Psyllid ID: psy14273

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MASKTPNEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDLEISKNETVSEDWIEQQSFEPTIR
Secondary Structure (PSIPRED)
cccccccccHHHHcccccccccccccccccccHHHHHHHHHHHHHHHccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHccccccc
Coil and Loop (DISEMBL)
masktpnedkefkeqrplaevpsefpfpfdaydiQSNFMKNLYYtldnskfgifesptgtgksLSLICGILKWYSDHKIAGLEKIEAEIKDLeisknetvsedwieqqsfeptir
Flexible Loop (DISEMBL)
masktpnedkefkeqrplaevpsefpFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDleisknetvsedwieqqsfeptir
Low Complexity Region (SEG)
MASKTPNEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDLEISKNETVSEDWIEQQSFEPTIR
Disordered region (IsUnstruct)
************************FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDLEI*********************
Disordered Region (DISOPRED)
********************VPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS****************************************
Disordered Region (DISEMBL)
******************AEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDLEISKNETVSEDW***********
Disordered Region (DISPRO)
*********************PSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDL***********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASKTPNEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGxxxxxxxxxxxxxxxxxxxxxDWIEQQSFEPTIR
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	115	2.2.26 [Sep-21-2011]
Q96FC9	970	Probable ATP-dependent RN	yes	N/A	0.573	0.068	0.579	3e-15
A8MPP1	907	Putative ATP-dependent RN	no	N/A	0.573	0.072	0.579	5e-15
Q1E5T3	861	ATP-dependent RNA helicas	N/A	N/A	0.469	0.062	0.629	9e-15
A1D8E4	861	ATP-dependent RNA helicas	N/A	N/A	0.573	0.076	0.5	2e-14
A2QY22	874	ATP-dependent RNA helicas	yes	N/A	0.530	0.069	0.524	6e-14
O14147	844	ATP-dependent RNA helicas	yes	N/A	0.739	0.100	0.439	2e-13
A5DUW8	892	ATP-dependent RNA helicas	N/A	N/A	0.539	0.069	0.523	2e-12
A7ERG1	902	ATP-dependent RNA helicas	N/A	N/A	0.539	0.068	0.532	6e-12
Q6CAX3	803	ATP-dependent RNA helicas	yes	N/A	0.478	0.068	0.545	1e-11
Q6CIF0	807	ATP-dependent RNA helicas	yes	N/A	0.556	0.079	0.470	2e-11

>sp|Q96FC9|DDX11_HUMAN Probable ATP-dependent RNA helicase DDX11 OS=Homo sapiens GN=DDX11 PE=1 SV=1

 Score = 80.5 bits (197), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 40/69 (57%), Positives = 45/69 (65%), Gaps = 3/69 (4%)

Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
          FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct: 13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query: 85 IEAEIKDLE 93
           E E + LE
Sbjct: 70 REEEARLLE 78

DNA helicase involved in cellular proliferation. Possesses DNA-dependent ATPase and helicase activities. This helicase translocates on single-stranded DNA in the 5' to 3' direction in the presence of ATP and, to a lesser extent, dATP. Its unwinding activity requires a 5'-single-stranded region for helicase loading, since flush-ended duplex structures do not support unwinding. The helicase activity is capable of displacing duplex regions up to 100 bp, which can be extended to 500 bp by RPA or the cohesion establishment factor, the Ctf18-RFC (replication factor C) complex activities. Stimulates the flap endonuclease activity of FEN1. Required for normal sister chromatid cohesion. Required for recruitment of bovine papillomavirus type 1 regulatory protein E2 to mitotic chrmosomes and for viral genome maintenance. Required for maintaining the chromosome segregation and is essential for embryonic development and the prevention of aneuploidy. May function during either S, G2, or M phase of the cell cycle. Binds to both single- and double-stranded DNA.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|A8MPP1|D11L8_HUMAN Putative ATP-dependent RNA helicase DDX11-like protein 8 OS=Homo sapiens GN=DDX11L8 PE=3 SV=1

 Score = 79.7 bits (195), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 40/69 (57%), Positives = 45/69 (65%), Gaps = 3/69 (4%)

Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
          FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct: 13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query: 85 IEAEIKDLE 93
           E E + LE
Sbjct: 70 REEEARLLE 78

Putative DNA helicase.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q1E5T3|CHL1_COCIM ATP-dependent RNA helicase CHL1 OS=Coccidioides immitis (strain RS) GN=CHL1 PE=3 SV=1

 Score = 79.0 bits (193), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 34/54 (62%), Positives = 39/54 (72%)

Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK 78
          F  P+  YDIQ  FM++LY  ++  K GIFESPTGTGKSLSLICG L W  DHK
Sbjct: 8  FYHPYSPYDIQVQFMRSLYTCIEECKVGIFESPTGTGKSLSLICGSLTWLRDHK 61

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Coccidioides immitis (strain RS) (taxid: 246410)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1D8E4|CHL1_NEOFI ATP-dependent RNA helicase chl1 OS=Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) GN=chl1 PE=3 SV=1

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 41/66 (62%)

Query: 18 LAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH 77
          +   P  F  P+  YDIQ  FM+ LY  L+  K  +FESPTGTGKSLSLICG + W  +H
Sbjct: 1  MGSQPQNFNHPYSPYDIQLQFMRALYTCLEEGKVAVFESPTGTGKSLSLICGSMTWLREH 60

Query: 78 KIAGLE 83
          K   L+
Sbjct: 61 KRKALQ 66

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A2QY22|CHL1_ASPNC ATP-dependent RNA helicase chl1 OS=Aspergillus niger (strain CBS 513.88 / FGSC A1513) GN=chl1 PE=3 SV=1

 Score = 75.9 bits (185), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 40/61 (65%)

Query: 23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGL 82
          ++F  P+  YDIQ   M+ LY  L+  K  +FESPTGTGKSLSLICG L W  DHK +  
Sbjct: 6  NDFHHPYSPYDIQLQLMRALYSCLEQGKVAVFESPTGTGKSLSLICGSLTWLRDHKRSAF 65

Query: 83 E 83
          +
Sbjct: 66 Q 66

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Aspergillus niger (strain CBS 513.88 / FGSC A1513) (taxid: 425011)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|O14147|CHL1_SCHPO ATP-dependent RNA helicase chl1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=chl1 PE=3 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/91 (43%), Positives = 54/91 (59%), Gaps = 6/91 (6%)

Query: 23  SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGL 82
           + F  P+  YDIQ  FM++LY ++ + K GIFESPTGTGKSLSLIC  L W  +H    L
Sbjct: 11  TNFHHPYTPYDIQLEFMRSLYSSISDGKIGIFESPTGTGKSLSLICASLTWLDEHGGVLL 70

Query: 83  EKIEAEIKDLEISKNETVSE--DWIEQQSFE 111
           E  E    +    K+ T S+  DW+ +Q  +
Sbjct: 71  EDNEKSNDN----KSNTSSKIPDWVLEQDLK 97

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DUW8|CHL1_LODEL ATP-dependent RNA helicase CHL1 OS=Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) GN=CHL1 PE=3 SV=1

