep_A           96 GQDEVFEEIAMLVQSALD-GYPVCIFAYGQTGSGKTFTMEG  135 (376)
T ss_dssp             CHHHHHHHHHHHHHGGGG-TCCEEEEEECSTTSSHHHHHTB
T ss_pred             cchhhhhhHHHHHHHhcC-CCceEEEEeCCCCCCCceEeec
Confidence            476666542       22 3223445559999999998864

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=88.31  E-value=0.1  Score=33.48  Aligned_cols=18  Identities=39%  Similarity=0.429  Sum_probs=14.7

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        25 e~~~liG~nGsGKSTLl~   42 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLE   42 (240)
T ss_dssp             SEEEEECCTTSSHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHH
Confidence            466689999999998763

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=88.28  E-value=0.17  Score=34.03  Aligned_cols=23  Identities=17%  Similarity=0.001  Sum_probs=17.6

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +....+++|+|+|||++...++.
T Consensus       129 g~vi~lvG~nGaGKTTll~~Lag  151 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAKLAN  151 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35677889999999988755543

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=88.21  E-value=0.11  Score=33.94  Aligned_cols=18  Identities=39%  Similarity=0.569  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        46 e~~~i~G~nGsGKSTLlk   63 (271)
T 2ixe_A           46 KVTALVGPNGSGKSTVAA   63 (271)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            577799999999998763

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=88.13  E-value=0.092  Score=35.64  Aligned_cols=19  Identities=21%  Similarity=0.011  Sum_probs=14.4

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...+..+.||||||+++..
T Consensus        82 ~tifAYGqTGSGKTyTm~G  100 (330)
T 2h58_A           82 VCIFAYGQTGAGKTYTMEG  100 (330)
T ss_dssp             EEEEEESSTTSSHHHHHTB
T ss_pred             EEEEeECCCCCCCcEEEec
Confidence            3455569999999988754

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=88.00  E-value=0.065  Score=38.22  Aligned_cols=18  Identities=39%  Similarity=0.233  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus        48 e~~~LvG~NGaGKSTLlk   65 (538)
T 1yqt_A           48 MVVGIVGPNGTGKSTAVK   65 (538)
T ss_dssp             SEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            577789999999998763

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=87.79  E-value=0.032  Score=34.29  Aligned_cols=21  Identities=19%  Similarity=-0.004  Sum_probs=16.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...|++|+|||||+++..++.
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~   24 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMP   24 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            355789999999988755543

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=87.65  E-value=0.15  Score=34.89  Aligned_cols=31  Identities=19%  Similarity=0.102  Sum_probs=21.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ....+++|+|+|||++...++...   ++++++.
T Consensus       158 ~vi~lvG~nGsGKTTll~~Lag~l~~~~G~V~l~  191 (359)
T 2og2_A          158 AVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVLMA  191 (359)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             eEEEEEcCCCChHHHHHHHHHhhccccCCEEEEe
Confidence            457788999999999886554432   3455444

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=87.58  E-value=0.031  Score=35.67  Aligned_cols=34  Identities=24%  Similarity=0.185  Sum_probs=24.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~   62 (67)
                      .--++.+|.|+|||.-.+..+..   .+.+++++.|.
T Consensus        21 ~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~   57 (195)
T 1w4r_A           21 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYA   57 (195)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEET
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccc
Confidence            45678899999999655554443   25678888765

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=87.54  E-value=0.15  Score=33.70  Aligned_cols=18  Identities=22%  Similarity=0.206  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      +...|.+|.|+|||+..-
T Consensus        65 e~~~i~G~NGsGKSTLlk   82 (290)
T 2bbs_A           65 QLLAVAGSTGAGKTSLLM   82 (290)
T ss_dssp             CEEEEEESTTSSHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHH
Confidence            567789999999998763

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=87.41  E-value=0.065  Score=35.89  Aligned_cols=20  Identities=20%  Similarity=0.140  Sum_probs=16.2

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|++|.|+|||+.+-.+
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L  190 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKL  190 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            57788999999999876433

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=87.40  E-value=0.18  Score=30.27  Aligned_cols=27  Identities=19%  Similarity=-0.007  Sum_probs=18.9

Q ss_pred             hcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         23 FGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        23 ~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +.-..+....+++++|+|||...-.++
T Consensus        21 ~~~~~~~~v~lvG~~g~GKSTLl~~l~   47 (210)
T 1pui_A           21 LPSDTGIEVAFAGRSNAGKSSALNTLT   47 (210)
T ss_dssp             SSCSCSEEEEEEECTTSSHHHHHTTTC
T ss_pred             CCCCCCcEEEEECCCCCCHHHHHHHHh
Confidence            433333678899999999998764443

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=87.39  E-value=0.029  Score=37.41  Aligned_cols=31  Identities=19%  Similarity=0.231  Sum_probs=23.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .-.+..+..|.|||+++..++..   .+.+++++
T Consensus        20 ~i~v~sgkGGvGKTTva~~LA~~lA~~G~rVllv   53 (329)
T 2woo_A           20 KWIFVGGKGGVGKTTTSCSLAIQMSKVRSSVLLI   53 (329)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHHHHHTSSSCEEEE
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHHHHHCCCeEEEE
Confidence            45667789999999999776654   36677765

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=87.38  E-value=0.028  Score=37.12  Aligned_cols=32  Identities=19%  Similarity=0.204  Sum_probs=22.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ....+++++|+|||+++..++...   +++++++.
T Consensus        99 ~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~  133 (295)
T 1ls1_A           99 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA  133 (295)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEec
Confidence            455567999999999887665442   45666543

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=87.33  E-value=0.041  Score=35.06  Aligned_cols=47  Identities=23%  Similarity=0.179  Sum_probs=27.5

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      |.-+.+.-+..-+.. ..-.+...-.|.|||+++..++..+   +.+++++
T Consensus         4 ~~~~~~~a~~l~~~~-~vI~v~s~kGGvGKTT~a~nLA~~la~~G~~Vlli   53 (262)
T 2ph1_A            4 RVTDEEIKERLGKIK-SRIAVMSGKGGVGKSTVTALLAVHYARQGKKVGIL   53 (262)
T ss_dssp             CCCHHHHHHHHTTCS-CEEEEECSSSCTTHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ecchhhhhhhhccCC-eEEEEEcCCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            444444444443322 1234445778999999998776543   4576654

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=87.31  E-value=0.081  Score=33.15  Aligned_cols=22  Identities=27%  Similarity=0.137  Sum_probs=17.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ....|.++.|||||+++-.+..
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4567889999999998855543

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=87.24  E-value=0.072  Score=32.63  Aligned_cols=21  Identities=24%  Similarity=0.257  Sum_probs=16.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...|.+++|||||+++-.+..
T Consensus         5 ~i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            5 NIALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            456889999999998855443

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=87.12  E-value=0.14  Score=33.70  Aligned_cols=21  Identities=24%  Similarity=0.235  Sum_probs=16.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....+++|+|+|||+..-.+.
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            567789999999998775443

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=87.10  E-value=0.029  Score=36.83  Aligned_cols=34  Identities=24%  Similarity=0.185  Sum_probs=25.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~   62 (67)
                      .--++.+|.|+|||+-++..+.+.   +.+++++-|.
T Consensus        20 ~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~   56 (234)
T 2orv_A           20 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYA   56 (234)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEET
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeec
Confidence            456677999999998887776553   5678877664

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=87.00  E-value=0.061  Score=36.08  Aligned_cols=23  Identities=22%  Similarity=-0.058  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....+++++|+|||+++..++..
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~  102 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMH  102 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            45778899999999998766543

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=86.94  E-value=0.14  Score=33.37  Aligned_cols=17  Identities=29%  Similarity=0.444  Sum_probs=14.8

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|.+|.|+|||+..
T Consensus        31 e~~~i~G~NGsGKSTLl   47 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLL   47 (263)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             EEEEEECCCCCCHHHHH
Confidence            57778999999999876

>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=86.92  E-value=0.15  Score=36.07  Aligned_cols=32  Identities=31%  Similarity=0.380  Sum_probs=22.7

Q ss_pred             HHHHHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         18 SLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        18 av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +++-.+.-+.+.+..|++|+|+|||+++..++
T Consensus       164 aID~~~pi~rGQr~~IvG~sG~GKTtLl~~Ia  195 (422)
T 3ice_A          164 VLDLASPIGRGQRGLIVAPPKAGKTMLLQNIA  195 (422)
T ss_dssp             HHHHHSCCBTTCEEEEECCSSSSHHHHHHHHH
T ss_pred             eeeeeeeecCCcEEEEecCCCCChhHHHHHHH
Confidence            34444444445789999999999999885443

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=86.89  E-value=0.024  Score=35.43  Aligned_cols=23  Identities=22%  Similarity=0.078  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...|.+|.|||||.++-.++.++
T Consensus         8 iI~i~g~~GsGk~ti~~~la~~l   30 (201)
T 3fdi_A            8 IIAIGREFGSGGHLVAKKLAEHY   30 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHT
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHh
Confidence            46678999999999987665544

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=86.60  E-value=0.06  Score=43.52  Aligned_cols=46  Identities=22%  Similarity=0.214  Sum_probs=33.4

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      ...+++++. .+  .+...+|.+|+|+|||..++.++..   .+.+++++.-
T Consensus        19 i~~LD~lL~~GGi~~G~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~t   70 (1706)
T 3cmw_A           19 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDA   70 (1706)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             cHHHHHHhhcCCcCCCeEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEe
Confidence            456788876 32  2467889999999999999877654   2457777653

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=86.56  E-value=0.23  Score=28.98  Aligned_cols=22  Identities=18%  Similarity=0.084  Sum_probs=9.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      -+.++++++|+|||.+...+..
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~   30 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSE   30 (183)
T ss_dssp             EEEEEECCCCC-----------
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4678899999999998876653

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=86.53  E-value=0.1  Score=33.05  Aligned_cols=24  Identities=21%  Similarity=0.080  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|.|+|||+++-.+...+
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l   50 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRL   50 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHH
Confidence            566778999999999886655443

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=86.53  E-value=0.19  Score=35.78  Aligned_cols=21  Identities=24%  Similarity=0.341  Sum_probs=16.7

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ++...|++|+|+|||+..-.+
T Consensus       369 G~~~~ivG~sGsGKSTLl~~l  389 (582)
T 3b60_A          369 GKTVALVGRSGSGKSTIASLI  389 (582)
T ss_dssp             TCEEEEEECTTSSHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            367789999999999877433

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=86.45  E-value=0.12  Score=36.08  Aligned_cols=19  Identities=16%  Similarity=-0.036  Sum_probs=14.5

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...+..+.||||||+++..
T Consensus       140 ~tifAYGqTGSGKTyTM~G  158 (412)
T 3u06_A          140 ICIFAYGQTGSGKTYTMDG  158 (412)
T ss_dssp             EEEEEESSTTSSHHHHHTE
T ss_pred             eEEEEecCCCCCCeeEecC
Confidence            3445559999999998754

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=86.42  E-value=0.19  Score=36.00  Aligned_cols=20  Identities=25%  Similarity=0.365  Sum_probs=16.3

Q ss_pred             ceeeeEEEeCCCCceeEeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~   47 (67)
                      ++...|++|+|+|||+..-.
T Consensus       381 G~~~~ivG~sGsGKSTll~~  400 (598)
T 3qf4_B          381 GQKVALVGPTGSGKTTIVNL  400 (598)
T ss_dssp             TCEEEEECCTTSSTTHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            36778999999999987643

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=86.40  E-value=0.082  Score=35.38  Aligned_cols=21  Identities=33%  Similarity=0.360  Sum_probs=16.7

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +....|++|+|+|||++.-.+
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll  100 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLL  100 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCchHHHHHHHH
Confidence            367789999999999877433

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=86.36  E-value=0.26  Score=29.90  Aligned_cols=22  Identities=23%  Similarity=0.134  Sum_probs=17.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...++++++|+|||.+...++.
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~   52 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIE   52 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH
Confidence            5677889999999988765554

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=86.30  E-value=0.033  Score=37.58  Aligned_cols=31  Identities=26%  Similarity=0.293  Sum_probs=23.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      ...++.+..|.|||+++.+++..   .+++++++
T Consensus        17 ~i~~~sgkGGvGKTt~a~~lA~~la~~g~~vlli   50 (334)
T 3iqw_A           17 RWIFVGGKGGVGKTTTSCSLAIQLAKVRRSVLLL   50 (334)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHTTSSSCEEEE
T ss_pred             EEEEEeCCCCccHHHHHHHHHHHHHhCCCcEEEE
Confidence            45667789999999999776654   35677665

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=86.30  E-value=0.28  Score=29.85  Aligned_cols=35  Identities=17%  Similarity=0.103  Sum_probs=22.0

Q ss_pred             hhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         16 EKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+.+.+.+........+++++.|+|||.+...++.
T Consensus        26 a~~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~   60 (226)
T 2hf9_A           26 ADKNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLID   60 (226)
T ss_dssp             HHHHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHH
Confidence            33334443322235677889999999988765543

>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=86.29  E-value=0.036  Score=35.36  Aligned_cols=31  Identities=16%  Similarity=0.163  Sum_probs=24.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      +..++..++|.|||+.++.++.+.   +.|++|+
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~v   62 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVV   62 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEE
Confidence            567777999999999998887763   6677776

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=86.19  E-value=0.16  Score=36.21  Aligned_cols=21  Identities=24%  Similarity=0.124  Sum_probs=16.6

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ++...|++|+|+|||+..-.+
T Consensus       367 G~~~~ivG~sGsGKSTll~~l  387 (578)
T 4a82_A          367 GETVAFVGMSGGGKSTLINLI  387 (578)
T ss_dssp             TCEEEEECSTTSSHHHHHTTT
T ss_pred             CCEEEEECCCCChHHHHHHHH
Confidence            367779999999999876433

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=86.17  E-value=0.027  Score=35.34  Aligned_cols=32  Identities=16%  Similarity=-0.002  Sum_probs=22.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE--EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT--VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~--~~~~~lil~   60 (67)
                      ...++++..|+|||+++..++..  .+.+++++-
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd   48 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   48 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEe
Confidence            34677899999999998766532  245665553

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=86.13  E-value=0.042  Score=35.73  Aligned_cols=34  Identities=15%  Similarity=0.006  Sum_probs=24.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p~   62 (67)
                      .--++.+|.|+|||+..+..+.+.   +.+++++.|.
T Consensus        29 ~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~kp~   65 (219)
T 3e2i_A           29 WIECITGSMFSGKSEELIRRLRRGIYAKQKVVVFKPA   65 (219)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEEEec
Confidence            567788999999998665555442   5678887764

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=86.09  E-value=0.044  Score=38.94  Aligned_cols=31  Identities=19%  Similarity=0.215  Sum_probs=23.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      +..++.+..|.|||+++.+++..   .+.|+|++
T Consensus         9 ~i~~~sgkGGvGKTT~a~~lA~~lA~~G~rVLlv   42 (589)
T 1ihu_A            9 PYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLV   42 (589)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEeCCCcCHHHHHHHHHHHHHHHCCCcEEEE
Confidence            45677799999999999877654   36678775

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=86.00  E-value=0.14  Score=40.09  Aligned_cols=22  Identities=32%  Similarity=0.282  Sum_probs=17.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ...-|++|||||||++...+..
T Consensus      1106 e~vaIVG~SGsGKSTL~~lL~r 1127 (1321)
T 4f4c_A         1106 QTLALVGPSGCGKSTVVALLER 1127 (1321)
T ss_dssp             CEEEEECSTTSSTTSHHHHHTT
T ss_pred             CEEEEECCCCChHHHHHHHHhc
Confidence            6777999999999998765543

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=85.96  E-value=0.043  Score=39.21  Aligned_cols=33  Identities=15%  Similarity=0.158  Sum_probs=24.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLCN   61 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~p   61 (67)
                      ...++++++|+|||+++..++..+   +.+++++..
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            356678999999999998777543   456666654

>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=85.74  E-value=0.041  Score=38.57  Aligned_cols=32  Identities=19%  Similarity=0.204  Sum_probs=22.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ...++++|.|+|||+++..++...   +++++++.
T Consensus        99 ~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd  133 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA  133 (425)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEee
Confidence            345667999999999987666543   45666543

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=85.66  E-value=0.087  Score=35.38  Aligned_cols=32  Identities=9%  Similarity=0.101  Sum_probs=23.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      .-.+..+..|.|||+++.+++..   .+.+++++-
T Consensus        27 ~i~v~sgKGGvGKTTvA~~LA~~lA~~G~rVLlvD   61 (349)
T 3ug7_A           27 KYIMFGGKGGVGKTTMSAATGVYLAEKGLKVVIVS   61 (349)
T ss_dssp             EEEEEECSSSTTHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             EEEEEeCCCCccHHHHHHHHHHHHHHCCCeEEEEe
Confidence            34666688999999999877654   366777653

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=85.66  E-value=0.043  Score=33.99  Aligned_cols=22  Identities=14%  Similarity=-0.097  Sum_probs=17.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...+.++.|||||++...++..
T Consensus         6 ~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            6 VWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            3567899999999988766654

>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=85.65  E-value=0.17  Score=36.33  Aligned_cols=20  Identities=15%  Similarity=0.064  Sum_probs=16.5

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      .+.+|.++||||||+..-.+
T Consensus       168 pHlLIaG~TGSGKSt~L~~l  187 (512)
T 2ius_A          168 PHLLVAGTTGSGASVGVNAM  187 (512)
T ss_dssp             CSEEEECCTTSSHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            57899999999999876443

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=85.63  E-value=0.22  Score=34.17  Aligned_cols=18  Identities=22%  Similarity=0.185  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        31 e~~~llGpsGsGKSTLLr   48 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLR   48 (359)
T ss_dssp             CEEEEEESTTSSHHHHHH
T ss_pred             CEEEEECCCCchHHHHHH
Confidence            577789999999998753

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=85.60  E-value=0.12  Score=37.26  Aligned_cols=23  Identities=22%  Similarity=0.143  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....+.++.|||||+++-.++..
T Consensus       370 ~iI~LiG~sGSGKSTLar~La~~  392 (552)
T 3cr8_A          370 FTVFFTGLSGAGKSTLARALAAR  392 (552)
T ss_dssp             EEEEEEESSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCChHHHHHHHHHHh
Confidence            56778899999999988665544

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12

Probab=85.47  E-value=0.13  Score=35.07  Aligned_cols=19  Identities=32%  Similarity=0.289  Sum_probs=15.6

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      +..+|++|+|+|||.+.-+
T Consensus        27 ~~~~i~G~nG~GKstll~a   45 (430)
T 1w1w_A           27 NFTSIIGPNGSGKSNMMDA   45 (430)
T ss_dssp             SEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            5678999999999987643

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=85.40  E-value=0.16  Score=33.68  Aligned_cols=36  Identities=11%  Similarity=-0.098  Sum_probs=23.6

Q ss_pred             hhhHHHH---HhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRK---MFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~---~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+++++.   .++.+....-++.+|.|+|||.++..++.
T Consensus         2 ~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~   40 (305)
T 2gno_A            2 AKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPE   40 (305)
T ss_dssp             --CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            5555544   44444345788899999999988866654

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=85.29  E-value=0.15  Score=33.50  Aligned_cols=20  Identities=20%  Similarity=0.150  Sum_probs=15.6

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....+.+|.|+|||++.-.+
T Consensus       170 eiv~l~G~sG~GKSTll~~l  189 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAI  189 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHh
Confidence            56778999999999776433

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=85.23  E-value=0.21  Score=42.63  Aligned_cols=18  Identities=28%  Similarity=0.348  Sum_probs=15.0

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      +..++++|||+|||.+.-
T Consensus       907 hGvmlVGp~gsGKTt~~~  924 (3245)
T 3vkg_A          907 HGVMMVGPSGGGKTTSWE  924 (3245)
T ss_dssp             SEEEEECSSSSSHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHH
Confidence            457888999999998864

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=85.10  E-value=0.2  Score=35.69  Aligned_cols=21  Identities=24%  Similarity=0.298  Sum_probs=16.7

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ++...|++|+|+|||+..-.+
T Consensus       369 G~~~~ivG~sGsGKSTll~~l  389 (582)
T 3b5x_A          369 GKTVALVGRSGSGKSTIANLF  389 (582)
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            367789999999999877443

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=84.94  E-value=0.082  Score=42.76  Aligned_cols=44  Identities=23%  Similarity=0.240  Sum_probs=31.4

Q ss_pred             hHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         17 KSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ..+++++. .+  .++..+|.+|+|+|||..++.++...   +++++|+.
T Consensus       369 ~~LD~lLg~GGl~~G~lilI~G~pGsGKTtLaLq~a~~~~~~G~~vlyis  418 (1706)
T 3cmw_A          369 LSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID  418 (1706)
T ss_dssp             HHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             HHHHHHhccCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEE
Confidence            45677776 32  24567888999999999998876653   45676664

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=84.78  E-value=0.13  Score=36.20  Aligned_cols=43  Identities=23%  Similarity=0.341  Sum_probs=27.6

Q ss_pred             HHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEee
Q psy11637         19 LRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCN   61 (67)
Q Consensus        19 v~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p   61 (67)
                      +++++..+  .+...+|.+|+|+|||+.+..++..   .+++++++..
T Consensus       270 ld~vL~g~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~~  317 (525)
T 1tf7_A          270 LDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY  317 (525)
T ss_dssp             HHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             HHHHhCCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEEE
Confidence            55665432  2356788899999999988665432   2345555543

>4h1g_A Maltose binding protein-cakar3 motor domain fusio; kinesin motor domain, motor protein, chimera; HET: MTT ADP EDO; 2.15A {Escherichia coli}

Probab=84.77  E-value=0.19  Score=36.81  Aligned_cols=27  Identities=11%  Similarity=0.083  Sum_probs=16.5

Q ss_pred             HHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         19 LRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        19 v~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      ++.++++ .+...+..+.||||||+++.
T Consensus       455 v~~~~~G-~n~~i~ayGqtgsGKT~Tm~  481 (715)
T 4h1g_A          455 IQCSLDG-TNVCVFAYGQTGSGKTFTMS  481 (715)
T ss_dssp             HHHHHTT-CCEEEEEESSTTSSHHHHHH
T ss_pred             HHHHhCC-ceEEEEccCCCCCchhhccC
Confidence            3444443 22334445999999998763

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=84.68  E-value=0.11  Score=37.64  Aligned_cols=18  Identities=33%  Similarity=0.220  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus       118 e~~~LiG~NGsGKSTLlk  135 (607)
T 3bk7_A          118 MVVGIVGPNGTGKTTAVK  135 (607)
T ss_dssp             SEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCChHHHHHH
Confidence            567789999999998763

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=84.54  E-value=0.25  Score=34.71  Aligned_cols=18  Identities=28%  Similarity=0.178  Sum_probs=15.5

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|++|.|+|||+..-
T Consensus       139 e~v~IvGpnGsGKSTLlr  156 (460)
T 2npi_A          139 PRVVIVGGSQTGKTSLSR  156 (460)
T ss_dssp             CCEEEEESTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            678899999999998763

>4aby_A DNA repair protein RECN; hydrolase, double strand break repair, ATPase, nucleotide binding domain; HET: DNA; 3.00A {Deinococcus radiodurans}

Probab=84.54  E-value=0.054  Score=36.39  Aligned_cols=17  Identities=29%  Similarity=0.266  Sum_probs=14.8

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      +...|++|+|+|||++.
T Consensus        61 G~~~lvG~NGaGKStLl   77 (415)
T 4aby_A           61 GFCAFTGETGAGKSIIV   77 (415)
T ss_dssp             SEEEEEESHHHHHHHHT
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            36778999999999887

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=84.53  E-value=0.039  Score=35.50  Aligned_cols=24  Identities=21%  Similarity=0.299  Sum_probs=17.8

Q ss_pred             eCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         36 PCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        36 pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      -.|.|||+++..++..+   +.+++++
T Consensus        45 KGGvGKTT~a~nLA~~la~~G~rVlli   71 (298)
T 2oze_A           45 KGGVGKSKLSTMFAYLTDKLNLKVLMI   71 (298)
T ss_dssp             SSSSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCCchHHHHHHHHHHHHHhCCCeEEEE
Confidence            67999999998776543   5577654

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=84.48  E-value=0.077  Score=33.70  Aligned_cols=23  Identities=17%  Similarity=0.068  Sum_probs=18.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-.++.++.|+|||.+++.++.+
T Consensus        17 ~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45677899999999998877653

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=84.43  E-value=0.22  Score=34.04  Aligned_cols=18  Identities=22%  Similarity=0.274  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        42 e~~~llGpnGsGKSTLLr   59 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILR   59 (355)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHH
Confidence            577789999999998763

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=84.33  E-value=0.23  Score=30.99  Aligned_cols=21  Identities=19%  Similarity=-0.047  Sum_probs=16.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ....|.+|.|||||+.+-.+.
T Consensus        21 ~~i~i~G~~GsGKSTl~~~L~   41 (230)
T 2vp4_A           21 FTVLIEGNIGSGKTTYLNHFE   41 (230)
T ss_dssp             EEEEEECSTTSCHHHHHHTTG
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            456678999999998775443

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=84.29  E-value=0.24  Score=33.91  Aligned_cols=18  Identities=28%  Similarity=0.312  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        30 e~~~llGpnGsGKSTLLr   47 (362)
T 2it1_A           30 EFMALLGPSGSGKSTLLY   47 (362)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCchHHHHHH
Confidence            567789999999998763

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=84.21  E-value=0.23  Score=33.97  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=15.1

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        30 e~~~llGpnGsGKSTLLr   47 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLL   47 (359)
T ss_dssp             CEEEEECSTTSSHHHHHH
T ss_pred             CEEEEEcCCCchHHHHHH
Confidence            567789999999998763

>2o5v_A DNA replication and repair protein RECF; ABC ATPase, walker A motif, P-loop, signature motif, replication/recombination complex; HET: DNA; 1.61A {Deinococcus radiodurans}

Probab=84.13  E-value=0.19  Score=34.29  Aligned_cols=19  Identities=26%  Similarity=0.059  Sum_probs=15.4

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      +...+++|+|+|||.+.-+
T Consensus        27 g~~~i~G~nG~GKttll~a   45 (359)
T 2o5v_A           27 GVTGIYGENGAGKTNLLEA   45 (359)
T ss_dssp             EEEEEECCTTSSHHHHHHH
T ss_pred             CeEEEECCCCCChhHHHHH
Confidence            4677899999999987643

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=84.05  E-value=0.15  Score=36.19  Aligned_cols=34  Identities=24%  Similarity=0.315  Sum_probs=24.8

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+++.++--+.+.+..|.+|.|+|||.++..++.
T Consensus       164 raID~l~PigrGQR~lIfg~~g~GKT~Ll~~Ia~  197 (427)
T 3l0o_A          164 RLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIAN  197 (427)
T ss_dssp             HHHHHHSCCBTTCEEEEEECTTCCHHHHHHHHHH
T ss_pred             hhhhhcccccCCceEEEecCCCCChhHHHHHHHH
Confidence            4455555444558999999999999998855544

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=84.01  E-value=0.28  Score=34.49  Aligned_cols=34  Identities=18%  Similarity=0.243  Sum_probs=24.4

Q ss_pred             hhhHHHHHhc-C-CcceeeeEEEeCCCCceeEeeee
Q psy11637         15 QEKSLRKMFG-N-GRARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        15 Q~~av~~~~~-~-~~~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      -..+++.+.- . ..+....|.+|+|+|||+.+..+
T Consensus        24 g~~~Ld~i~~G~i~~Ge~~~l~G~nGsGKSTL~~~~   59 (525)
T 1tf7_A           24 MIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQF   59 (525)
T ss_dssp             CCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHH
T ss_pred             CchhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHH
Confidence            3557777664 2 23467889999999999988653

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=83.84  E-value=0.24  Score=35.47  Aligned_cols=21  Identities=19%  Similarity=0.112  Sum_probs=16.8

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ++...|++|+|+|||+..-.+
T Consensus       369 Ge~~~ivG~sGsGKSTll~~l  389 (587)
T 3qf4_A          369 GSLVAVLGETGSGKSTLMNLI  389 (587)
T ss_dssp             TCEEEEECSSSSSHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHH
Confidence            367789999999999877443

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=83.84  E-value=0.36  Score=27.16  Aligned_cols=19  Identities=32%  Similarity=0.345  Sum_probs=15.3

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      +.++.+++|+|||.+...+
T Consensus         5 ~i~v~G~~~~GKssl~~~l   23 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQL   23 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5678999999999876444

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=83.82  E-value=0.29  Score=33.77  Aligned_cols=17  Identities=24%  Similarity=0.184  Sum_probs=15.0

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|.+|.|+|||+..
T Consensus        48 e~~~llGpsGsGKSTLL   64 (390)
T 3gd7_A           48 QRVGLLGRTGSGKSTLL   64 (390)
T ss_dssp             CEEEEEESTTSSHHHHH
T ss_pred             CEEEEECCCCChHHHHH
Confidence            67789999999999876

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=83.81  E-value=0.33  Score=27.49  Aligned_cols=19  Identities=32%  Similarity=0.048  Sum_probs=15.2

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      +.++.+++|+|||.+...+
T Consensus         3 ki~v~G~~~~GKSsli~~l   21 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRL   21 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            5678999999999876444

>2yc2_C IFT27, small RAB-related GTPase; transport protein, cilium, IFT complex; 2.59A {Chlamydomonas reinhardtii} PDB: 2yc4_C

Probab=83.75  E-value=0.26  Score=29.21  Aligned_cols=23  Identities=17%  Similarity=-0.002  Sum_probs=4.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      -+.++++++|+|||.+...+...
T Consensus        21 ~~i~v~G~~~~GKssli~~l~~~   43 (208)
T 2yc2_C           21 CKVAVVGEATVGKSALISMFTSK   43 (208)
T ss_dssp             EEEEEC-----------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46788899999999988766544

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=83.70  E-value=0.25  Score=33.88  Aligned_cols=17  Identities=24%  Similarity=0.350  Sum_probs=14.8

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|.+|.|+|||+..
T Consensus        30 e~~~llGpnGsGKSTLL   46 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTL   46 (372)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCcHHHHHH
Confidence            57778999999999876

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=83.69  E-value=0.075  Score=34.99  Aligned_cols=44  Identities=5%  Similarity=-0.105  Sum_probs=28.8

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~   60 (67)
                      ..+|+++..+  .+...++.+.+|+|||+.++.++..   .+.+++++.
T Consensus         8 ~~LD~~l~GGl~~gs~~li~g~p~~~~~~l~~qfl~~g~~~Ge~~~~~~   56 (260)
T 3bs4_A            8 EELDREIGKIKKHSLILIHEEDASSRGKDILFYILSRKLKSDNLVGMFS   56 (260)
T ss_dssp             HHHHHHHCCBCTTCEEEEEECSGGGCHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             HHHHHHhCCCCCCCcEEEEEeCCCccHHHHHHHHHHHHHHCCCcEEEEE
Confidence            3567788754  2344556568899998777666543   366777765

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=83.67  E-value=0.26  Score=34.06  Aligned_cols=18  Identities=39%  Similarity=0.346  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        30 e~~~llGpsGsGKSTLLr   47 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLR   47 (381)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEEcCCCchHHHHHH
Confidence            577789999999998763

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=83.54  E-value=0.12  Score=34.02  Aligned_cols=30  Identities=20%  Similarity=0.243  Sum_probs=20.2

Q ss_pred             eeeEEEe-CCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         30 SGVIVLP-CGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        30 ~~~i~~p-TGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      ..++..+ .|.|||+++..++..   .++++++|
T Consensus       106 vI~vts~kgG~GKTtva~nLA~~lA~~G~rVLLI  139 (299)
T 3cio_A          106 ILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFI  139 (299)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEECCCCCCChHHHHHHHHHHHHhCCCcEEEE
Confidence            3434444 689999999776654   35677765

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=83.53  E-value=0.39  Score=28.74  Aligned_cols=18  Identities=28%  Similarity=0.187  Sum_probs=14.7

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      -...+++|.|+|||.+.-
T Consensus        30 ~kv~lvG~~g~GKSTLl~   47 (191)
T 1oix_A           30 FKVVLIGDSGVGKSNLLS   47 (191)
T ss_dssp             EEEEEEECTTSSHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHH
Confidence            356789999999998763

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=83.50  E-value=0.039  Score=33.90  Aligned_cols=27  Identities=11%  Similarity=-0.020  Sum_probs=19.7

Q ss_pred             EEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         34 VLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        34 ~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      ..-+|.|||+++..++..+   +.+++++=
T Consensus         8 s~kgGvGKTt~a~nLa~~la~~G~rVll~d   37 (224)
T 1byi_A            8 GTDTEVGKTVASCALLQAAKAAGYRTAGYK   37 (224)
T ss_dssp             ESSTTSCHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCCEEEEc
Confidence            3457999999998777543   56777753

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=83.49  E-value=0.27  Score=33.76  Aligned_cols=17  Identities=29%  Similarity=0.339  Sum_probs=14.7

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|.+|.|+|||+..
T Consensus        38 e~~~llGpnGsGKSTLL   54 (372)
T 1v43_A           38 EFLVLLGPSGCGKTTTL   54 (372)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCChHHHHH
Confidence            57778999999999876

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=83.14  E-value=0.23  Score=31.04  Aligned_cols=24  Identities=25%  Similarity=-0.042  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.++.|||||+.+-.+...+
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHc
Confidence            345678999999999886665544

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=83.11  E-value=0.12  Score=38.01  Aligned_cols=34  Identities=21%  Similarity=0.344  Sum_probs=25.0

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+++.++--+++++..|.++.|+|||+++..++.
T Consensus       221 rvID~l~PigrGqr~~Ifgg~g~GKT~L~~~ia~  254 (600)
T 3vr4_A          221 RVIDTFFPVTKGGAAAVPGPFGAGKTVVQHQIAK  254 (600)
T ss_dssp             HHHHHHSCCBTTCEEEEECCTTSCHHHHHHHHHH
T ss_pred             hhhhccCCccCCCEEeeecCCCccHHHHHHHHHh
Confidence            4566665444557889999999999988765543

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=83.10  E-value=0.17  Score=32.78  Aligned_cols=23  Identities=17%  Similarity=0.005  Sum_probs=17.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.-+.+|+|||||+.+..++..
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~   31 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEK   31 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHHH
Confidence            45567899999999988655443