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 17 PLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYS 75
          P A    ++  P+D YDIQ  FM  LY TL N  K G+FESPTGTGK+LS+IC  + W  
Sbjct: 7  PSARTCRDYHHPYDPYDIQLQFMDALYETLQNGYKIGMFESPTGTGKTLSIICSSMTWLR 66

Query: 76 DHK 78
          D+K
Sbjct: 67 DYK 69

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (taxid: 379508)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A7ERG1|CHL1_SCLS1 ATP-dependent RNA helicase CHL1 OS=Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) GN=CHL1 PE=3 SV=1

 Score = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 38/62 (61%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLE 83
          +F  P+  Y IQ  FM+ +Y  L+  K GI ESPTGTGKSLSLICG L W  D K    E
Sbjct: 18 DFHHPYTPYPIQEKFMQTVYDVLEQGKIGILESPTGTGKSLSLICGSLTWLRDFKRKEFE 77

Query: 84 KI 85
           I
Sbjct: 78 GI 79

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) (taxid: 665079)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6CAX3|CHL1_YARLI ATP-dependent RNA helicase CHL1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=CHL1 PE=3 SV=1

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 30/55 (54%), Positives = 39/55 (70%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK 78
          EF  P+  Y IQ +FM+ LY  +++ K GIFESPTGTGK+LSLICG + W   +K
Sbjct: 8  EFSHPYTPYPIQVDFMEALYDCIESYKVGIFESPTGTGKTLSLICGSMTWLRKNK 62

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Yarrowia lipolytica (strain CLIB 122 / E 150) (taxid: 284591)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6CIF0|CHL1_KLULA ATP-dependent RNA helicase CHL1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=CHL1 PE=3 SV=1

 Score = 67.8 bits (164), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 47/68 (69%), Gaps = 4/68 (5%)

Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLICGILKWYSDHKIAGLE 83
          F  P+  YDIQ+  M+++Y  L++ K  GIFESPTGTGK+LSLIC  + W  +HK   LE
Sbjct: 5  FHHPYQPYDIQTQLMEHIYELLNSGKKVGIFESPTGTGKTLSLICSTVTWLREHK---LE 61

Query: 84 KIEAEIKD 91
          K+ +++ +
Sbjct: 62 KLNSKVDN 69

Important for chromosome transmission and normal cell cycle progression in G(2)/M. May have a role in changing DNA topology to allow the loading of proteins involved in maintaining sister chromatid cohesion in the vicinity of the centromeres. Has a specific role in chromosome segregation during meiosis II.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	115
91081131	861	PREDICTED: similar to regulator of telom	0.8	0.106	0.489	4e-20
270006445	817	DEAD/H (Asp-Glu-Ala-Asp/His) box polypep	0.8	0.112	0.489	4e-20
307191862	862	Probable ATP-dependent RNA helicase DDX1	0.773	0.103	0.559	8e-20
332029639	857	Putative ATP-dependent RNA helicase DDX1	0.739	0.099	0.494	8e-19
340378232	886	PREDICTED: putative ATP-dependent RNA he	0.739	0.095	0.521	2e-18
242025010	852	conserved hypothetical protein [Pediculu	0.817	0.110	0.494	7e-18
443709796	875	hypothetical protein CAPTEDRAFT_175213 [	0.756	0.099	0.5	1e-17
383850034	861	PREDICTED: putative ATP-dependent RNA he	0.747	0.099	0.522	3e-17
198436769	907	PREDICTED: similar to DEAD/H (Asp-Glu-Al	0.756	0.095	0.5	5e-17
432863481	859	PREDICTED: putative ATP-dependent RNA he	0.6	0.080	0.579	2e-16

>gi|91081131|ref|XP_975541.1| PREDICTED: similar to regulator of telomere elongation helicase 1 rtel1 [Tribolium castaneum]

 Score =  102 bits (253), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 46/94 (48%), Positives = 65/94 (69%), Gaps = 2/94 (2%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI 79
           EVP+ F FPF  Y IQ  FM+NL+  ++N KFGIFESPTGTGKSLS++CG ++W  DH +
Sbjct: 2   EVPNNFEFPFQPYPIQHAFMRNLFEVIENKKFGIFESPTGTGKSLSILCGAIRWLKDHNM 61

Query: 80  AGLEKIEAEIKDLEISKNETV--SEDWIEQQSFE 111
              E ++ +I++LE+ K +    S DW+  Q+ E
Sbjct: 62  YERENLKLQIEELELKKRKVSGNSSDWLSAQAQE 95

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270006445|gb|EFA02893.1| DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 [Tribolium castaneum]

 Score =  101 bits (252), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 46/94 (48%), Positives = 65/94 (69%), Gaps = 2/94 (2%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI 79
           EVP+ F FPF  Y IQ  FM+NL+  ++N KFGIFESPTGTGKSLS++CG ++W  DH +
Sbjct: 2   EVPNNFEFPFQPYPIQHAFMRNLFEVIENKKFGIFESPTGTGKSLSILCGAIRWLKDHNM 61

Query: 80  AGLEKIEAEIKDLEISKNETV--SEDWIEQQSFE 111
              E ++ +I++LE+ K +    S DW+  Q+ E
Sbjct: 62  YERENLKLQIEELELKKRKVSGNSSDWLSAQAQE 95

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307191862|gb|EFN75286.1| Probable ATP-dependent RNA helicase DDX11 [Harpegnathos saltator]

 Score =  100 bits (250), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 52/93 (55%), Positives = 61/93 (65%), Gaps = 4/93 (4%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH-- 77
           E+P EFPFPF AY+IQ  FMK LY  L+  K G+FESPTGTGKSLSLICG LKW  DH  
Sbjct: 2   ELPQEFPFPFPAYEIQKQFMKELYNCLEGGKLGLFESPTGTGKSLSLICGALKWLVDHEK 61

Query: 78  -KIAGLEKIEAEIKDLEISKNETVSEDWIEQQS 109
            K   L  + +EI D +I   E  S+DW   Q+
Sbjct: 62  YKKQELSSVISEIDD-KIKNCEKPSDDWFSVQT 93

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332029639|gb|EGI69528.1| Putative ATP-dependent RNA helicase DDX11-like protein [Acromyrmex echinatior]

 Score = 97.8 bits (242), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 48/97 (49%), Positives = 63/97 (64%), Gaps = 12/97 (12%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK- 78
           E+P EFPFPF AY+IQ  FM+ LY  L + K G+FESPTGTGKSLSLICG LKW  DH+ 
Sbjct: 2   ELPQEFPFPFPAYEIQKRFMRELYACLKDGKLGLFESPTGTGKSLSLICGALKWLVDHER 61

Query: 79  ------IAGLEKIEAEIKDLEISKNETVSEDWIEQQS 109
                 I+ + KI+ ++K       E +S++W   Q+
Sbjct: 62  WRKEELISTIAKIDDKLKSC-----EKLSDNWFTVQT 93

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340378232|ref|XP_003387632.1| PREDICTED: putative ATP-dependent RNA helicase DDX11-like protein 8-like [Amphimedon queenslandica]

 Score = 96.7 bits (239), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 48/92 (52%), Positives = 65/92 (70%), Gaps = 7/92 (7%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI 79
           E P++FPFPF  Y IQ++FM++LY TL+  K G+FESPTGTGKSLS+ICG LKW  DH+ 
Sbjct: 5   EAPADFPFPFKPYSIQTDFMRSLYSTLEEGKVGLFESPTGTGKSLSIICGCLKWLMDHQE 64