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=82.92  E-value=0.41  Score=27.24  Aligned_cols=20  Identities=25%  Similarity=0.203  Sum_probs=15.6

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      -+.++++++|+|||.+...+
T Consensus         4 ~~i~v~G~~~~GKssli~~l   23 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRF   23 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHH
Confidence            35788999999999876443

---

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	67
d2fz4a1	206	c.37.1.19 (A:24-229) DNA repair protein RAD25 {Arc	3e-08
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	6e-05
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	0.001
d1z3ix2	298	c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fis	0.003

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 45.6 bits (107), Expect = 3e-08
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)

Query: 2   TIDLKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN 61
           T        LR YQEK+L +   + R   G IVLP G+GK+ V + A   +    L++  
Sbjct: 62  TPYFDAEISLRDYQEKALERWLVDKR---GCIVLPTGSGKTHVAMAAINELSTPTLIVVP 118

Query: 62  S 62
           +
Sbjct: 119 T 119

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 36.3 bits (82), Expect = 6e-05
 Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 4/40 (10%)

Query: 11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC 50
           R YQE    K        + +IVLP G GK+L+ +    
Sbjct: 10 PRIYQEVIYAKCKE----TNCLIVLPTGLGKTLIAMMIAE 45

>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 = 32.7 bits (73), Expect = 0.001
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLC 60
           RP QE+ +  +      R  ++V+P G GKSL        +    +V+ 
Sbjct: 26 FRPGQEEIIDTVLSG---RDCLVVMPTGGGKSLCYQIPALLLNGLTVVVS 72

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 298

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]

 Score = 31.6 bits (70), Expect = 0.003
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 1   MTIDLKPSAVLRPYQEKSLRKMFGNGRARS------GVIVLPCGAGKSLVGVTACCTVRK 54
           + +D   S VLRP+Q + ++ ++     R        ++    G GK+L  +T   T+ K
Sbjct: 46  VVVDPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLK 105

Query: 55  R 55
           +
Sbjct: 106 Q 106

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	67
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.67
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.5
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.45
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.44
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.33
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.26
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.8
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.73
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.55
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.52
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.51
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	98.51
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.48
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.41
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.38
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.38
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	98.35
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.35
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.34
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.26
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	98.25
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.19
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	98.01
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.88
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	97.76
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.67
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	97.56
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.36
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.29
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.27
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.25
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	97.25
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.19
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.16
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.1
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.02
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.99
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	96.96
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.84
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	96.82
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.8
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	96.79
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	96.79
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.77
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.7
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.67
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.65
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.59
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.55
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	96.52
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.46
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.43
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.36
d1okkd2	207	GTPase domain of the signal recognition particle r	96.35
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.24
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.24
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.22
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.21
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.15
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	96.11
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.08
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.06
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.05
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.05
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.02
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.02
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.97
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.94
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.94
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	95.94
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	95.93
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	95.91
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.82
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.8
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	95.78
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.77
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.76
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	95.75
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.65
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.64
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.64
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	95.63
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	95.6
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.51
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	95.49
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.43
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.36
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	95.29
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.26
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.2
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.18
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	95.15
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	95.14
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	95.12
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.07
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.99
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	94.92
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	94.84
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	94.84
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	94.79
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	94.67
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.65
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	94.63
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.51
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.48
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	94.35
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	94.26
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.15
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	94.11
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	94.03
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	94.02
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	93.96
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	93.85
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	93.84
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	93.4
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	92.9
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	92.65
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	92.53
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	92.52
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.4
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	92.09
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	92.08
d1tuea_	205	Replication protein E1 helicase domain {Human papi	91.95
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	91.86
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.83
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	91.71
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	91.68
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	91.67
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	91.64
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	91.6
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	91.51
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	91.39
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	91.13
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	91.13
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	91.09
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	91.02
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	90.84
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	90.49
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	90.33
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	90.31
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	90.31
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	90.24
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	90.12
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	90.09
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	90.02
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	89.98
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	89.94
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	89.83
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	89.8
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	89.71
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	89.56
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	89.13
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	88.81
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	88.81
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	88.58
d1xpua3	289	Transcription termination factor Rho, ATPase domai	88.57
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	88.48
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	88.38
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	88.05
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	87.64
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	87.62
d2awna2	232	Maltose transport protein MalK, N-terminal domain	87.61
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	87.57
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	87.27
d1g2912	240	Maltose transport protein MalK, N-terminal domain	86.9
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	86.76
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	86.72
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	86.45
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	86.29
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	86.09
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	85.99
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	85.83
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	85.81
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	85.67
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	85.66
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	85.61
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	85.56
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	85.55
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	85.53
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	85.43
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	85.31
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	85.23
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	84.92
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	84.35
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	84.18
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	83.92
d2fh5b1	207	Signal recognition particle receptor beta-subunit	83.69
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	83.64
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	83.35
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	83.04
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	82.86
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	82.76
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	82.75
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	82.0
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	81.93
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	81.83
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	81.67
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	81.52
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	81.22
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	81.1
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	80.73
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	80.46
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	80.19

>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=99.67  E-value=9.1e-19  Score=110.10  Aligned_cols=58  Identities=31%  Similarity=0.536  Sum_probs=51.6

Q ss_pred             cccceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637          5 LKPSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus         5 l~~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      ++..++|||||+++++.++++   +++++.+|||+|||++++.++.+.++++||+||+.++
T Consensus        65 ~~~~~~Lr~yQ~eav~~~~~~---~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p~~~L  122 (206)
T d2fz4a1          65 FDAEISLRDYQEKALERWLVD---KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLAL  122 (206)
T ss_dssp             CCCCCCCCHHHHHHHHHHTTT---SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESSHHH
T ss_pred             CCCCCCcCHHHHHHHHHHHhC---CCcEEEeCCCCCceehHHhHHHHhcCceeEEEcccch
Confidence            345689999999999999986   5889999999999999999888889999999998654

>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=99.50  E-value=1.2e-16  Score=104.98  Aligned_cols=57  Identities=19%  Similarity=0.258  Sum_probs=48.6

Q ss_pred             cceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeecceee
Q psy11637          7 PSAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVVF   66 (67)
Q Consensus         7 ~~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~v   66 (67)
                      ..++|||||++|++.++++   +++++.+|||+|||+++..++..    .+.++||+||+..+|
T Consensus       110 ~~~~~rdyQ~~av~~~l~~---~~~il~~pTGsGKT~i~~~i~~~~~~~~~~k~Liivp~~~Lv  170 (282)
T d1rifa_         110 KRIEPHWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYYLENYEGKILIIVPTTALT  170 (282)
T ss_dssp             EECCCCHHHHHHHHHHHHH---SEEEECCCTTSCHHHHHHHHHHHHHHHCSSEEEEECSSHHHH
T ss_pred             CccccchHHHHHHHHHHhc---CCceeEEEcccCccHHHHHHHHHhhhcccceEEEEEcCchhH
Confidence            3689999999999999987   68999999999999998877643    356899999997653

>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=99.45  E-value=5.6e-16  Score=95.03  Aligned_cols=54  Identities=28%  Similarity=0.322  Sum_probs=44.6

Q ss_pred             ceeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      .+++|+||+++++.+.+    ++.++++|||+|||++++.++..    .+++++|++|+..+
T Consensus         7 ~~~pr~~Q~~~~~~~~~----~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P~~~L   64 (200)
T d1wp9a1           7 LIQPRIYQEVIYAKCKE----TNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPL   64 (200)
T ss_dssp             HHCCCHHHHHHHHHGGG----SCEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECSSHHH
T ss_pred             CCCCCHHHHHHHHHHhc----CCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcCchHH
Confidence            46899999999998865    47899999999999988766543    36789999998654

>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=99.44  E-value=3.8e-16  Score=96.79  Aligned_cols=53  Identities=25%  Similarity=0.364  Sum_probs=47.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      .|||||+++++.++++   ++.++++|||||||.++...+....+++++++|+..+
T Consensus        25 ~~rp~Q~~ai~~~l~g---~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v~P~~~L   77 (206)
T d1oywa2          25 QFRPGQEEIIDTVLSG---RDCLVVMPTGGGKSLCYQIPALLLNGLTVVVSPLISL   77 (206)
T ss_dssp             SCCTTHHHHHHHHHTT---CCEEEECSCHHHHHHHHHHHHHHSSSEEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEcCCCCCCcchhhhhhhhccCceEEeccchhh
Confidence            7899999999999886   6899999999999999977777778899999998754

>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=99.33  E-value=4.4e-15  Score=91.95  Aligned_cols=53  Identities=23%  Similarity=0.372  Sum_probs=44.1

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      +|||||+++++.++++   ++.++.+|||+|||.++...+..   ..+++++++|+..+
T Consensus        25 ~l~~~Q~~ai~~l~~~---~~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P~~~L   80 (202)
T d2p6ra3          25 ELFPPQAEAVEKVFSG---KNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRAL   80 (202)
T ss_dssp             CCCCCCHHHHHHHTTC---SCEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEcCCCCchhHHHHHHHHHHhhccCcceeecccHHH
Confidence            6999999999999986   68999999999999987544332   36789999999754

>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=99.26  E-value=3.6e-14  Score=89.54  Aligned_cols=53  Identities=21%  Similarity=0.296  Sum_probs=44.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      +++|+|++++++++++   ++.++++|||+|||.+++..+..   .+++++|++|+..+
T Consensus        43 ~p~~~Q~~~i~~~l~g---~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~Pt~~L   98 (237)
T d1gkub1          43 EPRAIQKMWAKRILRK---ESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLL   98 (237)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEESCHHH
T ss_pred             CCCHHHHHHHHHHHCC---CCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEeccHHH
Confidence            6789999999999986   68999999999999877654433   36799999999764

>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=98.80  E-value=4.6e-11  Score=69.37  Aligned_cols=37  Identities=27%  Similarity=0.244  Sum_probs=32.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~~~   65 (67)
                      +.++|++|||||||+++..++...+.+++|++|+..+
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~~~l   45 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPSVAA   45 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESCHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcChHHH
Confidence            7899999999999998876677778899999999754

>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=98.73  E-value=9.8e-11  Score=73.29  Aligned_cols=57  Identities=28%  Similarity=0.297  Sum_probs=42.9

Q ss_pred             ceeeccchhhHHHHHhcCC-cceeeeEEEeCCCCceeEeeeeEEEE-----eeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFGNG-RARSGVIVLPCGAGKSLVGVTACCTV-----RKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~~~-~~~~~~i~~pTGsGKT~i~~~~~~~~-----~~~~lil~p~~~   64 (67)
                      +..|||||.+++....... .+..+++..++|.|||.++++++...     ..++||+||...
T Consensus        10 ~~~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~~~~~~~~~LIv~p~~l   72 (230)
T d1z63a1          10 KANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAKKENELTPSLVICPLSV   72 (230)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHHHTTCCSSEEEEECSTT
T ss_pred             hcchhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhhhcccccccceecchhh
Confidence            3479999999997644321 12567888899999999998777643     368999999753

>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=98.55  E-value=9e-10  Score=68.61  Aligned_cols=53  Identities=19%  Similarity=0.206  Sum_probs=42.7

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-E-----eeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-V-----RKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-~-----~~~~lil~p~~~~   65 (67)
                      .+.|-|++++-.++++   ++.++.+|||||||..++..+.. .     +.+++|++|+..+
T Consensus        23 ~pt~iQ~~aip~il~g---~dvl~~A~TGsGKTla~~lp~l~~~~~~~~~~~~lil~PtreL   81 (207)
T d1t6na_          23 HPSEVQHECIPQAILG---MDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVSVLVMCHTREL   81 (207)
T ss_dssp             CCCHHHHHHHHHHHTT---CCEEEECCTTSCHHHHHHHHHHHHCCCCTTCCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCeEEEeccccccccccccceeeeecccCCCceEEEEeccchh
Confidence            5788899999999987   68999999999999998654432 1     3468999998643

>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=98.52  E-value=4.9e-10  Score=63.57  Aligned_cols=37  Identities=32%  Similarity=0.313  Sum_probs=29.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEeeccee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCNSGVV   65 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p~~~~   65 (67)
                      ++.+|++|||+|||.+++..+..    .+.++++++|+...
T Consensus         8 ~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~vli~~p~~~l   48 (140)
T d1yksa1           8 MTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVV   48 (140)
T ss_dssp             CEEEECCCTTSSTTTTHHHHHHHHHHHTTCCEEEEESSHHH
T ss_pred             CcEEEEcCCCCChhHHHHHHHHHHhhhcCceeeeeecchhH
Confidence            78999999999999888654432    35689999998654

>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=98.51  E-value=6.2e-10  Score=70.56  Aligned_cols=43  Identities=28%  Similarity=0.330  Sum_probs=31.3

Q ss_pred             HHhcCCcceeeeEEEeCCCCceeEee-eeEEE---EeeeeEEEeeccee
Q psy11637         21 KMFGNGRARSGVIVLPCGAGKSLVGV-TACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus        21 ~~~~~~~~~~~~i~~pTGsGKT~i~~-~~~~~---~~~~~lil~p~~~~   65 (67)
                      ++++.+  ++.++.+|||||||+.++ .++..   .+.++||++|+..+
T Consensus         4 ~~~~~~--~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~lvi~Ptr~L   50 (305)
T d2bmfa2           4 DIFRKK--RLTIMDLHPGAGKTKRYLPAIVREAIKRGLRTLILAPTRVV   50 (305)
T ss_dssp             SSSSTT--CEEEECCCTTSSTTTTHHHHHHHHHHHHTCCEEEEESSHHH
T ss_pred             HHhhcC--CcEEEEECCCCCHHHHHHHHHHHHHHhcCCEEEEEccHHHH
Confidence            345544  789999999999998664 23222   36689999999764

>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=98.51  E-value=1.2e-09  Score=67.89  Aligned_cols=54  Identities=15%  Similarity=0.068  Sum_probs=42.0

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-----~~~~~lil~p~~~~   65 (67)
                      .+.|.|++++..+++++  .+.++.+|||+|||.++...+..     .+.+++|++|+..+
T Consensus        26 ~pt~iQ~~~ip~~l~g~--~d~iv~a~TGsGKT~~~~l~~~~~~~~~~~~~~lil~pt~~l   84 (208)
T d1hv8a1          26 KPTDIQMKVIPLFLNDE--YNIVAQARTGSGKTASFAIPLIELVNENNGIEAIILTPTREL   84 (208)
T ss_dssp             SCCHHHHHHHHHHHHTC--SEEEEECCSSSSHHHHHHHHHHHHSCSSSSCCEEEECSCHHH
T ss_pred             CCCHHHHHHHHHHHcCC--CCeeeechhcccccceeecccccccccccCcceEEEeecccc
Confidence            46778999999988753  47888899999999988654432     24589999999754

>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=98.48  E-value=3.3e-09  Score=65.92  Aligned_cols=52  Identities=21%  Similarity=0.166  Sum_probs=42.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~   64 (67)
                      .+.|-|++++..++++   ++.++.+|||||||..++..+..      .+.+++|++|+..
T Consensus        25 ~pt~iQ~~aip~il~g---~dvl~~a~TGsGKTlayllP~l~~~~~~~~~~~~lil~pt~e   82 (206)
T d1veca_          25 KPSPIQEESIPIALSG---RDILARAKNGTGKSGAYLIPLLERLDLKKDNIQAMVIVPTRE   82 (206)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCSSSTTHHHHHHHHHHHCCTTSCSCCEEEECSCHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEeeccCccccccccccchhhcccccccCcceEEEeecch
Confidence            6778899999999986   68999999999999988654432      2457899999864

>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=98.41  E-value=2.8e-09  Score=66.98  Aligned_cols=53  Identities=15%  Similarity=0.135  Sum_probs=42.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~~   65 (67)
                      .+.|-|++++-.++++   ++.++.+|||||||..++..+..      ...++||++||..+
T Consensus        34 ~pt~iQ~~aip~il~g---~dvl~~a~TGsGKTlayllp~l~~i~~~~~~~~alil~Pt~eL   92 (218)
T d2g9na1          34 KPSAIQQRAILPCIKG---YDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTREL   92 (218)
T ss_dssp             SCCHHHHHHHHHHHHT---CCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEEcccchhhhhhhhhhhhheecccccCccEEEEcccchh
Confidence            4667799999999976   68999999999999999654432      24579999999653

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=98.38  E-value=6e-09  Score=67.28  Aligned_cols=56  Identities=23%  Similarity=0.380  Sum_probs=40.3

Q ss_pred             eeeccchhhHHHHHhc----C--CcceeeeEEEeCCCCceeEeeeeEEEE----------eeeeEEEeecce
Q psy11637          9 AVLRPYQEKSLRKMFG----N--GRARSGVIVLPCGAGKSLVGVTACCTV----------RKRALVLCNSGV   64 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~----~--~~~~~~~i~~pTGsGKT~i~~~~~~~~----------~~~~lil~p~~~   64 (67)
                      ..|||||.++++...+    .  .....+++.-.+|.|||+.+++++...          ..++|||||.+.
T Consensus        54 ~~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~~~~~~~~~~~~~~LIV~P~sl  125 (298)
T d1z3ix2          54 KVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSL  125 (298)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHCCTTSSCSCSCEEEEECHHH
T ss_pred             ccccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHHHhcccccCCCCcEEEEccchh
Confidence            4699999999975432    1  123568888999999999876655431          246999999753

>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=98.38  E-value=7.3e-09  Score=65.41  Aligned_cols=52  Identities=15%  Similarity=0.231  Sum_probs=41.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecce
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSGV   64 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~~   64 (67)
                      .+.|-|++++..++++   ++.++.+|||||||..++..+..      ...+.+|++||..
T Consensus        39 ~pt~IQ~~aIp~il~g---~dvi~~a~TGSGKTlayllPil~~l~~~~~~~~~lil~Ptre   96 (222)
T d2j0sa1          39 KPSAIQQRAIKQIIKG---RDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRE   96 (222)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHTCCTTSCSCCEEEECSSHH
T ss_pred             CCCHHHHHHHHHHHCC---CCeEEEcCcchhhhhhhcccccccccccccCceeEEecchHH
Confidence            5667899999999986   68999999999999988654332      2446899999864

>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=98.35  E-value=3.4e-09  Score=66.99  Aligned_cols=52  Identities=13%  Similarity=0.138  Sum_probs=38.9

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeecceee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVVF   66 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~v   66 (67)
                      +|.|-|+++++.  ..   +..+|.+|+|||||.+.+.-+..       -..++|++++|++|+
T Consensus         1 ~L~~eQ~~av~~--~~---~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn~a~   59 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VT---GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAA   59 (306)
T ss_dssp             CCCHHHHHHHHC--CS---SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSHHHH
T ss_pred             CcCHHHHHHHhC--CC---CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcHHHH
Confidence            477899999964  12   57889999999999987643322       135899999998764

>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=98.35  E-value=8.9e-09  Score=66.08  Aligned_cols=58  Identities=19%  Similarity=0.230  Sum_probs=46.2

Q ss_pred             ceeeccchhhHHHHHhc---CCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeeccee
Q psy11637          8 SAVLRPYQEKSLRKMFG---NGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGVV   65 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~---~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~~   65 (67)
                      .+.+-+-|+++++++.+   .+...+.++.+.||||||.+++.++..   .++.+++++|+..+
T Consensus        53 P~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~L  116 (233)
T d2eyqa3          53 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLL  116 (233)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHH
T ss_pred             ccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHh
Confidence            45666779999988765   333457899999999999999887766   47899999998653

>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=98.34  E-value=9.6e-09  Score=64.17  Aligned_cols=53  Identities=15%  Similarity=0.141  Sum_probs=42.2

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-E-----EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-T-----VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-~-----~~~~~lil~p~~~~   65 (67)
                      .+.|-|++++..++++   ++.++.+|||||||..++..+. +     .+..++|++|+..+
T Consensus        32 ~pt~iQ~~aip~il~g---~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~~~~~lil~pt~el   90 (212)
T d1qdea_          32 EPSAIQQRAIMPIIEG---HDVLAQAQSGTGKTGTFSIAALQRIDTSVKAPQALMLAPTREL   90 (212)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHCCTTCCSCCEEEECSSHHH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEeecccccchhhhhHhhhHhhhhccCCCcceEEEcccHHH
Confidence            5677899999999987   6899999999999998865432 2     24578999998643

>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=98.26  E-value=1.2e-08  Score=64.59  Aligned_cols=53  Identities=15%  Similarity=0.245  Sum_probs=41.3

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---------------EeeeeEEEeeccee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---------------VRKRALVLCNSGVV   65 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---------------~~~~~lil~p~~~~   65 (67)
                      .+-|-|.+++..++++   ++.++.+|||||||..++..+..               ...+++|++|+..+
T Consensus        43 ~pt~iQ~~~ip~il~g---~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~~~alil~pt~el  110 (238)
T d1wrba1          43 RPTPIQKNAIPAILEH---RDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTREL  110 (238)
T ss_dssp             SCCHHHHHHHHHHHTT---CCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBCCSEEEECSSHHH
T ss_pred             CCCHHHHHHhhhhhCC---CCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCCceEEEeccchhh
Confidence            5566799999999986   68999999999999988643321               12469999998643

>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=98.25  E-value=1.7e-08  Score=65.70  Aligned_cols=57  Identities=12%  Similarity=0.177  Sum_probs=45.8

Q ss_pred             ceeeccchhhHHHHHhc---CCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecce
Q psy11637          8 SAVLRPYQEKSLRKMFG---NGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSGV   64 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~---~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~~   64 (67)
                      .++|=+-|+++++++.+   .+...+.++.+.||||||.|++.++..   .+..+++++||..
T Consensus        81 PFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~  143 (264)
T d1gm5a3          81 PFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSI  143 (264)
T ss_dssp             SSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHH
T ss_pred             cccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHh
Confidence            35666779999999875   333467899999999999999877765   4778999999864

>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=98.19  E-value=4e-08  Score=60.10  Aligned_cols=37  Identities=19%  Similarity=0.087  Sum_probs=31.4

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      .+.|-|++++..++++   ++.++.+|||||||..++..+
T Consensus        23 ~pt~iQ~~aip~~l~G---~dvii~a~TGSGKTlayllp~   59 (209)
T d1q0ua_          23 KPTEIQERIIPGALRG---ESMVGQSQTGTGKTHAYLLPI   59 (209)
T ss_dssp             SCCHHHHHHHHHHHHT---CCEEEECCSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHCC---CCeEeecccccccceeeeeee
Confidence            5778899999999986   689999999999998765443

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=98.01  E-value=8.5e-08  Score=61.08  Aligned_cols=52  Identities=17%  Similarity=0.141  Sum_probs=38.8

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE-------EeeeeEEEeecceee
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT-------VRKRALVLCNSGVVF   66 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~-------~~~~~lil~p~~~~v   66 (67)
                      .|-+-|+++++..  .   +..+|.+++|||||++++.-+..       ...+++++++|+.++
T Consensus        11 ~L~~eQ~~~v~~~--~---g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~~aa   69 (318)
T d1pjra1          11 HLNKEQQEAVRTT--E---GPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTNKAA   69 (318)
T ss_dssp             TSCHHHHHHHHCC--S---SCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSHHHH
T ss_pred             hCCHHHHHHHhCC--C---CCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccHHHH
Confidence            3778999999742  1   57889999999999988653321       135799999987653

>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=97.88  E-value=2.8e-07  Score=61.62  Aligned_cols=52  Identities=19%  Similarity=0.118  Sum_probs=40.0

Q ss_pred             eccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE-------EEeeeeEEEeeccee
Q psy11637         11 LRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC-------TVRKRALVLCNSGVV   65 (67)
Q Consensus        11 lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~-------~~~~~~lil~p~~~~   65 (67)
                      +=+.|++|+..++.+   +..+|.+|+|+|||++...++.       ..+.++++.+||..|
T Consensus       149 ~~~~Q~~A~~~al~~---~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkA  207 (359)
T d1w36d1         149 EINWQKVAAAVALTR---RISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKA  207 (359)
T ss_dssp             SCCHHHHHHHHHHTB---SEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHH
T ss_pred             cccHHHHHHHHHHcC---CeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHH
Confidence            345799999999876   6899999999999988744322       124589999999754

>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=97.76  E-value=1.3e-06  Score=53.47  Aligned_cols=51  Identities=20%  Similarity=0.212  Sum_probs=38.6

Q ss_pred             eeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE------EeeeeEEEeecc
Q psy11637         10 VLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT------VRKRALVLCNSG   63 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~------~~~~~lil~p~~   63 (67)
                      .+.|-|++++-.++++   ++.++.+|||||||..++..+..      .+.+.++++|+.
T Consensus        23 ~pt~iQ~~aip~il~g---~dvi~~a~tGsGKTlay~lp~i~~~~~~~~~~~~~~~~~~~   79 (206)
T d1s2ma1          23 KPSPIQEEAIPVAITG---RDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR   79 (206)
T ss_dssp             SCCHHHHHHHHHHHHT---CCEEEECCTTSCHHHHHHHHHHHHCCTTSCSCCEEEECSSH
T ss_pred             CCCHHHHHHHHHHHcC---CCEEEecCCcchhhhhhccccccccccccccccceeeccch
Confidence            5778899999999987   68999999999999887543321      234567777764

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.67  E-value=2.1e-06  Score=52.57  Aligned_cols=50  Identities=12%  Similarity=0.062  Sum_probs=33.7

Q ss_pred             Cccccccceeecc-----chhhH---HHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637          1 MTIDLKPSAVLRP-----YQEKS---LRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus         1 ~~~~l~~~~~lR~-----yQ~~a---v~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+++|.+++.++.     .|++.   +..|++.+...+.++.+|+|+|||.++-.++.
T Consensus         1 ~~~pw~eKyrP~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~   58 (224)
T d1sxjb2           1 LQLPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAH   58 (224)
T ss_dssp             CCCCHHHHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCchHhHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHH
Confidence            5667776655544     25544   45577665445689999999999988765543

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=97.56  E-value=1.9e-06  Score=58.74  Aligned_cols=61  Identities=16%  Similarity=0.213  Sum_probs=48.8

Q ss_pred             cccccceeeccchhhHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecc
Q psy11637          3 IDLKPSAVLRPYQEKSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSG   63 (67)
Q Consensus         3 ~~l~~~~~lR~yQ~~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~   63 (67)
                      |.+..++.+=--|-+|++++.++-  ..+..+|.+-||||||++++.++...++++|||+|+.
T Consensus         4 f~~~~~~~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~   66 (413)
T d1t5la1           4 FQLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNK   66 (413)
T ss_dssp             CCCCCSSCCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSH
T ss_pred             eEEecCCCCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            455555666566999999888641  1256788999999999999999999999999999985

>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=97.36  E-value=9.7e-06  Score=49.29  Aligned_cols=49  Identities=18%  Similarity=0.164  Sum_probs=31.4

Q ss_pred             cccccceeecc-----chhhHH---HHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637          3 IDLKPSAVLRP-----YQEKSL---RKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus         3 ~~l~~~~~lR~-----yQ~~av---~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++|..++.++-     .|++++   ..|++.+.-.+.++.+|+|+|||.++..++.+
T Consensus         2 ~pw~ekyrP~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~   58 (227)
T d1sxjc2           2 LPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALARE   58 (227)
T ss_dssp             CCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHH
T ss_pred             CchhhhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHH
Confidence            44555544433     245544   45766654346899999999999888666543

>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=97.29  E-value=2.5e-05  Score=47.39  Aligned_cols=44  Identities=18%  Similarity=0.116  Sum_probs=30.2

Q ss_pred             eeeccchhhHHHHHhcC------CcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637          9 AVLRPYQEKSLRKMFGN------GRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~------~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.=|+.|.+.+.+++..      ....+.++.+|+|+|||.++-.++..+
T Consensus        18 l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l   67 (276)
T d1fnna2          18 LPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELY   67 (276)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHH
Confidence            33466777777766642      123578999999999998886665543

>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=97.27  E-value=8.4e-06  Score=50.01  Aligned_cols=32  Identities=13%  Similarity=0.127  Sum_probs=24.3

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ....++.+|||+|||.++-.++...+...+.+
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i   63 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVI   63 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhhcceEEE
Confidence            34577889999999999977777666555554

>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=97.25  E-value=1.4e-05  Score=53.65  Aligned_cols=43  Identities=14%  Similarity=0.174  Sum_probs=33.0

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEE
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..+-+.|.+.++++....+ +-.++.+|||||||++..+++...
T Consensus       140 LG~~~~~~~~l~~l~~~~~-GliLvtGpTGSGKSTTl~~~l~~~  182 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKRPH-GIILVTGPTGSGKSTTLYAGLQEL  182 (401)
T ss_dssp             SCCCHHHHHHHHHHHTSSS-EEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHhhhh-ceEEEEcCCCCCccHHHHHHhhhh
Confidence            4566788888988887632 567778999999999987776643

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.19  E-value=1.7e-05  Score=48.69  Aligned_cols=41  Identities=17%  Similarity=0.212  Sum_probs=31.1

Q ss_pred             eeccchhhHHHHHhc---CCc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         10 VLRPYQEKSLRKMFG---NGR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~---~~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .++|||+++++++.+   .+. ++.-++.+|+|+|||.++..++.
T Consensus         2 ~~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~   46 (207)
T d1a5ta2           2 RWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSR   46 (207)
T ss_dssp             CCCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHH
Confidence            567999999988654   222 34578899999999999876554

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.16  E-value=4e-05  Score=46.35  Aligned_cols=40  Identities=15%  Similarity=0.112  Sum_probs=29.2

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ++...+.++.|++.+...+.++.+|+|+|||.++-.++.+
T Consensus        17 ~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~   56 (237)
T d1sxjd2          17 QDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKE   56 (237)
T ss_dssp             CCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHH
Confidence            3445666777887654456899999999999887666543

>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=97.10  E-value=6.1e-06  Score=46.49  Aligned_cols=27  Identities=33%  Similarity=0.434  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ++-++.+|+|+|||+++-.++.+++.+
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~~~   29 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLNME   29 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            567888999999999998877765544

>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=97.02  E-value=1.8e-05  Score=45.56  Aligned_cols=31  Identities=13%  Similarity=0.024  Sum_probs=23.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      +-.++.+|+|||||+++-.+..+.+.+.+.+
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~~lg~~~~~~   35 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALANLPGVPKVHF   35 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEe
Confidence            4567889999999999977777666665544

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.99  E-value=4.5e-05  Score=46.38  Aligned_cols=36  Identities=19%  Similarity=0.275  Sum_probs=25.7

Q ss_pred             hhhHHH---HHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLR---KMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~---~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |+++++   .|++.+...+.++.+|+|+|||.++-.++.
T Consensus        29 ~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          29 QEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             CHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            555554   466554445689999999999988866554

>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=96.96  E-value=1.4e-05  Score=48.89  Aligned_cols=31  Identities=16%  Similarity=0.205  Sum_probs=23.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .+.++.+|+|+|||.++-.++.+.+...+++
T Consensus        36 ~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~   66 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLAHIIASELQTNIHVT   66 (238)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             CeEEEECCCCCcHHHHHHHHHhccCCCcccc
Confidence            5789999999999999877766655544443

>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=96.84  E-value=9.3e-06  Score=52.62  Aligned_cols=32  Identities=13%  Similarity=0.221  Sum_probs=24.0

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .++.++.+|||+|||.++-+++...+.+...+
T Consensus        49 ~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i   80 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIARRLAKLANAPFIKV   80 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHTCCEEEE
T ss_pred             CceEEEECCCCCCHHHHHHHHhhccccchhcc
Confidence            36788899999999999977776655544433

>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=96.82  E-value=2.2e-05  Score=53.62  Aligned_cols=32  Identities=13%  Similarity=0.221  Sum_probs=25.3

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ..|.++++|||+|||.++-.++..++-|++++
T Consensus        49 ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~   80 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIARRLAKLANAPFIKV   80 (443)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHTTCCEEEE
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHhCCCEEEe
Confidence            45899999999999999977776666665544

>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=96.80  E-value=1.5e-05  Score=45.65  Aligned_cols=27  Identities=15%  Similarity=0.160  Sum_probs=21.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      +-+|.+|+|||||+++-.++.+++.+.
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~   32 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKY   32 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcE
Confidence            467889999999999987776655443

>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=96.79  E-value=3.5e-05  Score=47.15  Aligned_cols=30  Identities=20%  Similarity=0.231  Sum_probs=23.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALV   58 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~li   58 (67)
                      ...++.+|+|+|||.++-+++...+.....
T Consensus        53 ~~lll~GPpG~GKTt~a~~la~~~~~~~~~   82 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAHLVAQELGYDILE   82 (253)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhhhhc
Confidence            468889999999999998777765555443

>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=96.79  E-value=5.5e-05  Score=51.16  Aligned_cols=54  Identities=19%  Similarity=0.196  Sum_probs=43.2

Q ss_pred             eeccchhhHHHHHhcC--CcceeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeecc
Q psy11637         10 VLRPYQEKSLRKMFGN--GRARSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNSG   63 (67)
Q Consensus        10 ~lR~yQ~~av~~~~~~--~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~~   63 (67)
                      .++.-|-+|++++++.  ...+...+.+.+||+|+++.++++...++++|||+|+.
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~~   63 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNK   63 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            5566788899887653  11134678899999999999999988999999999974

>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=96.77  E-value=4.7e-05  Score=49.98  Aligned_cols=31  Identities=13%  Similarity=0.198  Sum_probs=23.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE--eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV--RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~--~~~~lil   59 (67)
                      .+.+|++|||||||+...+++...  ..|++.+
T Consensus       167 ~nili~G~tgSGKTT~l~al~~~i~~~~rivti  199 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIMEFIPKEERIISI  199 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEE
T ss_pred             CCEEEEeeccccchHHHHHHhhhcccccceeec
Confidence            688999999999999887666543  3454444

>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=96.70  E-value=2.2e-05  Score=44.70  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=19.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      -.+|.+|+|||||+++-.+....+.
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~~~   28 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQLDN   28 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCC
Confidence            4578899999999998766655443

>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=96.67  E-value=6.1e-05  Score=45.98  Aligned_cols=41  Identities=17%  Similarity=0.180  Sum_probs=27.2