Query: 80  AGLEKIEA----EIKDLEIS-KNE--TVSEDW 104
              ++ EA    ++  L +S KNE  +V +DW
Sbjct: 65  KETKRCEAILSGDVSVLPLSDKNEKKSVVDDW 96

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|242025010|ref|XP_002432919.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212518428|gb|EEB20181.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score = 94.4 bits (233), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 47/95 (49%), Positives = 62/95 (65%), Gaps = 1/95 (1%)

Query: 22  PSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG 81
           P +FPFPF+ Y IQ++ MKNLY  L+  K GIFESPTGTGKS+SLICG LKW  D +   
Sbjct: 11  PEKFPFPFNPYLIQNDLMKNLYEALEGKKLGIFESPTGTGKSMSLICGSLKWLLDAQERI 70

Query: 82  LEKIEAEIKDLEIS-KNETVSEDWIEQQSFEPTIR 115
              +E  IK+L    KN ++  +W+E+ S    +R
Sbjct: 71  KNDLELNIKNLNDELKNTSLGSNWLEEHSSLTKLR 105

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443709796|gb|ELU04301.1| hypothetical protein CAPTEDRAFT_175213 [Capitella teleta]

 Score = 93.6 bits (231), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 47/94 (50%), Positives = 60/94 (63%), Gaps = 7/94 (7%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH-- 77
           EVP++F FPF+ Y IQ  FM NLY  ++  + GIFESPTGTGKSLSLICG L W  D+  
Sbjct: 2   EVPAKFAFPFEPYGIQEAFMHNLYSAIEGGQMGIFESPTGTGKSLSLICGALTWLQDYEE 61

Query: 78  ----KIAGLEKIEAEIKDLEISKNETVSEDWIEQ 107
               ++  L  I+ EIK   IS+   V  DW++Q
Sbjct: 62  KQRNELEALLSIKQEIKKY-ISRYAFVEPDWVQQ 94

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|383850034|ref|XP_003700633.1| PREDICTED: putative ATP-dependent RNA helicase DDX11-like protein 8-like [Megachile rotundata]

 Score = 92.4 bits (228), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 46/88 (52%), Positives = 55/88 (62%), Gaps = 2/88 (2%)

Query: 24  EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLE 83
           EFPFPF  Y IQ  FMK LY  L+N+K GIFESPTGTGKS+S+ICG LKW  DH+     
Sbjct: 6   EFPFPFPPYSIQVQFMKELYNCLENAKLGIFESPTGTGKSMSIICGALKWLLDHEEFQKN 65

Query: 84  KIEAEIKDLE--ISKNETVSEDWIEQQS 109
           ++   I D E  I K    S +W   Q+
Sbjct: 66  QLTKAISDFEEKIKKCTNSSTNWFSVQT 93

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198436769|ref|XP_002122486.1| PREDICTED: similar to DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 [Ciona intestinalis]

 Score = 91.7 bits (226), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 44/88 (50%), Positives = 59/88 (67%), Gaps = 1/88 (1%)

Query: 21  VPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA 80
            PS+F FPF+ Y IQ +FMK+LY+ +++ K GIFESPTGTGKSLSLICG L W  DH+  
Sbjct: 13  APSKFAFPFEPYSIQVDFMKSLYHAIEDKKIGIFESPTGTGKSLSLICGSLTWLKDHEER 72

Query: 81  GLEKIEAEIKDLEISKN-ETVSEDWIEQ 107
             ++ +     L   K+ ET   DWI++
Sbjct: 73  EEKRCQEITNKLTTEKSKETCDFDWIQE 100

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|432863481|ref|XP_004070088.1| PREDICTED: putative ATP-dependent RNA helicase DDX11-like protein 8-like [Oryzias latipes]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 40/69 (57%), Positives = 49/69 (71%)

Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
          FPFP+  YDIQ  FM+ LY  LD SK GIFESPTGTGKSLSLICG L W  DH+   +++
Sbjct: 8  FPFPYQPYDIQEQFMQALYRALDQSKVGIFESPTGTGKSLSLICGALSWLRDHEEKTIQE 67

Query: 85 IEAEIKDLE 93
            A +++ E
Sbjct: 68 AAALLQEGE 76

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	115
UNIPROTKB|F5GXL6	192	DDX11 "Probable ATP-dependent	0.573	0.343	0.579	5.4e-15
UNIPROTKB|F5GYY1	171	DDX11 "Probable ATP-dependent	0.573	0.385	0.579	5.4e-15
UNIPROTKB|F5H235	297	DDX11 "Probable ATP-dependent	0.573	0.222	0.579	6.3e-15
UNIPROTKB|C9K0E8	302	DDX11 "Probable ATP-dependent	0.573	0.218	0.579	7.2e-15
UNIPROTKB|B4DMS8	304	DDX11 "Probable ATP-dependent	0.573	0.217	0.579	7.5e-15
UNIPROTKB|F1SK82	210	F1SK82 "Uncharacterized protei	0.591	0.323	0.550	1.4e-14
ZFIN|ZDB-GENE-041114-191	890	ddx11 "DEAD/H (Asp-Glu-Ala-Asp	0.713	0.092	0.467	1.8e-14
MGI|MGI:2443590	880	Ddx11 "DEAD/H (Asp-Glu-Ala-Asp	0.530	0.069	0.593	6.2e-14
RGD|1306675	882	Ddx11 "DEAD/H (Asp-Glu-Ala-Asp	0.530	0.069	0.593	1e-13
UNIPROTKB|A8MPP1	907	DDX11L8 "Putative ATP-dependen	0.573	0.072	0.579	1.1e-13

UNIPROTKB|F5GXL6 DDX11 "Probable ATP-dependent RNA helicase DDX11" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 40/69 (57%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    49 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 105

Query:    85 IEAEIKDLE 93
              E E + LE
Sbjct:   106 REEEARLLE 114

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

UNIPROTKB|F5GYY1 DDX11 "Probable ATP-dependent RNA helicase DDX11" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 40/69 (57%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query:    85 IEAEIKDLE 93
              E E + LE
Sbjct:    70 REEEARLLE 78

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

UNIPROTKB|F5H235 DDX11 "Probable ATP-dependent RNA helicase DDX11" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 6.3e-15, P = 6.3e-15
 Identities = 40/69 (57%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query:    85 IEAEIKDLE 93
              E E + LE
Sbjct:    70 REEEARLLE 78

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|C9K0E8 DDX11 "Probable ATP-dependent RNA helicase DDX11" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 7.2e-15, P = 7.2e-15
 Identities = 40/69 (57%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query:    85 IEAEIKDLE 93
              E E + LE
Sbjct:    70 REEEARLLE 78

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|B4DMS8 DDX11 "Probable ATP-dependent RNA helicase DDX11" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 7.5e-15, P = 7.5e-15
 Identities = 40/69 (57%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query:    85 IEAEIKDLE 93
              E E + LE
Sbjct:    70 REEEARLLE 78

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1SK82 F1SK82 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 186 (70.5 bits), Expect = 1.4e-14, P = 1.4e-14
 Identities = 38/69 (55%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    ++
Sbjct:    13 FPFPFTPYPIQKDFMAALYQVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFEQKKRQE 72

Query:    85 IEAEIKDLE 93
              EA + + E
Sbjct:    73 -EARLLEAE 80

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

ZFIN|ZDB-GENE-041114-191 ddx11 "DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11" [Danio rerio (taxid:7955)]

 Score = 197 (74.4 bits), Expect = 1.8e-14, P = 1.8e-14
 Identities = 43/92 (46%), Positives = 54/92 (58%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH----KIA 80
             FPFPF  Y IQ +FM+ LY  LD  K GIFESPTGTGKSLSLICG L W  D+    K  
Sbjct:     8 FPFPFQPYPIQESFMEALYTALDQRKVGIFESPTGTGKSLSLICGALTWLRDYEEQRKQE 67

Query:    81 GLEKIEAEIKDLEISKNETVSE-----DWIEQ 107
                 +E + KD ++ K +  +      DW+ +
Sbjct:    68 AARLLEGQ-KDSDVVKEKNSNSGPPEPDWVSE 98

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0032508 "DNA duplex unwinding" evidence=IEA

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

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

MGI|MGI:2443590 Ddx11 "DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11" [Mus musculus (taxid:10090)]

 Score = 192 (72.6 bits), Expect = 6.2e-14, P = 6.2e-14
 Identities = 38/64 (59%), Positives = 44/64 (68%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFPPYPIQKDFMAELYKVLEGGKIGIFESPTGTGKSLSLICGALSWLRDFE---KKK 69

Query:    85 IEAE 88
             ++AE
Sbjct:    70 LQAE 73

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=ISO

GO:0000922 "spindle pole" evidence=ISO

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0007062 "sister chromatid cohesion" evidence=ISO

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

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

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0030496 "midbody" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0051536 "iron-sulfur cluster binding" evidence=IEA

GO:0051539 "4 iron, 4 sulfur cluster binding" evidence=IEA

RGD|1306675 Ddx11 "DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11" [Rattus norvegicus (taxid:10116)]

 Score = 190 (71.9 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 38/64 (59%), Positives = 44/64 (68%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFPPYPIQKDFMAELYKVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query:    85 IEAE 88
             ++AE
Sbjct:    70 LQAE 73

GO:0000790 "nuclear chromatin" evidence=ISO

GO:0000922 "spindle pole" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0007062 "sister chromatid cohesion" evidence=ISO

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

GO:0030496 "midbody" evidence=ISO

UNIPROTKB|A8MPP1 DDX11L8 "Putative ATP-dependent RNA helicase DDX11-like protein 8" [Homo sapiens (taxid:9606)]

 Score = 190 (71.9 bits), Expect = 1.1e-13, P = 1.1e-13
 Identities = 40/69 (57%), Positives = 45/69 (65%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEK 84
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    +K
Sbjct:    13 FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFE---QKK 69

Query:    85 IEAEIKDLE 93
              E E + LE
Sbjct:    70 REEEARLLE 78

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q96FC9	DDX11_HUMAN	3, ., 6, ., 4, ., 1, 3	0.5797	0.5739	0.0680	yes	N/A
A2QY22	CHL1_ASPNC	3, ., 6, ., 4, ., 1, 3	0.5245	0.5304	0.0697	yes	N/A
Q6AXC6	DDX11_MOUSE	3, ., 6, ., 4, ., 1, 3	0.5818	0.4521	0.0590	yes	N/A
Q6CAX3	CHL1_YARLI	3, ., 6, ., 4, ., 1, 3	0.5454	0.4782	0.0684	yes	N/A
Q6BZD9	CHL1_DEBHA	3, ., 6, ., 4, ., 1, 3	0.5090	0.4782	0.0670	yes	N/A
Q750G3	CHL1_ASHGO	3, ., 6, ., 4, ., 1, 3	0.5081	0.5217	0.0749	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	115
smart00488	289	smart00488, DEXDc2, DEAD-like helicases superfamil	2e-21
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	2e-08
TIGR00604	705	TIGR00604, rad3, DNA repair helicase (rad3)	3e-08
PRK08074	928	PRK08074, PRK08074, bifunctional ATP-dependent DNA	0.001

>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily

 Score = 85.5 bits (212), Expect = 2e-21
 Identities = 28/55 (50%), Positives = 33/55 (60%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK 78
           F FP++ Y IQ  FM+ L   LD  K GI ESPTGTGK+LSL+C  L W     
Sbjct: 2  LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFP 56

Length = 289

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 50.2 bits (120), Expect = 2e-08
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW 73
           FP  F+    Q    + +   L   +  + E+PTGTGK+L+ +   L +
Sbjct: 10 AFP-GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAY 58

Length = 654

>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3)

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 12/78 (15%)

Query: 27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW-----------Y 74
          FP++  Y  Q ++M++L  +LD     I E P+GTGK++SL+  IL +           Y
Sbjct: 6  FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPEVRKIIY 65

Query: 75 SDHKIAGLEKIEAEIKDL 92
          +    + LE+   E++ L
Sbjct: 66 ASRTHSQLEQATEELRKL 83

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) [DNA metabolism, DNA replication, recombination, and repair]. Length = 705

>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 9/72 (12%)

Query: 2   ASKTPNEDKEFKEQR--PLAEVPSE----FPFPFDAYDI---QSNFMKNLYYTLDNSKFG 52
           A +    +K  +E           +           Y+    Q   MK +Y  L +S+  
Sbjct: 220 ALRKREVEKNLEETCRSDFDAFLEKTEEKLSLAMPKYEKREGQQEMMKEVYTALRDSEHA 279