Q ss_pred             hhhHHHH---Hhc----C-CcceeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         15 QEKSLRK---MFG----N-GRARSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        15 Q~~av~~---~~~----~-~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      |++++++   |++    . ....+.++.+|+|+|||..+-.++.+.+..
T Consensus        14 q~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~   62 (239)
T d1ixsb2          14 QERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVN   62 (239)
T ss_dssp             CHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            7666654   432    1 123578899999999999887666544333

>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=96.65  E-value=8.2e-05  Score=42.84  Aligned_cols=35  Identities=23%  Similarity=0.249  Sum_probs=26.7

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.+|+++..+  .+...+|.+|+|+|||.+++.++..
T Consensus        10 ~~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          10 KELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             HHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHH
Confidence            4678888753  2467888999999999998776643

>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=96.59  E-value=0.00012  Score=43.64  Aligned_cols=34  Identities=24%  Similarity=0.280  Sum_probs=26.0

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +.+|+++..+  .+...+|.+|+|+|||.+++.++.
T Consensus        21 ~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~   56 (251)
T d1szpa2          21 KNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAV   56 (251)
T ss_dssp             HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTT
T ss_pred             HHHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHH
Confidence            4577788753  346788889999999999986654

>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=96.55  E-value=0.0001  Score=44.65  Aligned_cols=43  Identities=23%  Similarity=0.368  Sum_probs=32.0

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      .+++.+..+  .+...+|.+|+|+|||.+++.++...   +.+++++.
T Consensus        14 ~LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          14 RLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             HHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             HHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            477888753  24568888999999999998887763   45666664

>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=96.52  E-value=0.00013  Score=44.29  Aligned_cols=44  Identities=14%  Similarity=0.141  Sum_probs=28.4

Q ss_pred             ceeeccchhhHHHHHhc----CCc-cee----eeEEEeCCCCceeEeeeeEEE
Q psy11637          8 SAVLRPYQEKSLRKMFG----NGR-ARS----GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus         8 ~~~lR~yQ~~av~~~~~----~~~-~~~----~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.-|+.|.+.+.+++.    ++. ..+    .++++|+|+|||.++-.++..
T Consensus        17 ~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~   69 (287)
T d1w5sa2          17 ELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR   69 (287)
T ss_dssp             SCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHH
Confidence            45567888888876542    221 111    234599999999988766654

>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=96.46  E-value=3e-05  Score=44.35  Aligned_cols=27  Identities=15%  Similarity=0.121  Sum_probs=21.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ++.+|.+|+|+|||+++-.++.+.+.+
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~~~~   34 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVFNTT   34 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            578899999999999997776655443

>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=96.43  E-value=5.5e-05  Score=43.20  Aligned_cols=28  Identities=18%  Similarity=-0.016  Sum_probs=21.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      +-.+|.+|+|||||+++-.+...++.+.
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~l~~~~   31 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSVLPEPW   31 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCe
Confidence            3466779999999999987776655443

>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=96.36  E-value=0.00021  Score=43.06  Aligned_cols=33  Identities=27%  Similarity=0.392  Sum_probs=25.1

Q ss_pred             HHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE
Q psy11637         18 SLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        18 av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+++++..+  .+.-.+|.+|+|+|||..++.++.
T Consensus        24 ~LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~   58 (254)
T d1pzna2          24 SLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAV   58 (254)
T ss_dssp             HHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHH
T ss_pred             HHHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHH
Confidence            456777653  246788889999999999986654

>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=96.35  E-value=6.2e-05  Score=46.89  Aligned_cols=31  Identities=19%  Similarity=0.122  Sum_probs=21.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      +..++++|||+|||++.+-++...   ++++.++
T Consensus         7 ~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~li   40 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFC   40 (207)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            456779999999999987665442   4455544

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.24  E-value=0.00032  Score=42.50  Aligned_cols=36  Identities=17%  Similarity=0.127  Sum_probs=24.0

Q ss_pred             hhhHHHHHhcCCc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRKMFGNGR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..+.+..++..+. ..+.++.+|+|+|||.++..++.
T Consensus        19 ~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2          19 LTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             HHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHH
T ss_pred             HHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            3444444554332 34678999999999998866654

>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=96.24  E-value=0.0001  Score=46.05  Aligned_cols=23  Identities=17%  Similarity=0.040  Sum_probs=14.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...++++|||+|||++.+-++..
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~~   35 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAYF   35 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            45667899999999998766654

>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=96.22  E-value=0.00022  Score=40.22  Aligned_cols=21  Identities=19%  Similarity=-0.018  Sum_probs=16.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      -.++.+|+|||||+++-.++.
T Consensus         4 lIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356789999999998765543

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.21  E-value=0.00011  Score=45.88  Aligned_cols=31  Identities=16%  Similarity=0.034  Sum_probs=21.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ...++++|||+|||++.+-++.+.   +.++.++
T Consensus        12 ~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~li   45 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLA   45 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEE
Confidence            456778999999999987665442   3455444

>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=96.15  E-value=0.00011  Score=45.94  Aligned_cols=32  Identities=16%  Similarity=0.036  Sum_probs=22.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      .-.++++|||+|||++.+-++.+.   +.++.+++
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit   44 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAA   44 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            446678999999999987766442   34554443

>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=96.11  E-value=0.00017  Score=47.95  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .+.++.+|||.|||.++-.++..
T Consensus        69 ~niLfiGPTGvGKTElAk~LA~~   91 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMAQTLAKH   91 (364)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHH
T ss_pred             cceeeeCCCCccHHHHHHHHHhh
Confidence            56899999999999988555443

>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=96.08  E-value=0.00012  Score=41.62  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=19.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ++.+|.+|+|+|||+++..++..+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            578899999999999887776543

>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=96.06  E-value=0.00031  Score=42.06  Aligned_cols=34  Identities=21%  Similarity=0.341  Sum_probs=26.3

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +.+|+++..+  .+...+|.+|+|+|||.+++.++.
T Consensus        24 ~~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~   59 (258)
T d1v5wa_          24 QEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCV   59 (258)
T ss_dssp             HHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHH
T ss_pred             HHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4577888753  345788889999999999987764

>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=96.05  E-value=0.0001  Score=45.78  Aligned_cols=31  Identities=19%  Similarity=0.207  Sum_probs=21.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      -.++++|||+|||++.+-++.+.   +.++.+++
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit   45 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVA   45 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            35668999999999987666543   44555443

>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=96.05  E-value=0.00012  Score=46.50  Aligned_cols=33  Identities=18%  Similarity=0.326  Sum_probs=25.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLCN   61 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p   61 (67)
                      +..++++|+|+|||.++-+++...+.+.+.+-.
T Consensus        46 ~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~   78 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISG   78 (256)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHTCCEEEECS
T ss_pred             CeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEh
Confidence            568889999999999998887766666655544

>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=96.02  E-value=9.5e-05  Score=46.53  Aligned_cols=34  Identities=18%  Similarity=0.259  Sum_probs=26.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEeec
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLCNS   62 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~p~   62 (67)
                      +..++.+|+|+|||.++-+++...+.+++.+.++
T Consensus        39 ~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~   72 (258)
T d1e32a2          39 RGILLYGPPGTGKTLIARAVANETGAFFFLINGP   72 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHH
T ss_pred             ceeEEecCCCCCchHHHHHHHHHhCCeEEEEEch
Confidence            5678889999999998877777666666665543

>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=96.02  E-value=8.6e-05  Score=43.24  Aligned_cols=23  Identities=22%  Similarity=0.130  Sum_probs=18.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-+|.+|+|||||+++..++.+.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            35788999999999987665543

>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=95.98  E-value=0.00012  Score=45.98  Aligned_cols=31  Identities=13%  Similarity=0.059  Sum_probs=23.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      ++.++.+|+|+|||.++-+++...+.+++-+
T Consensus        41 ~~vLL~GppGtGKT~la~alA~~~~~~~~~i   71 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKIAEESNFPFIKI   71 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTCSEEEE
T ss_pred             eEEEEECcCCCCHHHHHHHHhhccccccccc
Confidence            5678899999999999987776665554433

>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=95.97  E-value=0.00048  Score=39.25  Aligned_cols=24  Identities=25%  Similarity=0.264  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +-.++.+|+|||||+++-.+..++
T Consensus         7 ~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            456778999999999987665544

>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=95.94  E-value=0.00024  Score=46.03  Aligned_cols=43  Identities=21%  Similarity=0.219  Sum_probs=29.6

Q ss_pred             chhhHHHHHhc----------C-Cc-ceeeeEEEeCCCCceeEeeeeEEEEeeee
Q psy11637         14 YQEKSLRKMFG----------N-GR-ARSGVIVLPCGAGKSLVGVTACCTVRKRA   56 (67)
Q Consensus        14 yQ~~av~~~~~----------~-~~-~~~~~i~~pTGsGKT~i~~~~~~~~~~~~   56 (67)
                      .|.+|++.+..          . +. ..+.++++|||+|||.++-.++..++.+.
T Consensus        26 GQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~   80 (315)
T d1r6bx3          26 GQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIEL   80 (315)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEE
T ss_pred             ChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhccCCe
Confidence            49999886431          1 11 23577889999999999877766555543

>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=95.94  E-value=0.00038  Score=39.69  Aligned_cols=25  Identities=16%  Similarity=0.135  Sum_probs=19.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      -+-+|.+|+|+|||+++-.+..+++
T Consensus         6 ~~I~i~G~~GsGKTT~~~~La~~l~   30 (174)
T d1y63a_           6 INILITGTPGTGKTSMAEMIAAELD   30 (174)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHhC
Confidence            4678889999999999876665543

>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=95.94  E-value=0.00014  Score=45.88  Aligned_cols=32  Identities=19%  Similarity=0.262  Sum_probs=25.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      +..++.+|+|+|||.++-+++.+.+.+++.+-
T Consensus        43 ~giLl~GppGtGKT~la~aia~~~~~~~~~i~   74 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAGEARVPFITAS   74 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTCCEEEEE
T ss_pred             ceEEEecCCCCChhHHHHHHHHHcCCCEEEEE
Confidence            45788999999999999888776666655553

>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=95.93  E-value=0.00021  Score=47.49  Aligned_cols=32  Identities=19%  Similarity=0.162  Sum_probs=25.7

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEEEEeeeeEEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACCTVRKRALVL   59 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil   59 (67)
                      .+..++.+|+|+|||.++.+++..++.+++-+
T Consensus       154 ~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~i  185 (362)
T d1svma_         154 KRYWLFKGPIDSGKTTLAAALLELCGGKALNV  185 (362)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCEEECC
T ss_pred             cCeEEEECCCCCCHHHHHHHHHHHcCCCEEEE
Confidence            35678889999999999998888777766543

>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=95.91  E-value=0.00018  Score=42.56  Aligned_cols=24  Identities=13%  Similarity=0.040  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...+|.+|+|||||+++-.++.+.
T Consensus         7 ~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           7 NVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            456788999999999987666543

>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=95.82  E-value=0.00012  Score=42.78  Aligned_cols=24  Identities=21%  Similarity=0.170  Sum_probs=18.7

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +-++.+++|+|||+++-.++..++
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~   25 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLD   25 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhC
Confidence            467889999999999876665543

>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=95.80  E-value=0.00049  Score=40.70  Aligned_cols=34  Identities=21%  Similarity=0.378  Sum_probs=26.0

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .-+|+++..+  .+.-.+|.+|+|+|||.+++.++.
T Consensus        21 ~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~   56 (258)
T d2i1qa2          21 SELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCV   56 (258)
T ss_dssp             HHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHH
T ss_pred             HHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHH
Confidence            3467777653  246788899999999999987765

>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=95.78  E-value=0.00061  Score=39.70  Aligned_cols=22  Identities=14%  Similarity=-0.081  Sum_probs=17.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.++.+|+|||||+++-.++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4578899999999998666544

>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=95.77  E-value=0.00012  Score=42.82  Aligned_cols=26  Identities=19%  Similarity=0.166  Sum_probs=19.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      .-++.+++|+|||+++-.++.+++-+
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~Lg~~   29 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARALGYE   29 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTCE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            45778999999999997776654433

>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=95.76  E-value=0.00058  Score=40.17  Aligned_cols=24  Identities=25%  Similarity=0.261  Sum_probs=18.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -+.++.+|+|||||+++-.++.+.
T Consensus         4 ~riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           4 VRAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            466788999999999987665543

>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=95.75  E-value=0.00013  Score=42.86  Aligned_cols=23  Identities=22%  Similarity=0.052  Sum_probs=18.3

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.+|.+|+|||||+++..++.+.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            35788999999999987666554

>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=95.65  E-value=0.00023  Score=42.69  Aligned_cols=25  Identities=20%  Similarity=0.161  Sum_probs=19.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      -+.+|.+|+|||||+++..++.+.+
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~g   31 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHFE   31 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHBC
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHHC
Confidence            4677889999999999977766543

>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=95.64  E-value=0.00072  Score=39.79  Aligned_cols=23  Identities=13%  Similarity=-0.116  Sum_probs=18.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      -+.+|.+|+|||||+++-.++.+
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999988665544

>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=95.64  E-value=0.00055  Score=40.38  Aligned_cols=44  Identities=16%  Similarity=0.295  Sum_probs=30.4

Q ss_pred             hHHHHHhcCC--cceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEe
Q psy11637         17 KSLRKMFGNG--RARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLC   60 (67)
Q Consensus        17 ~av~~~~~~~--~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~   60 (67)
                      +.+|+.+..+  .+...+|.+++|+|||..++.++..    .+.+++++.
T Consensus        13 ~~LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s   62 (242)
T d1tf7a1          13 EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVT   62 (242)
T ss_dssp             TTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEE
T ss_pred             HHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCccccc
Confidence            3467777643  3467888999999999998766543    234566654

>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=95.63  E-value=0.00081  Score=38.01  Aligned_cols=24  Identities=13%  Similarity=0.027  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ....+++++|||||+++-.+..++
T Consensus         7 ~~I~l~G~~GsGKTTia~~La~~L   30 (183)
T d1m8pa3           7 FTIFLTGYMNSGKDAIARALQVTL   30 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            345577999999999987666543

>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=95.60  E-value=0.00068  Score=39.57  Aligned_cols=23  Identities=26%  Similarity=0.314  Sum_probs=18.2

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.+|.+|+|||||+++-.++...
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            45788999999999987665543

>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=95.51  E-value=0.00024  Score=42.19  Aligned_cols=24  Identities=17%  Similarity=0.016  Sum_probs=19.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...++.+|+|||||+++-.++.+.
T Consensus         9 ~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           9 KIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            457788999999999987666543

>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=95.49  E-value=0.00022  Score=41.98  Aligned_cols=24  Identities=25%  Similarity=0.171  Sum_probs=18.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -+.++.+|+|||||+++-.++.+.
T Consensus         3 mrIvl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            356788999999999987666543

>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=95.43  E-value=0.00069  Score=39.99  Aligned_cols=24  Identities=17%  Similarity=-0.029  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ...+|.+|+|||||+++-.++.+.
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            346677999999999987665543

>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=95.36  E-value=0.00081  Score=39.47  Aligned_cols=23  Identities=17%  Similarity=0.018  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..+|.+|+|||||+++-.++.+.
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            35788999999999987666543

>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=95.29  E-value=0.0018  Score=37.24  Aligned_cols=19  Identities=21%  Similarity=0.067  Sum_probs=15.4

Q ss_pred             EEEeCCCCceeEeeeeEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+|+|||||+++-.+...
T Consensus        27 I~G~~GSGKSTla~~L~~~   45 (198)
T d1rz3a_          27 IDGLSRSGKTTLANQLSQT   45 (198)
T ss_dssp             EEECTTSSHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHH
Confidence            6799999999998766543

>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=95.26  E-value=0.00021  Score=41.54  Aligned_cols=24  Identities=29%  Similarity=0.337  Sum_probs=18.4

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +.++.+++|+|||+++-.++.+++
T Consensus         3 ~IvliG~~G~GKSTig~~La~~l~   26 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRRLAKALG   26 (165)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhC
Confidence            456779999999999876655543

>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=95.20  E-value=0.0011  Score=37.60  Aligned_cols=23  Identities=17%  Similarity=0.069  Sum_probs=18.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +-.+|.+|+|||||+++-.+..+
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~   24 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDN   24 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999988766554

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=95.18  E-value=0.00025  Score=41.97  Aligned_cols=22  Identities=27%  Similarity=0.240  Sum_probs=17.0

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -.|.+|+||||++++-.++.+.
T Consensus         6 I~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3566999999999987666543

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=95.15  E-value=0.0046  Score=38.00  Aligned_cols=40  Identities=13%  Similarity=0.111  Sum_probs=30.2

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+-..+-+..++.+....+.++++|+|.|||.+.-.++.+
T Consensus        27 Rd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~r   66 (195)
T d1jbka_          27 RDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHH
Confidence            5555556667777655578999999999999988666654

>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=95.14  E-value=0.00034  Score=44.14  Aligned_cols=32  Identities=16%  Similarity=0.251  Sum_probs=24.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEeeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~~~lil~   60 (67)
                      +..++++|+|+|||.++-+++...+.+.+.+.
T Consensus        42 ~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~   73 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLLAKAIANECQANFISIK   73 (265)
T ss_dssp             CEEEEBCCTTSSHHHHHHHHHHHTTCEEEEEC
T ss_pred             CeEEEECCCCCcchhHHHHHHHHhCCcEEEEE
Confidence            46778899999999999888777666655544

>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=95.12  E-value=0.00094  Score=40.02  Aligned_cols=40  Identities=20%  Similarity=0.134  Sum_probs=25.4

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEEEeee
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      .++-++++.+.. .+..+|.+|.|+|||.++..++...+..
T Consensus        17 R~~el~~l~~~~-~~~i~i~G~~G~GKTsLl~~~~~~~~~~   56 (283)
T d2fnaa2          17 REKEIEKLKGLR-APITLVLGLRRTGKSSIIKIGINELNLP   56 (283)
T ss_dssp             CHHHHHHHHHTC-SSEEEEEESTTSSHHHHHHHHHHHHTCC
T ss_pred             hHHHHHHHHhcc-CCEEEEEcCCCCcHHHHHHHHHHHCCCC
Confidence            334445544432 2567788999999998886665544333

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=95.07  E-value=0.00031  Score=41.96  Aligned_cols=22  Identities=27%  Similarity=0.172  Sum_probs=17.3

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..|.+|+|||||+++-.++.++
T Consensus         6 IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3467999999999997766554

>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=94.99  E-value=0.0018  Score=41.29  Aligned_cols=32  Identities=19%  Similarity=0.048  Sum_probs=21.5

Q ss_pred             chhhHHHHHhc---CCcceeeeEEEeCCCCceeEe
Q psy11637         14 YQEKSLRKMFG---NGRARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        14 yQ~~av~~~~~---~~~~~~~~i~~pTGsGKT~i~   45 (67)
                      .|+++..+++-   ....++.++.+|+|+|||.++
T Consensus        11 Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~la   45 (333)
T d1g8pa_          11 GQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAV   45 (333)
T ss_dssp             SCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHH
T ss_pred             CcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHH
Confidence            37776665331   111257899999999999765

>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=94.92  E-value=0.0013  Score=38.86  Aligned_cols=20  Identities=35%  Similarity=0.064  Sum_probs=15.8

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      .-.++++++|||||+.+-.+
T Consensus        15 ~liil~G~pGsGKST~a~~l   34 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFIQEH   34 (172)
T ss_dssp             CEEEEECCTTSSHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            45677899999999887544

>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=94.84  E-value=0.0026  Score=36.27  Aligned_cols=20  Identities=20%  Similarity=0.127  Sum_probs=15.9

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +.+|.+|+|+|||+.+-.++
T Consensus         2 ki~I~G~~G~GKSTLl~~i~   21 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIV   21 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCcHHHHHHHHHH
Confidence            35789999999999875544

>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=94.84  E-value=0.0025  Score=38.94  Aligned_cols=36  Identities=22%  Similarity=0.200  Sum_probs=24.3

Q ss_pred             hhhHHHH---HhcCCc-ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         15 QEKSLRK---MFGNGR-ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        15 Q~~av~~---~~~~~~-~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      |++.++.   |++.+. .+..++.+|+|+|||.++..++.
T Consensus        17 ~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~   56 (239)
T d1njfa_          17 QEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAK   56 (239)
T ss_dssp             CHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHH
Confidence            6666654   554433 34468899999999988765543

>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=94.79  E-value=0.00048  Score=39.02  Aligned_cols=22  Identities=14%  Similarity=0.013  Sum_probs=17.8

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      ..|+++.|||||+.+-.++.++
T Consensus         5 i~itG~~GSGKTTL~~~L~~~l   26 (170)
T d1np6a_           5 LAFAAWSGTGKTTLLKKLIPAL   26 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH
Confidence            4578999999999987777653

>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=94.67  E-value=0.0011  Score=40.81  Aligned_cols=44  Identities=11%  Similarity=0.003  Sum_probs=29.5

Q ss_pred             HHHHHhcC-CcceeeeEEEeCCCCceeEeeeeEEE----EeeeeEEEee
Q psy11637         18 SLRKMFGN-GRARSGVIVLPCGAGKSLVGVTACCT----VRKRALVLCN   61 (67)
Q Consensus        18 av~~~~~~-~~~~~~~i~~pTGsGKT~i~~~~~~~----~~~~~lil~p   61 (67)
                      .+++.+.. ..+.-.+|.++||+|||..++.++..    .+.+++++..
T Consensus        24 ~lD~~~~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~   72 (277)
T d1cr2a_          24 GINDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (277)
T ss_dssp             THHHHHCSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             hHHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee
Confidence            34555532 12356788899999999888776643    3567887753

>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=94.65  E-value=0.001  Score=43.27  Aligned_cols=31  Identities=23%  Similarity=0.260  Sum_probs=21.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      ++.+|.++||+|||.....++..   .+.+++|+
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iii   84 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIV   84 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEE
Confidence            57899999999999875444433   23445544

>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=94.63  E-value=0.0026  Score=36.20  Aligned_cols=22  Identities=27%  Similarity=0.226  Sum_probs=17.4

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|.+++|+|||+++-.+...+
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L   25 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEIL   25 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            4678999999999987665543

>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=94.51  E-value=0.00039  Score=40.94  Aligned_cols=23  Identities=30%  Similarity=0.164  Sum_probs=17.7

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +-.+|++|.|+|||+++-.+..+
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHhh
Confidence            45678899999999987655443

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=94.48  E-value=0.0085  Score=38.18  Aligned_cols=40  Identities=15%  Similarity=0.197  Sum_probs=28.7

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+--.+-+..++.+....+.++++|+|.|||.+.-.++.+
T Consensus        23 Rd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~r   62 (268)
T d1r6bx2          23 REKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWR   62 (268)
T ss_dssp             CHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHH
Confidence            4444445556676554578999999999999888766654

>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=94.35  E-value=0.0011  Score=38.35  Aligned_cols=22  Identities=23%  Similarity=0.119  Sum_probs=16.9

Q ss_pred             eeeEEEeCCCCceeEeeeeEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ..++++++|||||+++-.+..+
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~   42 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEY   42 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3446699999999999776554

>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=94.26  E-value=0.0006  Score=40.47  Aligned_cols=23  Identities=30%  Similarity=0.242  Sum_probs=18.0

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      -.+|++|+|+|||.++-.++...
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            46789999999999876665543

>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=94.15  E-value=0.0022  Score=38.20  Aligned_cols=19  Identities=21%  Similarity=0.076  Sum_probs=15.4

Q ss_pred             EEEeCCCCceeEeeeeEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+|+|||||+++-.+...
T Consensus         7 I~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           7 VSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             EECSTTSSHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHH
Confidence            6799999999998666544

>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=94.11  E-value=0.004  Score=37.65  Aligned_cols=37  Identities=14%  Similarity=-0.060  Sum_probs=30.7

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+.++++++.+...+-++.+|.|+|||.++..++..
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~   38 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEY   38 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            7788899998766678999999999999998765543

>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=94.03  E-value=0.0042  Score=40.09  Aligned_cols=38  Identities=26%  Similarity=0.357  Sum_probs=25.4

Q ss_pred             chhhHHHHHhc----------C-Cc-ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         14 YQEKSLRKMFG----------N-GR-ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        14 yQ~~av~~~~~----------~-~~-~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .|.+|++.+..          . .+ ....++++|||+|||.++-.++..
T Consensus        27 GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~   76 (315)
T d1qvra3          27 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAAT   76 (315)
T ss_dssp             SCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHH
Confidence            48888876432          1 11 124567799999999998766554

>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=94.02  E-value=0.00082  Score=43.62  Aligned_cols=52  Identities=13%  Similarity=0.191  Sum_probs=36.3

Q ss_pred             eeeccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE---EeeeeEEEeecc
Q psy11637          9 AVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT---VRKRALVLCNSG   63 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~---~~~~~lil~p~~   63 (67)
                      ..+|||..+.+-.+.-+   ...+.-|.||-|||+++...+..   .++.+.|++.+.
T Consensus        77 lG~RhyDVQLiGgi~L~---~G~iaem~TGEGKTL~a~l~a~l~al~g~~vhvvTvNd  131 (273)
T d1tf5a3          77 TGMFPFKVQLMGGVALH---DGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNE  131 (273)
T ss_dssp             HSCCCCHHHHHHHHHHH---TTSEEECCTTSCHHHHHHHHHHHHHTTSSCEEEEESSH
T ss_pred             hceEEehhHHHHHHHHH---hhhheeecCCCcchhHHHHHHHHHHhcCCCceEEecCc
Confidence            45788877777765443   23567899999999998765543   366777776554

>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=93.96  E-value=0.0029  Score=36.83  Aligned_cols=21  Identities=19%  Similarity=0.039  Sum_probs=17.0

Q ss_pred             eeEEEeCCCCceeEeeeeEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .++++.+|||||+++-.++..
T Consensus         5 i~l~GlpgsGKSTla~~L~~~   25 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRY   25 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999776643

>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=93.85  E-value=0.0085  Score=36.43  Aligned_cols=41  Identities=15%  Similarity=0.040  Sum_probs=25.9

Q ss_pred             eccchhhHH---HHHhcCC-c-ceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         11 LRPYQEKSL---RKMFGNG-R-ARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        11 lR~yQ~~av---~~~~~~~-~-~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-+..+.|.   +++.+.. . .....|.+|+|+|||+.+.+++.+
T Consensus        14 vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~   59 (213)
T d1l8qa2          14 VGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE   59 (213)
T ss_dssp             CCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHH
Confidence            344455544   4455432 1 123678899999999998776654

>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=93.84  E-value=0.0006  Score=40.75  Aligned_cols=22  Identities=32%  Similarity=0.217  Sum_probs=17.3

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .+|++|+|+|||.++-.++...
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            5788999999999876665543

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=92.90  E-value=0.021  Score=37.84  Aligned_cols=40  Identities=13%  Similarity=0.116  Sum_probs=28.9

Q ss_pred             ccchhhHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEEE
Q psy11637         12 RPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        12 R~yQ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      |+.-.+-+..+|.+....+.++++|+|.|||.+.-.++.+
T Consensus        27 r~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~   66 (387)
T d1qvra2          27 RDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQR   66 (387)
T ss_dssp             CHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHH
Confidence            5555555566676544578999999999999887655543

>d1w1wa_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.65  E-value=0.0083  Score=38.02  Aligned_cols=19  Identities=32%  Similarity=0.289  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      +-.+|++|+|+|||.+.-+
T Consensus        26 ~l~~i~G~NGsGKS~ileA   44 (427)
T d1w1wa_          26 NFTSIIGPNGSGKSNMMDA   44 (427)
T ss_dssp             SEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHH
Confidence            4578999999999977543

>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=92.53  E-value=0.0044  Score=39.26  Aligned_cols=44  Identities=23%  Similarity=0.265  Sum_probs=30.7

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ..+++.++. .+  .++-..+.+|+|+|||.+++.++...   +++++|+
T Consensus        39 ~~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyi   88 (263)
T d1u94a1          39 SLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFI   88 (263)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CHHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEE
Confidence            346788886 43  24568888999999999998776653   3444444

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

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: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=92.52  E-value=0.011  Score=38.08  Aligned_cols=34  Identities=18%  Similarity=0.135  Sum_probs=20.7

Q ss_pred             chhhHHHHH--------hcCCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKM--------FGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~--------~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+..        +..+.....+..+.||||||+++..
T Consensus        63 ~q~~vy~~~~~plv~~~~~~G~n~~i~aYGqTGSGKTyTm~G  104 (330)
T d1ry6a_          63 DNFTVYENTIKPLIIDLYENGCVCSCFAYGQTGSGKTYTMLG  104 (330)
T ss_dssp             CHHHHHHHHTHHHHHHHHHHCCEEEEEEECCTTSSHHHHHHB
T ss_pred             CHHHHHHHHHHHHHHHHHhcCCCeEEEeeeccccccceeeec
Confidence            477666542        2223223344559999999988753

>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=92.09  E-value=0.0034  Score=36.62  Aligned_cols=31  Identities=10%  Similarity=0.042  Sum_probs=21.9

Q ss_pred             eeeeEEEe-CCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLP-CGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~p-TGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ++-+|.+- ||.|||++++.++..+   +.+++++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~i   36 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGY   36 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEE
Confidence            34556655 5999999998877653   5677665

>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=92.08  E-value=0.0023  Score=36.75  Aligned_cols=20  Identities=15%  Similarity=0.002  Sum_probs=16.9

Q ss_pred             EEEeCCCCceeEeeeeEEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~~   52 (67)
                      |+++.|||||+....++.++
T Consensus         6 I~G~~gSGKTTli~~l~~~L   25 (165)
T d1xjca_           6 VVGYKHSGKTTLMEKWVAAA   25 (165)
T ss_dssp             EECCTTSSHHHHHHHHHHHH
T ss_pred             EEeCCCCCHHHHHHHHHHHH
Confidence            78999999999998777654

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

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 protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=91.95  E-value=0.002  Score=40.19  Aligned_cols=47  Identities=17%  Similarity=0.280  Sum_probs=28.8

Q ss_pred             eeeccchhhHH-------HHHhcCCccee-eeEEEeCCCCceeEeeeeEEEEeee
Q psy11637          9 AVLRPYQEKSL-------RKMFGNGRARS-GVIVLPCGAGKSLVGVTACCTVRKR   55 (67)
Q Consensus         9 ~~lR~yQ~~av-------~~~~~~~~~~~-~~i~~pTGsGKT~i~~~~~~~~~~~   55 (67)
                      ..+-.||..-+       +.++++...++ .++.+|+++|||..+.+++.-+++.
T Consensus        26 ~~~l~~q~i~~~~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~   80 (205)
T d1tuea_          26 VQFLRYQQIEFITFLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFIQGA   80 (205)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHHTCE
T ss_pred             HHHHHhcCccHHHHHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHhCCE
Confidence            34444665433       34554433344 5667999999999987776554443

>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=91.86  E-value=0.011  Score=34.90  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=18.0

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +-.+|++|+|+|||.+.-.++.+
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~   26 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITK   26 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHh
Confidence            35678899999999988665544

>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=91.71  E-value=0.022  Score=36.35  Aligned_cols=34  Identities=15%  Similarity=0.005  Sum_probs=21.9

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..++...       .|.....+..++||||||++...
T Consensus        55 ~q~~vf~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyT~~G   95 (323)
T d1bg2a_          55 SQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG   95 (323)
T ss_dssp             CHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCcceeeecccCCCCceeccC
Confidence            46666654321       23334566669999999988753

>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=91.68  E-value=0.0058  Score=37.24  Aligned_cols=22  Identities=36%  Similarity=0.650  Sum_probs=18.6

Q ss_pred             eeeeEEEeCCCCceeEeeeeEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .-.+|.+++|+|||..++.++.
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            5788999999999998876654

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=91.67  E-value=0.011  Score=34.45  Aligned_cols=15  Identities=40%  Similarity=0.417  Sum_probs=12.3

Q ss_pred             EEEeCCCCceeEeee
Q psy11637         33 IVLPCGAGKSLVGVT   47 (67)
Q Consensus        33 i~~pTGsGKT~i~~~   47 (67)
                      |.++.|||||+++-.
T Consensus         8 itG~~gSGKstva~~   22 (191)
T d1uf9a_           8 ITGNIGSGKSTVAAL   22 (191)
T ss_dssp             EEECTTSCHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            569999999998743

>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=91.64  E-value=0.014  Score=35.23  Aligned_cols=24  Identities=29%  Similarity=0.227  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      .-.+|++|.|+|||.+.-.++...
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            456788999999999886665543

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {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: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=91.60  E-value=0.0015  Score=36.91  Aligned_cols=20  Identities=25%  Similarity=0.074  Sum_probs=15.8

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +-.+|++|+|||||.+.-++
T Consensus        25 ~~tvi~G~NGsGKStil~Ai   44 (222)
T d1qhla_          25 LVTTLSGGNGAGKSTTMAAF   44 (222)
T ss_dssp             HHHHHHSCCSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHH
Confidence            45678899999999877444

>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=91.51  E-value=0.012  Score=38.43  Aligned_cols=25  Identities=8%  Similarity=-0.047  Sum_probs=19.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVR   53 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~   53 (67)
                      +..++.+|+|+|||.++-+++.+.+
T Consensus       124 g~~l~~G~pG~GKT~la~ala~~~~  148 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGEALG  148 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHHHHH
T ss_pred             ceEEEECCCCccHHHHHHHHHHHhc
Confidence            3455579999999999977776653

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=91.39  E-value=0.006  Score=37.35  Aligned_cols=31  Identities=10%  Similarity=0.070  Sum_probs=22.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      +-.++++--|.|||+++..++..+   +.++|++
T Consensus        21 ~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllv   54 (279)
T d1ihua2          21 GLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLT   54 (279)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEE
Confidence            556667999999999997776543   5566654

>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=91.13  E-value=0.029  Score=36.58  Aligned_cols=34  Identities=18%  Similarity=0.047  Sum_probs=21.1

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..++...       .|.+...+..+.||||||+++..
T Consensus        93 ~Q~~Vy~~~~~plv~~~l~G~n~tifaYGqTGSGKTyTm~G  133 (362)
T d1v8ka_          93 SNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGG  133 (362)
T ss_dssp             CHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHHHHhccCceEEeeccCCCCCceeeee
Confidence            37766655321       23323444559999999988755

>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=91.09  E-value=0.023  Score=35.14  Aligned_cols=20  Identities=25%  Similarity=0.238  Sum_probs=16.2