Query: 53  IFESPTGTGKSL 64
           + E+ TGTGKSL
Sbjct: 280 LIEAGTGTGKSL 291

Length = 928

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
KOG1133|consensus	821		99.81
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.73
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.73
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.61
KOG1132|consensus	945		99.48
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.46
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.45
KOG1131|consensus	755		99.38
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.38
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.24
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.09
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.9
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.78
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	98.74
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	98.72
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.68
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.68
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	98.67
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.66
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	98.65
PTZ00424	401	helicase 45; Provisional	98.63
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	98.58
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	98.58
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.58
PTZ00110	545	helicase; Provisional	98.55
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.54
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	98.54
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	98.52
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.45
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	98.38
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.37
KOG0348|consensus	708		98.36
KOG0345|consensus	567		98.36
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.36
PRK13767	876	ATP-dependent helicase; Provisional	98.34
COG1201	814	Lhr Lhr-like helicases [General function predictio	98.31
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.3
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.3
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.29
PRK01172	674	ski2-like helicase; Provisional	98.28
PRK02362	737	ski2-like helicase; Provisional	98.2
PRK00254	720	ski2-like helicase; Provisional	98.16
COG1205	851	Distinct helicase family with a unique C-terminal	98.09
KOG0335|consensus	482		97.96
KOG0331|consensus	519		97.96
PRK10689	1147	transcription-repair coupling factor; Provisional	97.95
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.93
KOG0344|consensus	593		97.93
KOG0350|consensus	620		97.89
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	97.87
KOG0330|consensus	476		97.8
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	97.79
PRK09694	878	helicase Cas3; Provisional	97.79
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.77
PRK09401	1176	reverse gyrase; Reviewed	97.71
COG1204	766	Superfamily II helicase [General function predicti	97.7
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	97.67
KOG0346|consensus	569		97.67
PRK05580	679	primosome assembly protein PriA; Validated	97.65
PRK14701	1638	reverse gyrase; Provisional	97.61
PHA02653	675	RNA helicase NPH-II; Provisional	97.58
PHA02558	501	uvsW UvsW helicase; Provisional	97.57
KOG0338|consensus	691		97.57
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	97.53
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	97.52
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	97.52
KOG0354|consensus	746		97.46
KOG0342|consensus	543		97.46
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.44
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	97.43
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.43
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	97.41
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	97.4
PRK13766	773	Hef nuclease; Provisional	97.4
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	97.37
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	97.35
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.35
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	97.33
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.29
PF13245	76	AAA_19: Part of AAA domain	97.27
KOG0334|consensus	997		97.26
KOG0340|consensus	442		97.26
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	97.25
KOG0952|consensus	1230		97.17
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.08
KOG0352|consensus	641		97.08
PRK09200	790	preprotein translocase subunit SecA; Reviewed	97.05
COG4096	875	HsdR Type I site-specific restriction-modification	97.02
KOG0333|consensus	673		97.01
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.93
KOG0343|consensus	758		96.86
PHA02244	383	ATPase-like protein	96.85
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	96.82
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.81
PRK10536	262	hypothetical protein; Provisional	96.79
PRK12402	337	replication factor C small subunit 2; Reviewed	96.76
KOG0989|consensus	346		96.76
PRK15483	986	type III restriction-modification system StyLTI en	96.75
PRK06835	329	DNA replication protein DnaC; Validated	96.75
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	96.74
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.72
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.66
KOG0351|consensus	941		96.65
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.64
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.63
KOG0336|consensus	629		96.62
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.61
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	96.48
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.45
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.43
PRK08181	269	transposase; Validated	96.42
PLN03025	319	replication factor C subunit; Provisional	96.38
smart00382	148	AAA ATPases associated with a variety of cellular	96.37
PRK13531	498	regulatory ATPase RavA; Provisional	96.36
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.26
KOG0326|consensus	459		96.2
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.2
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.18
KOG0327|consensus	397		96.16
KOG0337|consensus	529		96.16
PRK10436	462	hypothetical protein; Provisional	96.15
COG0714	329	MoxR-like ATPases [General function prediction onl	96.15
PRK06526	254	transposase; Provisional	96.07
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.02
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	96.02
KOG0991|consensus	333		96.01
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.01
PRK13107	908	preprotein translocase subunit SecA; Reviewed	96.0
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	95.95
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	95.87
PRK00440	319	rfc replication factor C small subunit; Reviewed	95.85
PRK13851	344	type IV secretion system protein VirB11; Provision	95.84
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.82
PRK12904	830	preprotein translocase subunit SecA; Reviewed	95.78
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	95.76
TIGR00376	637	DNA helicase, putative. The gene product may repre	95.73
KOG1803|consensus	649		95.73
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.63
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.62
PRK08939	306	primosomal protein DnaI; Reviewed	95.58
KOG0353|consensus	695		95.57
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	95.56
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	95.53
COG4889	1518	Predicted helicase [General function prediction on	95.52
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	95.51
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	95.5
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	95.47
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	95.47
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.4
KOG0347|consensus	731		95.4
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	95.38
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	95.36
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	95.36
TIGR02533	486	type_II_gspE general secretory pathway protein E.	95.32
PRK08116	268	hypothetical protein; Validated	95.32
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	95.31
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	95.29
PF12846	304	AAA_10: AAA-like domain	95.28
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	95.28
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	95.27
PRK07952	244	DNA replication protein DnaC; Validated	95.23
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	95.21
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	95.18
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.14
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	95.13
KOG0328|consensus	400		95.13
PRK09183	259	transposase/IS protein; Provisional	95.13
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	95.09
PRK06921	266	hypothetical protein; Provisional	95.07
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.07
PRK13764	602	ATPase; Provisional	95.06
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.04
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	95.02
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.01
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	94.99
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.95
PRK12326	764	preprotein translocase subunit SecA; Reviewed	94.93
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.91
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	94.88
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	94.86
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	94.79
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	94.74
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	94.73
PRK13342	413	recombination factor protein RarA; Reviewed	94.71
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	94.69
TIGR00595	505	priA primosomal protein N'. All proteins in this f	94.68
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	94.67
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	94.57
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	94.54
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	94.5
KOG0951|consensus	1674		94.49
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	94.38
PRK00411	394	cdc6 cell division control protein 6; Reviewed	94.37
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	94.35
PRK12377	248	putative replication protein; Provisional	94.31
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	94.31
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	94.3
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	94.3
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	94.29
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	94.23
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	94.18
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.18
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	94.18
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	94.18
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	94.16
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	94.15
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	94.1
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	94.07
PRK08903	227	DnaA regulatory inactivator Hda; Validated	94.07
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	94.01
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	94.01
) 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	93.98
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	93.92
PF00004	132	AAA: ATPase family associated with various cellula	93.92
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	93.89
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	93.82
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	93.78
cd01368	345	KISc_KIF23_like Kinesin motor domain, KIF23-like s	93.76
PRK04195	482	replication factor C large subunit; Provisional	93.75
cd01373	337	KISc_KLP2_like Kinesin motor domain, KLP2-like sub	93.74
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	93.74
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	93.73
cd01375	334	KISc_KIF9_like Kinesin motor domain, KIF9-like sub	93.71
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	93.7
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	93.68
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	93.66
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	93.62
COG0606	490	Predicted ATPase with chaperone activity [Posttran	93.61
cd01370	338	KISc_KIP3_like Kinesin motor domain, KIP3-like sub	93.6
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	93.59
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	93.58
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	93.57
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	93.51
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	93.5
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	93.5
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	93.47
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	93.46
PHA02544	316	44 clamp loader, small subunit; Provisional	93.43
KOG0947|consensus	1248		93.43
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	93.4
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	93.4
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	93.39
PRK13765	637	ATP-dependent protease Lon; Provisional	93.34
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	93.31
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	93.3
cd01376	319	KISc_KID_like Kinesin motor domain, KIF22/Kid-like	93.3
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	93.28
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	93.25
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.24
PRK08727	233	hypothetical protein; Validated	93.23
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	93.21
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	93.19
PRK13850	670	type IV secretion system protein VirD4; Provisiona	93.17
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	93.15
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	93.15
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	93.13
KOG0341|consensus	610		93.07
PF05729	166	NACHT: NACHT domain	93.04
PRK13897	606	type IV secretion system component VirD4; Provisio	93.04
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	93.03
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	93.03
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	93.0
KOG0243|consensus	1041		93.0
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	92.98
PRK06620	214	hypothetical protein; Validated	92.97
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	92.96
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	92.94
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	92.94
PRK10865	857	protein disaggregation chaperone; Provisional	92.9
PRK11608	326	pspF phage shock protein operon transcriptional ac	92.9
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	92.89
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	92.88
PF13555	62	AAA_29: P-loop containing region of AAA domain	92.83
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	92.83
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	92.8
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	92.75
CHL00095	821	clpC Clp protease ATP binding subunit	92.7
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	92.69
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	92.69
cd01367	322	KISc_KIF2_like Kinesin motor domain, KIF2-like gro	92.68
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	92.66
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	92.58
PRK13341	725	recombination factor protein RarA/unknown domain f	92.58
cd01365	356	KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like p	92.57
PRK08769	319	DNA polymerase III subunit delta'; Validated	92.56
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	92.51
KOG0349|consensus	725		92.49
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	92.43
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	92.39
PRK13876	663	conjugal transfer coupling protein TraG; Provision	92.37
CHL00181	287	cbbX CbbX; Provisional	92.35
PRK13880	636	conjugal transfer coupling protein TraG; Provision	92.33
cd01366	329	KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/	92.31
KOG1802|consensus	935		92.29
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	92.28
PRK13889	988	conjugal transfer relaxase TraA; Provisional	92.27
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	92.26
cd01372	341	KISc_KIF4 Kinesin motor domain, KIF4-like subfamil	92.25
cd01369	325	KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy	92.24
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	92.24
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	92.22
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	92.21
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	92.17
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	92.16
COG1198	730	PriA Primosomal protein N' (replication factor Y)	92.13
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	92.12
KOG1805|consensus	1100		92.11
KOG0922|consensus	674		92.04
cd01364	352	KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spind	92.03
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	91.98
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	91.97
CHL00122	870	secA preprotein translocase subunit SecA; Validate	91.96
PRK08084	235	DNA replication initiation factor; Provisional	91.93
PRK07471	365	DNA polymerase III subunit delta'; Validated	91.91
PRK07940	394	DNA polymerase III subunit delta'; Validated	91.87
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	91.86
KOG0239|consensus	670		91.84
PRK09112	351	DNA polymerase III subunit delta'; Validated	91.79
PRK00300	205	gmk guanylate kinase; Provisional	91.79
cd01374	321	KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like	91.75
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	91.73
PRK06893	229	DNA replication initiation factor; Validated	91.73
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	91.72
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	91.71
COG0324	308	MiaA tRNA delta(2)-isopentenylpyrophosphate transf	91.71
PRK04296	190	thymidine kinase; Provisional	91.69
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	91.67
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	91.65
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	91.64
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	91.64
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	91.62
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	91.57
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	91.56
PLN03188	1320	kinesin-12 family protein; Provisional	91.53
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	91.48
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	91.47
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	91.42
cd01371	333	KISc_KIF3 Kinesin motor domain, kinesins II or KIF	91.39
PRK03992	389	proteasome-activating nucleotidase; Provisional	91.39
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	91.37
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	91.32
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	91.26
KOG0339|consensus	731		91.22
KOG0332|consensus	477		91.21
PRK13822	641	conjugal transfer coupling protein TraG; Provision	91.2
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	91.13
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	91.13
KOG0743|consensus	457		91.11
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	91.07
PRK10416	318	signal recognition particle-docking protein FtsY;	91.07
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	91.03
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	91.01
KOG1970|consensus	634		91.0
PTZ00112	1164	origin recognition complex 1 protein; Provisional	90.99
PRK07399	314	DNA polymerase III subunit delta'; Validated	90.98
PRK14974	336	cell division protein FtsY; Provisional	90.94
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	90.89
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	90.87
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	90.81
PRK00698	205	tmk thymidylate kinase; Validated	90.76
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	90.76
PF07726	131	AAA_3: ATPase family associated with various cellu	90.74
PF00225	335	Kinesin: Kinesin motor domain; InterPro: IPR001752	90.7
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	90.67
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	90.64
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	90.64
PRK10875	615	recD exonuclease V subunit alpha; Provisional	90.63
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	90.62
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	90.6
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	90.59
PF00005	137	ABC_tran: ABC transporter This structure is on hol	90.52
PF13173	128	AAA_14: AAA domain	90.49
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	90.47
KOG0926|consensus	1172		90.47
PRK05541	176	adenylylsulfate kinase; Provisional	90.45
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	90.37
PRK08058	329	DNA polymerase III subunit delta'; Validated	90.27
cd03115	173	SRP The signal recognition particle (SRP) mediates	90.25
PRK05022	509	anaerobic nitric oxide reductase transcription reg	90.23
COG1221	403	PspF Transcriptional regulators containing an AAA-	90.17
TIGR00665	434	DnaB replicative DNA helicase. This model describe	90.16
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	90.13
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	90.1
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	90.04
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	90.01
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	89.99
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	89.98
TIGR03744	893	traC_PFL_4706 conjugative transfer ATPase, PFL_470	89.97
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	89.91
TIGR02237	209	recomb_radB DNA repair and recombination protein R	89.91
cd03241	276	ABC_RecN RecN ATPase involved in DNA repair; ABC (	89.91
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	89.89
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	89.86
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	89.86
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	89.84
TIGR00064	272	ftsY signal recognition particle-docking protein F	89.83
KOG0744|consensus	423		89.82
PRK05973	237	replicative DNA helicase; Provisional	89.76
KOG0923|consensus	902		89.64
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	89.62
KOG4284|consensus	980		89.59
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	89.59
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	89.44
PRK00771	437	signal recognition particle protein Srp54; Provisi	89.44
COG3973	747	Superfamily I DNA and RNA helicases [General funct	89.41
CHL00176	638	ftsH cell division protein; Validated	89.4
cd00106	328	KISc Kinesin motor domain. This catalytic (head) d	89.39
PLN02165	334	adenylate isopentenyltransferase	89.38
PRK10869	553	recombination and repair protein; Provisional	89.36
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	89.31
cd01394	218	radB RadB. The archaeal protein radB shares simila	89.29
smart00129	335	KISc Kinesin motor, catalytic domain. ATPase. Micr	89.22
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	89.19
KOG0390|consensus	776		89.16
PRK00131	175	aroK shikimate kinase; Reviewed	89.14
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	89.13
TIGR00618	1042	sbcc exonuclease SbcC. This family is based on the	89.11
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	89.1
KOG1533|consensus	290		89.09
PRK05298	652	excinuclease ABC subunit B; Provisional	89.05
COG2256	436	MGS1 ATPase related to the helicase subunit of the	89.03
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	88.98
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	88.97
COG1202	830	Superfamily II helicase, archaea-specific [General	88.9
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	88.9
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	88.88
PRK06871	325	DNA polymerase III subunit delta'; Validated	88.83
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	88.73
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	88.72
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	88.72
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	88.69
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	88.67
PRK08533	230	flagellar accessory protein FlaH; Reviewed	88.63
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	88.6
PRK13973	213	thymidylate kinase; Provisional	88.57
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	88.53
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	88.52
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	88.51
PRK08233	182	hypothetical protein; Provisional	88.37
PRK10867	433	signal recognition particle protein; Provisional	88.35
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	88.35
KOG2373|consensus	514		88.31
PHA00729	226	NTP-binding motif containing protein	88.29
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	88.23
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	88.22
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	88.21
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	88.14
PRK05564	313	DNA polymerase III subunit delta'; Validated	88.11
PRK15424	538	propionate catabolism operon regulatory protein Pr	88.05
PRK13975	196	thymidylate kinase; Provisional	88.03
PF01935	229	DUF87: Domain of unknown function DUF87; InterPro:	88.0
PRK05595	444	replicative DNA helicase; Provisional	87.99
PRK06547	172	hypothetical protein; Provisional	87.98
KOG0731|consensus	774		87.96
PRK00091	307	miaA tRNA delta(2)-isopentenylpyrophosphate transf	87.93
PRK13768	253	GTPase; Provisional	87.9
KOG0060|consensus	659		87.87
COG3587	985	Restriction endonuclease [Defense mechanisms]	87.82
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	87.81
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	87.79
PRK14088	440	dnaA chromosomal replication initiation protein; P	87.78
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	87.72
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	87.71
PRK11054	684	helD DNA helicase IV; Provisional	87.7
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	87.64
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	87.61
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	87.56
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	87.53
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	87.47
PRK00149	450	dnaA chromosomal replication initiation protein; R	87.47
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	87.45
PRK13826	1102	Dtr system oriT relaxase; Provisional	87.43
PRK06067	234	flagellar accessory protein FlaH; Validated	87.42
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	87.35
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	87.31
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	87.28
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	87.17
cd03242	270	ABC_RecF RecF is a recombinational DNA repair ATPa	87.11
PRK06090	319	DNA polymerase III subunit delta'; Validated	87.06
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	87.05
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	87.02
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	87.01
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	86.99
KOG0745|consensus	564		86.99
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	86.98
PRK14738	206	gmk guanylate kinase; Provisional	86.96
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	86.95
PRK05748	448	replicative DNA helicase; Provisional	86.88
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	86.83
cd01363	186	Motor_domain Myosin and Kinesin motor domain. Thes	86.8
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	86.76
PRK14737	186	gmk guanylate kinase; Provisional	86.67
PRK10246	1047	exonuclease subunit SbcC; Provisional	86.67
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	86.66
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	86.65
PHA02562	562	46 endonuclease subunit; Provisional	86.65
PRK08760	476	replicative DNA helicase; Provisional	86.64
COG4133	209	CcmA ABC-type transport system involved in cytochr	86.62
CHL00195	489	ycf46 Ycf46; Provisional	86.57
cd03269	210	ABC_putative_ATPase This subfamily is involved in	86.48