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ...+|.+++|+||+.+|-.+
T Consensus        24 ~pvlI~Ge~GtGK~~~A~~i   43 (247)
T d1ny5a2          24 CPVLITGESGVGKEVVARLI   43 (247)
T ss_dssp             SCEEEECSTTSSHHHHHHHH
T ss_pred             CCEEEECCCCcCHHHHHHHH
Confidence            56888899999999877443

>d1e69a_ c.37.1.12 (A:) Smc head 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: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.02  E-value=0.018  Score=35.34  Aligned_cols=17  Identities=47%  Similarity=0.526  Sum_probs=14.5

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      +-.++++|.|+|||.+.
T Consensus        25 ~lnvlvG~NgsGKS~iL   41 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNII   41 (308)
T ss_dssp             SEEEEECCTTTCSTHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            35689999999999885

>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=90.84  E-value=0.039  Score=35.42  Aligned_cols=33  Identities=18%  Similarity=0.075  Sum_probs=20.4

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..++...       .|.....+..++||||||+++.
T Consensus        60 ~q~~vy~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyTm~   99 (345)
T d1x88a1          60 KQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTME   99 (345)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHHT
T ss_pred             CHHHHHHHHHHHhHHHHhccCCceEEeeeeccccceEEee
Confidence            36666554321       2333345556999999998764

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {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: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=90.49  E-value=0.0065  Score=37.20  Aligned_cols=32  Identities=19%  Similarity=0.243  Sum_probs=24.8

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE---eeeeEEEe
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV---RKRALVLC   60 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil~   60 (67)
                      +..++++--|.|||+++.+++..+   ++|+|++-
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD   43 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVS   43 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEe
Confidence            566778999999999998776653   67887653

>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=90.33  E-value=0.032  Score=36.07  Aligned_cols=34  Identities=24%  Similarity=0.130  Sum_probs=20.8

Q ss_pred             chhhHHHHHhc-------CCcceeeeEEEeCCCCceeEeee
Q psy11637         14 YQEKSLRKMFG-------NGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        14 yQ~~av~~~~~-------~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      -|++..+....       .|.....+..++||||||+++..
T Consensus        59 ~q~~vy~~~~~plv~~~l~G~n~ti~aYG~tgSGKT~Tm~G   99 (354)
T d1goja_          59 KQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMMG   99 (354)
T ss_dssp             CHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             CHHHHHHHHHHHHHHHhhccCceeEEecccCCCCcceeeec
Confidence            36666654321       23223455559999999988654

>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=90.31  E-value=0.032  Score=36.33  Aligned_cols=18  Identities=17%  Similarity=0.041  Sum_probs=13.8

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ...+..++||||||+++.
T Consensus        76 ~~i~aYGqTGSGKTyTm~   93 (364)
T d1sdma_          76 VCIFAYGQTGSGKTFTIY   93 (364)
T ss_dssp             EEEEEECSTTSSHHHHHT
T ss_pred             eeeeccccCCCCcccccc
Confidence            345555999999998864

>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=90.31  E-value=0.029  Score=35.00  Aligned_cols=20  Identities=30%  Similarity=0.154  Sum_probs=16.4

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|++|+|||||+..-.+
T Consensus        30 e~vaIvG~sGsGKSTLl~ll   49 (241)
T d2pmka1          30 EVIGIVGRSGSGKSTLTKLI   49 (241)
T ss_dssp             CEEEEECSTTSSHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHH
Confidence            67889999999999876433

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=90.24  E-value=0.1  Score=29.71  Aligned_cols=29  Identities=24%  Similarity=0.275  Sum_probs=20.9

Q ss_pred             HHhcCCcceeeeEEEeCCCCceeEeeeeE
Q psy11637         21 KMFGNGRARSGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        21 ~~~~~~~~~~~~i~~pTGsGKT~i~~~~~   49 (67)
                      ..+...+.-+.++++++|+|||.+...+.
T Consensus        10 ~l~~~~k~~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          10 KLWGSNKELRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             GGTTCSSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             HHhCCCceEEEEEECCCCCCHHHHHHHHh
Confidence            34444445678899999999998776553

>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=90.12  E-value=0.025  Score=34.08  Aligned_cols=23  Identities=17%  Similarity=0.115  Sum_probs=18.5

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-.++.+|.|+|||.+++.++.+
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            45677899999999999876653

>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=90.09  E-value=0.034  Score=34.58  Aligned_cols=20  Identities=25%  Similarity=0.187  Sum_probs=16.2

Q ss_pred             ceeeeEEEeCCCCceeEeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~   47 (67)
                      +....|++|+|||||+..-.
T Consensus        28 Ge~vaivG~sGsGKSTLl~l   47 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSL   47 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHH
Confidence            36778999999999987643

>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=90.02  E-value=0.03  Score=36.10  Aligned_cols=32  Identities=28%  Similarity=0.255  Sum_probs=20.9

Q ss_pred             hhhHHHH--------HhcCCcceeeeEEEeCCCCceeEeee
Q psy11637         15 QEKSLRK--------MFGNGRARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        15 Q~~av~~--------~~~~~~~~~~~i~~pTGsGKT~i~~~   47 (67)
                      |++..+.        +++ |.+...+..+.||||||+++..
T Consensus        67 Q~~vy~~~~~plv~~~l~-G~n~ti~aYGqTgSGKT~Tm~G  106 (349)
T d2zfia1          67 QKQVYRDIGEEMLQHAFE-GYNVCIFAYGQTGAGKSYTMMG  106 (349)
T ss_dssp             HHHHHHHTHHHHHHHHHT-TCCEEEEEECSTTSSHHHHHTB
T ss_pred             HHHHHHHhhHHHHHHHHh-ccCceeeeeccCCCCCceeecc
Confidence            6666554        333 3334455569999999988753

>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=89.98  E-value=0.031  Score=34.91  Aligned_cols=21  Identities=33%  Similarity=0.420  Sum_probs=17.0

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +....|++|+|||||++.-.+
T Consensus        40 Ge~vaivG~sGsGKSTLl~li   60 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALL   60 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHHHH
Confidence            367889999999999887443

>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=89.94  E-value=0.042  Score=34.37  Aligned_cols=20  Identities=25%  Similarity=0.350  Sum_probs=16.5

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|++|+|||||+..-.+
T Consensus        42 e~iaivG~sGsGKSTLl~ll   61 (253)
T d3b60a1          42 KTVALVGRSGSGKSTIASLI   61 (253)
T ss_dssp             CEEEEEECTTSSHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHH
Confidence            67889999999999877443

>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=89.83  E-value=0.027  Score=33.16  Aligned_cols=20  Identities=25%  Similarity=0.155  Sum_probs=15.7

Q ss_pred             eeEEEeCCCCceeEeeeeEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .+|.+|.|||||+..-.+..
T Consensus         3 i~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHH
Confidence            36789999999988766554

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {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: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=89.80  E-value=0.034  Score=33.45  Aligned_cols=23  Identities=17%  Similarity=0.014  Sum_probs=17.9

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ....+.+.+|||||+++-.+..+
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~   47 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQ   47 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            45667799999999998666543

>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=89.71  E-value=0.041  Score=35.84  Aligned_cols=32  Identities=16%  Similarity=0.075  Sum_probs=20.3

Q ss_pred             chhhHHH-------HHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLR-------KMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~-------~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..+       .+++ |.+...+..++||||||++..
T Consensus       105 ~Q~~Vy~~v~plv~~vl~-G~n~ti~aYGqtGSGKT~Tm~  143 (368)
T d2ncda_         105 SQSDIFEMVSPLIQSALD-GYNICIFAYGQTGSGKTYTMD  143 (368)
T ss_dssp             CHHHHHTTTHHHHHHHHT-TCEEEEEEECSTTSSHHHHHT
T ss_pred             CccchHHHHHHHHHHHhc-ccceeEEeeccCCCccceEec
Confidence            3666654       3343 333445556999999998764

>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=89.56  E-value=0.036  Score=33.36  Aligned_cols=20  Identities=25%  Similarity=0.125  Sum_probs=16.1

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ....|.+|.|+|||+..-.+
T Consensus        28 ei~~l~G~NGsGKSTLl~~i   47 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTI   47 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHH
Confidence            56778999999999877433

>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=89.13  E-value=0.049  Score=34.52  Aligned_cols=21  Identities=19%  Similarity=0.137  Sum_probs=16.4

Q ss_pred             ceeeeEEEeCCCCceeEeeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      +....|++|+|+|||+..-.+
T Consensus        62 Ge~vaivG~nGsGKSTLl~~i   82 (281)
T d1r0wa_          62 GEMLAITGSTGSGKTSLLMLI   82 (281)
T ss_dssp             TCEEEEEESTTSSHHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHHH
Confidence            367778999999999876433

>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=88.81  E-value=0.043  Score=34.43  Aligned_cols=20  Identities=25%  Similarity=0.144  Sum_probs=16.3

Q ss_pred             ceeeeEEEeCCCCceeEeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~   47 (67)
                      +....|++|+|||||++.-.
T Consensus        44 Ge~vaivG~sGsGKSTLl~l   63 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINL   63 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHH
Confidence            36788999999999987643

>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=88.81  E-value=0.031  Score=35.73  Aligned_cols=20  Identities=20%  Similarity=0.307  Sum_probs=16.7

Q ss_pred             ceeeeEEEeCCCCceeEeee
Q psy11637         28 ARSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~   47 (67)
                      +++.+|.+..|||||.+...
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~   35 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAA   35 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHH
Confidence            36889999999999987654

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

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: Deinococcus radiodurans [TaxId: 1299]

Probab=88.58  E-value=0.019  Score=36.32  Aligned_cols=44  Identities=23%  Similarity=0.307  Sum_probs=30.2

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ..+++..+. .+  .++-..+.+|.|+|||.+++.++...   +++++++
T Consensus        42 s~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yi   91 (268)
T d1xp8a1          42 SLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFI   91 (268)
T ss_dssp             CHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEE
Confidence            346788886 43  24567788999999999998776543   3445554

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, 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: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=88.57  E-value=0.029  Score=36.18  Aligned_cols=34  Identities=29%  Similarity=0.361  Sum_probs=25.2

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      .++|.++--+.+++..|.+|.|+|||++...++.
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~   65 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQ   65 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHH
Confidence            4566666444558999999999999988755544

>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=88.48  E-value=0.047  Score=33.88  Aligned_cols=17  Identities=35%  Similarity=0.350  Sum_probs=14.9

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....|++|.|+|||+..
T Consensus        32 e~~~iiG~sGsGKSTLl   48 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTML   48 (230)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCcchhh
Confidence            67889999999999775

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine 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: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.38  E-value=0.012  Score=34.84  Aligned_cols=26  Identities=19%  Similarity=-0.077  Sum_probs=20.2

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      +.-+|.++-|||||+.+-.+...+.+
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            45677899999999999777765543

>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=88.05  E-value=0.063  Score=33.49  Aligned_cols=17  Identities=29%  Similarity=0.229  Sum_probs=14.7

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      +...|.+|.|||||+..
T Consensus        32 e~~~iiG~sGsGKSTLl   48 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLI   48 (240)
T ss_dssp             CEEEEEESTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            67788999999999765

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {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: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=87.64  E-value=0.026  Score=33.46  Aligned_cols=15  Identities=20%  Similarity=0.302  Sum_probs=12.5

Q ss_pred             EEEeCCCCceeEeee
Q psy11637         33 IVLPCGAGKSLVGVT   47 (67)
Q Consensus        33 i~~pTGsGKT~i~~~   47 (67)
                      |.++.|||||+++-.
T Consensus         7 ITG~igSGKStv~~~   21 (205)
T d1jjva_           7 LTGGIGSGKTTIANL   21 (205)
T ss_dssp             EECSTTSCHHHHHHH
T ss_pred             EECCCCCCHHHHHHH
Confidence            679999999998643

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA 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: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=87.62  E-value=0.028  Score=33.46  Aligned_cols=14  Identities=36%  Similarity=0.377  Sum_probs=12.2

Q ss_pred             EEEeCCCCceeEee
Q psy11637         33 IVLPCGAGKSLVGV   46 (67)
Q Consensus        33 i~~pTGsGKT~i~~   46 (67)
                      |.++.|||||+++-
T Consensus         8 itG~igSGKStv~~   21 (208)
T d1vhta_           8 LTGGIGSGKSTVAN   21 (208)
T ss_dssp             EECCTTSCHHHHHH
T ss_pred             EECCCcCCHHHHHH
Confidence            67999999999874

>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=87.61  E-value=0.061  Score=33.42  Aligned_cols=17  Identities=41%  Similarity=0.405  Sum_probs=14.7

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ....+.+|.|+|||+..
T Consensus        27 ei~~liGpsGsGKSTLl   43 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLL   43 (232)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CEEEEECCCCChHHHHH
Confidence            67778999999999765

>d1f6ba_ c.37.1.8 (A:) SAR1 {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: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=87.57  E-value=0.12  Score=28.69  Aligned_cols=23  Identities=17%  Similarity=-0.113  Sum_probs=18.5

Q ss_pred             ceeeeEEEeCCCCceeEeeeeEE
Q psy11637         28 ARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..+.++++++|+|||.+...+..
T Consensus        13 ~~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          13 TGKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            36788999999999988765544

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {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: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.27  E-value=0.0096  Score=34.59  Aligned_cols=25  Identities=16%  Similarity=-0.071  Sum_probs=18.1

Q ss_pred             eeeEEEeCCCCceeEeeeeEEEEee
Q psy11637         30 SGVIVLPCGAGKSLVGVTACCTVRK   54 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~~~~~   54 (67)
                      ...|.++.|||||+.+-.+...++.
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~   35 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKND   35 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            4556699999999988666555433

>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=86.90  E-value=0.067  Score=33.39  Aligned_cols=17  Identities=24%  Similarity=0.350  Sum_probs=14.8

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ...-+++|.|+|||++.
T Consensus        30 e~~~liG~sGaGKSTll   46 (240)
T d1g2912          30 EFMILLGPSGCGKTTTL   46 (240)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCChHHHHH
Confidence            57778999999999875

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.76  E-value=0.035  Score=35.58  Aligned_cols=19  Identities=26%  Similarity=0.398  Sum_probs=14.3

Q ss_pred             EEEeCCCCceeEeeeeEEE
Q psy11637         33 IVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        33 i~~pTGsGKT~i~~~~~~~   51 (67)
                      |.+++|||||+++..+...
T Consensus        32 i~G~qGSGKSTl~~~l~~~   50 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNH   50 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHH
T ss_pred             eECCCCCCHHHHHHHHHHH
Confidence            4599999999888655443

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=86.72  E-value=0.093  Score=33.75  Aligned_cols=21  Identities=19%  Similarity=0.003  Sum_probs=15.8

Q ss_pred             eeEEEeCCCCceeEeeeeEEE
Q psy11637         31 GVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-|.++.|||||+++-.+...
T Consensus        83 IGIaG~sgSGKSTla~~L~~l  103 (308)
T d1sq5a_          83 ISIAGSVAVGKSTTARVLQAL  103 (308)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEeCCCCCCCcHHHHHHHHH
Confidence            335699999999988665544

>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=86.45  E-value=0.023  Score=34.52  Aligned_cols=31  Identities=19%  Similarity=0.075  Sum_probs=20.9

Q ss_pred             eeEEEeCCCCceeEeeeeEEEE-eeeeEEEee
Q psy11637         31 GVIVLPCGAGKSLVGVTACCTV-RKRALVLCN   61 (67)
Q Consensus        31 ~~i~~pTGsGKT~i~~~~~~~~-~~~~lil~p   61 (67)
                      .+|.+.-|||||+....++... +.|+.||++
T Consensus         6 ~iitGFLGaGKTTll~~lL~~~~~~riaVI~N   37 (222)
T d1nija1           6 TLLTGFLGAGKTTLLRHILNEQHGYKIAVIEN   37 (222)
T ss_dssp             EEEEESSSSSCHHHHHHHHHSCCCCCEEEECS
T ss_pred             EEEeeCCCCCHHHHHHHHHhcCCCCcEEEEEe
Confidence            4678999999998765554432 456666653

>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=86.29  E-value=0.022  Score=34.25  Aligned_cols=23  Identities=22%  Similarity=0.147  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-.++.++.|+|||.+++.++.+
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45677899999999998876643

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.09  E-value=0.03  Score=35.48  Aligned_cols=44  Identities=27%  Similarity=0.320  Sum_probs=29.8

Q ss_pred             hhHHHHHhc-CC--cceeeeEEEeCCCCceeEeeeeEEEE---eeeeEEE
Q psy11637         16 EKSLRKMFG-NG--RARSGVIVLPCGAGKSLVGVTACCTV---RKRALVL   59 (67)
Q Consensus        16 ~~av~~~~~-~~--~~~~~~i~~pTGsGKT~i~~~~~~~~---~~~~lil   59 (67)
                      ...++..+. .+  .++-..+.+|.|+|||.+++.++...   +..++++
T Consensus        45 ~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyI   94 (269)
T d1mo6a1          45 SIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFI   94 (269)
T ss_dssp             CHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEE
T ss_pred             CHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEE
Confidence            346788885 43  24567788999999999987766542   3444444

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {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: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=85.99  E-value=0.079  Score=33.12  Aligned_cols=17  Identities=41%  Similarity=0.460  Sum_probs=13.6