>KOG1133|consensus

Probab=99.81  E-value=3.7e-20  Score=163.63  Aligned_cols=95  Identities=41%  Similarity=0.707  Sum_probs=81.7

Q ss_pred             CCccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhhHHHHHHHHHH-hhhhcCCC
Q psy14273         21 VPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKD-LEISKNET   99 (115)
Q Consensus        21 ~~~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~~~~~~~~~~-~~~~~~~~   99 (115)
                      ..+.|+|||.||++|.++|++++++|++|+++|||+|||||||||+||+++.|+..++.++.+.+.+++.. +.-.....
T Consensus         6 ~~~~F~fPy~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~eek~~t~~~~~l~~v~~~~~d~k   85 (821)
T KOG1133|consen    6 GAIEFPFPYTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDFEEKKRTEEARLLETVTGPLHDEK   85 (821)
T ss_pred             cccccCCCCCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHhHHhhhhHHHhhhccCCCcccccc
Confidence            55789999999999999999999999999999999999999999999999999999999998887777766 11124455


Q ss_pred             CCcc----hHHHhhcccccC
Q psy14273        100 VSED----WIEQQSFEPTIR  115 (115)
Q Consensus       100 ~~pd----W~~e~~~~~~~~  115 (115)
                      ++||    |+.++.+++..|
T Consensus        86 de~d~~s~wl~~~~~~~~er  105 (821)
T KOG1133|consen   86 DESDSSSAWLTQFVQKKEER  105 (821)
T ss_pred             ccccchhHHHHHHHHHHHhh
Confidence            5677    999998876543

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.73  E-value=5.3e-18  Score=135.49  Aligned_cols=56  Identities=50%  Similarity=0.876  Sum_probs=53.4

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .|.|||+|||.|.+||+.|++++.+++++|+|||||||||++||+|++.|+..++.
T Consensus         2 ~~~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00488        2 LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            57899999999999999999999999999999999999999999999999987665

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.73  E-value=5.3e-18  Score=135.49  Aligned_cols=56  Identities=50%  Similarity=0.876  Sum_probs=53.4

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .|.|||+|||.|.+||+.|++++.+++++|+|||||||||++||+|++.|+..++.
T Consensus         2 ~~~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00489        2 LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            57899999999999999999999999999999999999999999999999987665

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.61  E-value=7.5e-16  Score=135.22  Aligned_cols=56  Identities=34%  Similarity=0.610  Sum_probs=52.9

Q ss_pred             ccccCCCCC-CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         23 SEFPFPFDA-YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        23 ~~~~fpf~~-r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ..++|||++ ||.|.++|+.|++++.+++++++|||||||||+|+|||+|.|+..++
T Consensus         2 ~~v~FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~   58 (705)
T TIGR00604         2 LLVYFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP   58 (705)
T ss_pred             CceecCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc
Confidence            468999995 99999999999999999999999999999999999999999998766

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).

>KOG1132|consensus

Probab=99.48  E-value=2.9e-14  Score=128.65  Aligned_cols=60  Identities=43%  Similarity=0.733  Sum_probs=57.4

Q ss_pred             CccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         22 PSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        22 ~~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |+.+.|||+||+.|+.||..|.++|.+..++++|+||||||||++||++++|.+.+..+.
T Consensus        13 Gv~V~fP~qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~   72 (945)
T KOG1132|consen   13 GVPVEFPFQPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRK   72 (945)
T ss_pred             CceeeccCCcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccc
Confidence            899999999999999999999999999999999999999999999999999999987443

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.46  E-value=7.7e-14  Score=123.12  Aligned_cols=57  Identities=23%  Similarity=0.233  Sum_probs=51.7

Q ss_pred             ccCC-CCCCHHHHHHHHHHHHHHhc-----CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         25 FPFP-FDAYDIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        25 ~~fp-f~~r~~Q~e~m~~I~~~l~~-----~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+| |++|++|.+||..|.+++.+     ++++++|||||||||++||+|++.|+...+++|
T Consensus        19 ~~~~~~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k~v   81 (697)
T PRK11747         19 EQLPGFIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKKKL   81 (697)
T ss_pred             HhCCCCCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCCeE
Confidence            3445 99999999999999999988     488999999999999999999999999887776

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

Probab=99.45  E-value=1e-13  Score=119.52  Aligned_cols=59  Identities=24%  Similarity=0.350  Sum_probs=53.4

Q ss_pred             ccccCC-CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         23 SEFPFP-FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        23 ~~~~fp-f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ....|| |++|+.|.+||..|..++.++.++++|||||||||++||+|++.|....++++
T Consensus         7 ~~~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~v   66 (654)
T COG1199           7 LAVAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV   66 (654)
T ss_pred             HHhhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcE
Confidence            344566 66999999999999999999999999999999999999999999998887765

>KOG1131|consensus

Probab=99.38  E-value=6e-13  Score=116.26  Aligned_cols=63  Identities=29%  Similarity=0.417  Sum_probs=59.5

Q ss_pred             CCCCCccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         18 LAEVPSEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        18 ~~~~~~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +.++++.++|||+ .||.|.++|.+++++|++++|+++|+|+|||||.|+|..+++|...++..
T Consensus         3 ~~id~l~v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~   66 (755)
T KOG1131|consen    3 FYIDDLLVYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDE   66 (755)
T ss_pred             eeecCeeEecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcc
Confidence            4578999999999 99999999999999999999999999999999999999999999998843