Q ss_pred             eeeEEEeCCCCceeEee
Q psy11637         30 SGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~   46 (67)
                      ...+.+|.|+|||+..-
T Consensus        26 ~~~liGpnGaGKSTll~   42 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLE   42 (240)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCChHHHHHH
Confidence            45578999999998763

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {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: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=85.83  E-value=0.19  Score=32.26  Aligned_cols=23  Identities=22%  Similarity=-0.096  Sum_probs=17.1

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      ...=|.+|+|+|||+..-.++..
T Consensus        55 ~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          55 LRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEeeCCCCCCHHHHHHHHHHH
Confidence            34457799999999888666543

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal 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: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.81  E-value=0.18  Score=31.09  Aligned_cols=31  Identities=16%  Similarity=0.170  Sum_probs=22.7

Q ss_pred             hhhHHHHHhcCCcceeeeEEEeCCCCceeEeeee
Q psy11637         15 QEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        15 Q~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      ..+.+.++++.   +..+++++.|.|||.+.-++
T Consensus        85 g~~~L~~~l~~---kt~~~~G~SGVGKSTLiN~L  115 (225)
T d1u0la2          85 GIEELKEYLKG---KISTMAGLSGVGKSSLLNAI  115 (225)
T ss_dssp             THHHHHHHHSS---SEEEEECSTTSSHHHHHHHH
T ss_pred             hHhhHHHHhcC---CeEEEECCCCCCHHHHHHhh
Confidence            34455566654   68899999999999877544

>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=85.67  E-value=0.089  Score=32.80  Aligned_cols=18  Identities=28%  Similarity=0.283  Sum_probs=15.3

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ....|.+|.|+|||+..-
T Consensus        33 e~~~liGpsGaGKSTLl~   50 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLR   50 (239)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCChHHHHHH
Confidence            577789999999998764

>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=85.66  E-value=0.029  Score=33.42  Aligned_cols=23  Identities=22%  Similarity=0.115  Sum_probs=18.4

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      .-.++.++.|+|||.+++.++.+
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            45677899999999988776654

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

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: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=85.61  E-value=0.085  Score=32.63  Aligned_cols=19  Identities=21%  Similarity=0.188  Sum_probs=15.6

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...-+.+|.|+|||++.-.
T Consensus        33 ei~~liGpnGaGKSTl~~~   51 (240)
T d1ji0a_          33 QIVTLIGANGAGKTTTLSA   51 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            5677899999999987743

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {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: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.56  E-value=0.1  Score=28.18  Aligned_cols=20  Identities=15%  Similarity=-0.097  Sum_probs=15.7

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +.++++++|+|||.....+.
T Consensus         2 KI~liG~~nvGKSSLln~l~   21 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLK   21 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            56789999999998765443

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=85.55  E-value=0.25  Score=27.40  Aligned_cols=27  Identities=22%  Similarity=0.239  Sum_probs=19.6

Q ss_pred             HHhcCCcceeeeEEEeCCCCceeEeeee
Q psy11637         21 KMFGNGRARSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        21 ~~~~~~~~~~~~i~~pTGsGKT~i~~~~   48 (67)
                      .+++.. ..+.++++.+|+|||.....+
T Consensus         9 ~~~~~k-~~kI~vvG~~~~GKSsLi~rl   35 (177)
T d1zj6a1           9 RLFNHQ-EHKVIIVGLDNAGKTTILYQF   35 (177)
T ss_dssp             HHHTTS-CEEEEEEESTTSSHHHHHHHH
T ss_pred             HHhCCC-eEEEEEECCCCCCHHHHHHHH
Confidence            455532 367889999999999776543

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {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: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=85.53  E-value=0.058  Score=33.85  Aligned_cols=19  Identities=26%  Similarity=0.142  Sum_probs=15.5

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...-|++|.|+|||+++-.
T Consensus        29 Ei~~iiG~sGsGKSTLl~~   47 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRC   47 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            6777899999999977643

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

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: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=85.43  E-value=0.16  Score=36.22  Aligned_cols=29  Identities=24%  Similarity=0.296  Sum_probs=21.4

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEe
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~   45 (67)
                      +|...++..+.+...++.+..|||||..+
T Consensus       112 ~Ay~~m~~~~~~QsIiisGeSGaGKTe~~  140 (794)
T d2mysa2         112 NAYQFMLTDRENQSILITGESGAGKTVNT  140 (794)
T ss_dssp             HHHHHHHHHTCCEEEEEEECTTSCHHHHH
T ss_pred             HHHHHHHHcCCCcEEEEEcCCCCCHHHHH
Confidence            45555665555578889999999999655

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=85.31  E-value=0.1  Score=33.42  Aligned_cols=33  Identities=12%  Similarity=0.161  Sum_probs=20.0

Q ss_pred             chhhHHHHH---hc---CCcceeeeEEEeCCCCceeEee
Q psy11637         14 YQEKSLRKM---FG---NGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        14 yQ~~av~~~---~~---~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      -|++..+.+   +.   .|.+...+..+.||||||+++.
T Consensus        63 ~q~~vy~~v~~~v~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          63 TNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             CHHHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             CHHHHHHHhhhhhcchhcccccceeeeeccCCccccccc
Confidence            376666542   22   1322344456999999998764

>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=85.23  E-value=0.13  Score=31.74  Aligned_cols=42  Identities=19%  Similarity=0.202  Sum_probs=27.6

Q ss_pred             eeeccchhhHHHHHhcC---CcceeeeEEEeCCCCceeEeeeeEE
Q psy11637          9 AVLRPYQEKSLRKMFGN---GRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus         9 ~~lR~yQ~~av~~~~~~---~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +--|+.-.+-+.+++..   .......|++..|.|||+++..+..
T Consensus        22 ~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~   66 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALS   66 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            33477766666555532   1123456889999999999976653

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

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: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=84.92  E-value=0.14  Score=35.92  Aligned_cols=30  Identities=23%  Similarity=0.251  Sum_probs=21.7

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      .|...+...+.+...++.+..|||||..+-
T Consensus        75 ~Ay~~l~~~~~~QsIiisGeSGsGKTe~~k  104 (684)
T d1lkxa_          75 DAYRSMRQSQENQCVIISGESGAGKTEASK  104 (684)
T ss_dssp             HHHHHHHHHCCCEEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHcCCCeEEEEEcCCCCCHHHHHH
Confidence            455555554445678889999999997663

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

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: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=84.35  E-value=0.16  Score=35.85  Aligned_cols=31  Identities=26%  Similarity=0.393  Sum_probs=22.1

Q ss_pred             hhHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         16 EKSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      +.|...+...+.+...++.+..|||||..+-
T Consensus        82 ~~Ay~~l~~~~~~Q~IiisGeSGsGKTe~~k  112 (730)
T d1w7ja2          82 EEAYKQMARDERNQSIIVSGESGAGKTVSAK  112 (730)
T ss_dssp             HHHHHHHHHHTCCEEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHhCCCeEEEEEeCCCCCHHHHHH
Confidence            4455555554445788889999999997653

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {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: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=84.18  E-value=0.16  Score=35.90  Aligned_cols=30  Identities=27%  Similarity=0.288  Sum_probs=21.3

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      .|...++..+.+...+|.+..|||||..+-
T Consensus       114 ~Ay~~m~~~~~nQsIiisGeSGaGKTe~~k  143 (712)
T d1d0xa2         114 VAYRSMLDDRQNQSLLITGESGAGKTENTK  143 (712)
T ss_dssp             HHHHHHHHHTCCEEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHhCCCceEEEeCCCCCCHHHHHH
Confidence            344555544445788899999999997653

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

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: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=83.92  E-value=0.17  Score=35.66  Aligned_cols=30  Identities=23%  Similarity=0.226  Sum_probs=21.5

Q ss_pred             hHHHHHhcCCcceeeeEEEeCCCCceeEee
Q psy11637         17 KSLRKMFGNGRARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        17 ~av~~~~~~~~~~~~~i~~pTGsGKT~i~~   46 (67)
                      .|..+++..+.+...++.+..|||||..+-
T Consensus        80 ~Ay~~m~~~~~~Q~IiisGeSGaGKTe~~k  109 (710)
T d1br2a2          80 TAYRSMLQDREDQSILCTGESGAGKTENTK  109 (710)
T ss_dssp             HHHHHHHHHTCCEEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHhCCCcEEEEEeCCCCCHHHHHH
Confidence            455555554445778889999999997653

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {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: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.69  E-value=0.14  Score=29.69  Aligned_cols=20  Identities=30%  Similarity=0.375  Sum_probs=15.9

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +.++++++|+|||.+.-.+.
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~   21 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLL   21 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            67899999999998765443

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {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: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=83.64  E-value=0.074  Score=32.60  Aligned_cols=17  Identities=41%  Similarity=0.333  Sum_probs=14.4

Q ss_pred             eeeeEEEeCCCCceeEe
Q psy11637         29 RSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~   45 (67)
                      ...-+.+|.|+|||+..
T Consensus        26 ei~~iiG~nGaGKSTLl   42 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLL   42 (231)
T ss_dssp             CEEECBCCTTSSHHHHH
T ss_pred             CEEEEECCCCCcHHHHH
Confidence            56778899999999865

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {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: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=83.35  E-value=0.098  Score=32.34  Aligned_cols=18  Identities=28%  Similarity=0.187  Sum_probs=14.6

Q ss_pred             eeeeEEEeCCCCceeEee
Q psy11637         29 RSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~   46 (67)
                      ...-+++|.|+|||+..-
T Consensus        29 ei~glvG~nGaGKSTLl~   46 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLR   46 (238)
T ss_dssp             CEEEEECCTTSSHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHH
Confidence            455689999999998763

>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=83.04  E-value=0.074  Score=32.99  Aligned_cols=19  Identities=42%  Similarity=0.419  Sum_probs=15.6

Q ss_pred             ceeeeEEEeCCCCceeEee
Q psy11637         28 ARSGVIVLPCGAGKSLVGV   46 (67)
Q Consensus        28 ~~~~~i~~pTGsGKT~i~~   46 (67)
                      +....+.+|.|+|||++.-
T Consensus        26 Ge~~~liGpsGaGKSTll~   44 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLE   44 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHH
T ss_pred             CCEEEEECCCCCcHHHHHH
Confidence            3677789999999998763

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=82.86  E-value=0.15  Score=27.59  Aligned_cols=20  Identities=20%  Similarity=-0.003  Sum_probs=15.5

Q ss_pred             eeeEEEeCCCCceeEeeeeE
Q psy11637         30 SGVIVLPCGAGKSLVGVTAC   49 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~   49 (67)
                      +.++++++|+|||...-.++
T Consensus         2 kivlvG~~~vGKSsLi~~l~   21 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLK   21 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            35789999999998775443

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

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: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=82.76  E-value=0.2  Score=35.77  Aligned_cols=30  Identities=23%  Similarity=0.317  Sum_probs=21.7

Q ss_pred             hhHHHHHhcCCcceeeeEEEeCCCCceeEe
Q psy11637         16 EKSLRKMFGNGRARSGVIVLPCGAGKSLVG   45 (67)
Q Consensus        16 ~~av~~~~~~~~~~~~~i~~pTGsGKT~i~   45 (67)
                      ++|...+...+.+...+|.+..|||||..+
T Consensus       109 ~~Ay~~m~~~~~nQ~IiisGESGaGKTe~~  138 (789)
T d1kk8a2         109 DNAYQNMVTDRENQSCLITGESGAGKTENT  138 (789)
T ss_dssp             HHHHHHHHHHTSEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHHHHhCCCcEEEEEeCCCCCHHHHH
Confidence            345555555555578889999999999654

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

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: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=82.75  E-value=0.072  Score=34.16  Aligned_cols=19  Identities=32%  Similarity=0.172  Sum_probs=12.0

Q ss_pred             eEEEeCCCCceeEeeeeEE
Q psy11637         32 VIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~   50 (67)
                      -|.+++|||||+++-.+..
T Consensus         8 gIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           8 SVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             EEESCC---CCTHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            3679999999999865544

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {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: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=82.00  E-value=0.19  Score=28.72  Aligned_cols=19  Identities=16%  Similarity=-0.039  Sum_probs=15.1

Q ss_pred             eeeEEEeCCCCceeEeeee
Q psy11637         30 SGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~   48 (67)
                      ...|++++|+|||...-.+
T Consensus        25 ~I~lvG~~n~GKSTLin~L   43 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSL   43 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHh
Confidence            4678899999999876444

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine 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: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.93  E-value=0.12  Score=30.45  Aligned_cols=24  Identities=25%  Similarity=-0.042  Sum_probs=18.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCTV   52 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~~   52 (67)
                      +.-+|.++-|||||+.+-.+...+
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l   26 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH
Confidence            456678999999999886665544

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {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: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=81.83  E-value=0.075  Score=31.60  Aligned_cols=19  Identities=11%  Similarity=-0.071  Sum_probs=14.8

Q ss_pred             eEEEeCCCCceeEeeeeEE
Q psy11637         32 VIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~   50 (67)
                      -|.++.|||||+++-.+..
T Consensus         5 giTG~igSGKsTva~~l~e   23 (241)
T d1deka_           5 FLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3679999999998865543

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=81.67  E-value=0.18  Score=27.97  Aligned_cols=20  Identities=15%  Similarity=-0.047  Sum_probs=16.0

Q ss_pred             eeeeEEEeCCCCceeEeeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVTA   48 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~   48 (67)
                      -+.++++++|+|||.....+
T Consensus         3 ~ki~ivG~~~~GKTsLi~~l   22 (165)
T d1ksha_           3 LRLLMLGLDNAGKTTILKKF   22 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHH
Confidence            46789999999999776544

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

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: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=81.52  E-value=0.041  Score=33.88  Aligned_cols=28  Identities=21%  Similarity=0.294  Sum_probs=20.3

Q ss_pred             eEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .|++--|.|||+++..++..   .+.++|+|
T Consensus         6 aisgKGGVGKTT~a~NLA~~LA~~G~rVLlI   36 (289)
T d2afhe1           6 AIYGKGGIGKSTTTQNLVAALAEMGKKVMIV   36 (289)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEE
Confidence            45678899999999766543   36677755

>d1g6ha_ c.37.1.12 (A:) MJ1267 {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: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=81.22  E-value=0.16  Score=31.43  Aligned_cols=19  Identities=32%  Similarity=0.377  Sum_probs=15.2

Q ss_pred             eeeeEEEeCCCCceeEeee
Q psy11637         29 RSGVIVLPCGAGKSLVGVT   47 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~   47 (67)
                      ...-+.+|.|+|||+..-.
T Consensus        31 ei~~liG~nGaGKSTLl~~   49 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINV   49 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHH
T ss_pred             CEEEEECCCCCcHHHHHHH
Confidence            5667899999999987643

>d4tmka_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=81.10  E-value=0.22  Score=29.01  Aligned_cols=23  Identities=30%  Similarity=0.112  Sum_probs=17.3

Q ss_pred             eeeeEEEeCCCCceeEeeeeEEE
Q psy11637         29 RSGVIVLPCGAGKSLVGVTACCT   51 (67)
Q Consensus        29 ~~~~i~~pTGsGKT~i~~~~~~~   51 (67)
                      +.-++.++-|||||+.+-.+...
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~   25 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVET   25 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHH
Confidence            34566799999999988666544

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

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: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=80.73  E-value=0.045  Score=33.24  Aligned_cols=28  Identities=25%  Similarity=0.222  Sum_probs=20.0

Q ss_pred             eEEEeCCCCceeEeeeeEEE---EeeeeEEE
Q psy11637         32 VIVLPCGAGKSLVGVTACCT---VRKRALVL   59 (67)
Q Consensus        32 ~i~~pTGsGKT~i~~~~~~~---~~~~~lil   59 (67)
                      .|.+--|.|||+++..++..   .+.+++++
T Consensus         5 ai~gKGGvGKTT~a~nLA~~LA~~G~rVllI   35 (269)
T d1cp2a_           5 AIYGKGGIGKSTTTQNLTSGLHAMGKTIMVV   35 (269)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEECCCcCCHHHHHHHHHHHHHhCCCcEEEE
Confidence            35678899999999776554   35666654

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {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: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.46  E-value=0.27  Score=27.63  Aligned_cols=21  Identities=19%  Similarity=0.138  Sum_probs=8.5

Q ss_pred             eeeEEEeCCCCceeEeeeeEE
Q psy11637         30 SGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        30 ~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      ..++++.+|+|||.+...++.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            467889999999998876664

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=80.19  E-value=0.7  Score=25.74  Aligned_cols=31  Identities=26%  Similarity=0.224  Sum_probs=21.6

Q ss_pred             HHHHhcCCcceeeeEEEeCCCCceeEeeeeEE
Q psy11637         19 LRKMFGNGRARSGVIVLPCGAGKSLVGVTACC   50 (67)
Q Consensus        19 v~~~~~~~~~~~~~i~~pTGsGKT~i~~~~~~   50 (67)
                      +++.+... .-+.+++++.|+|||.+...++.
T Consensus         4 ~~~~~~~k-~~kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_           4 LSKIFGNK-EMRILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             HHHHHTTC-CEEEEEEEETTSSHHHHHHHTTC
T ss_pred             hhhhhCCC-eEEEEEECCCCCCHHHHHHHHhc
Confidence            34555432 25788999999999988765543