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

Probab=99.38  E-value=6e-13  Score=120.55  Aligned_cols=53  Identities=26%  Similarity=0.409  Sum_probs=50.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |++|++|.+||..|.+++.++.++++|||||||||++||+|++.|+...+++|
T Consensus       256 ~e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~~~v  308 (928)
T PRK08074        256 YEKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKEEPV  308 (928)
T ss_pred             CcCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccCCeE
Confidence            89999999999999999999999999999999999999999999998776665

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

Probab=99.24  E-value=8.2e-12  Score=111.97  Aligned_cols=49  Identities=24%  Similarity=0.325  Sum_probs=46.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ..|++|+.|.+||+.|.+++.+++++++|||||||||++||+|++.++.
T Consensus       242 ~~~~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~  290 (850)
T TIGR01407       242 LGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI  290 (850)
T ss_pred             cCCccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc
Confidence            4588999999999999999999999999999999999999999999987

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.

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

Probab=99.09  E-value=1.5e-10  Score=104.15  Aligned_cols=47  Identities=19%  Similarity=0.247  Sum_probs=44.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .|++|++|.+||..|.+++.++.++++|||||||||++||+|++.++
T Consensus       243 ~~e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~  289 (820)
T PRK07246        243 GLEERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS  289 (820)
T ss_pred             CCccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc
Confidence            39999999999999999999999999999999999999999988765

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

Probab=98.90  E-value=1.7e-09  Score=95.57  Aligned_cols=43  Identities=30%  Similarity=0.513  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         34 IQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .|.+||..|++++.+++++++|||||||||++||+|++.|+..
T Consensus         1 ~Q~~~~~~i~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~   43 (636)
T TIGR03117         1 EQALFYLNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKE   43 (636)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHh
Confidence            4999999999999999999999999999999999999999874

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.

>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=98.78  E-value=1.2e-08  Score=72.30  Aligned_cols=47  Identities=21%  Similarity=0.393  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      |.+|+.|.+.+..+.+.+...   .++++.+|||+|||..++..+.....
T Consensus         2 ~~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~   51 (184)
T PF04851_consen    2 YKLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR   51 (184)
T ss_dssp             -EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc
Confidence            568999999999999999876   89999999999999998865555443

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 ....

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.74  E-value=1.7e-08  Score=83.16  Aligned_cols=48  Identities=17%  Similarity=0.141  Sum_probs=41.3

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..++|. |++.|.+.+..+    .+|+.+|+.||||||||++|++|++..+..
T Consensus        24 ~~~g~~~pt~iQ~~aip~i----l~g~dvi~~ApTGsGKTla~llp~l~~l~~   72 (423)
T PRK04837         24 EKKGFHNCTPIQALALPLT----LAGRDVAGQAQTGTGKTMAFLTATFHYLLS   72 (423)
T ss_pred             HHCCCCCCCHHHHHHHHHH----hCCCcEEEECCCCchHHHHHHHHHHHHHHh
Confidence            346787 999999988764    578999999999999999999999987754

>cd00268 DEADc DEAD-box helicases

Probab=98.72  E-value=2.9e-08  Score=72.98  Aligned_cols=47  Identities=23%  Similarity=0.323  Sum_probs=40.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++|. +++.|.+.+..+.    +++++++++|||+|||++|+.|++..+...
T Consensus        17 ~~~~~~~~~Q~~~~~~~~----~~~~~li~~~TG~GKT~~~~~~~l~~~~~~   64 (203)
T cd00268          17 LGFEKPTPIQARAIPPLL----SGRDVIGQAQTGSGKTAAFLIPILEKLDPS   64 (203)
T ss_pred             cCCCCCCHHHHHHHHHHh----cCCcEEEECCCCCcHHHHHHHHHHHHHHhh
Confidence            4566 8999999888765    388999999999999999999999888775

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.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.68  E-value=2.7e-08  Score=83.63  Aligned_cols=45  Identities=22%  Similarity=0.182  Sum_probs=39.0

Q ss_pred             cccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         24 EFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        24 ~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      ...|+|. +||.|.+.+..+    .+++.+++.||||+|||++|++|++.
T Consensus         4 ~~~~g~~~~r~~Q~~ai~~~----l~g~dvlv~apTGsGKTl~y~lp~l~   49 (470)
T TIGR00614         4 KTVFGLSSFRPVQLEVINAV----LLGRDCFVVMPTGGGKSLCYQLPALC   49 (470)
T ss_pred             HhhcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCCcHhHHHHHHHHH
Confidence            4578998 999999988765    46779999999999999999999874

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

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

Probab=98.68  E-value=4.5e-08  Score=69.20  Aligned_cols=41  Identities=24%  Similarity=0.421  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      |.|.++++.+.    +++++++.||||+|||++|+.+++..+...
T Consensus         2 ~~Q~~~~~~i~----~~~~~li~aptGsGKT~~~~~~~l~~~~~~   42 (169)
T PF00270_consen    2 PLQQEAIEAII----SGKNVLISAPTGSGKTLAYILPALNRLQEG   42 (169)
T ss_dssp             HHHHHHHHHHH----TTSEEEEECSTTSSHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHH----cCCCEEEECCCCCccHHHHHHHHHhhhccC
Confidence            78999888764    678899999999999999999999888775

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 ....

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

Probab=98.67  E-value=3.8e-08  Score=84.01  Aligned_cols=46  Identities=17%  Similarity=0.241  Sum_probs=39.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+|. |+|.|.+.+..+    .+|+++|+.||||||||++|++|++..+..
T Consensus       139 ~g~~~ptpiQ~~aip~i----l~g~dviv~ApTGSGKTlayllPil~~l~~  185 (518)
T PLN00206        139 AGYEFPTPIQMQAIPAA----LSGRSLLVSADTGSGKTASFLVPIISRCCT  185 (518)
T ss_pred             cCCCCCCHHHHHHHHHH----hcCCCEEEEecCCCCccHHHHHHHHHHHHh
Confidence            4676 999999988765    478899999999999999999999987653

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.66  E-value=4.3e-08  Score=82.03  Aligned_cols=48  Identities=17%  Similarity=0.180  Sum_probs=41.3

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+.|. |++.|.+.+..+    .+++.+|+.||||||||++|++|++..+...
T Consensus        18 ~~g~~~pt~iQ~~ai~~i----l~g~dvlv~apTGsGKTla~~lpil~~l~~~   66 (456)
T PRK10590         18 EQGYREPTPIQQQAIPAV----LEGRDLMASAQTGTGKTAGFTLPLLQHLITR   66 (456)
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCCCcHHHHHHHHHHHHhhhc
Confidence            45676 999999988865    4688999999999999999999999888653

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=98.65  E-value=4.9e-08  Score=80.51  Aligned_cols=47  Identities=21%  Similarity=0.281  Sum_probs=40.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+|. |++.|.+.+..+.    +++.+++.||||+|||++|++|++..+...
T Consensus        19 ~g~~~p~~iQ~~ai~~~~----~g~d~l~~apTGsGKT~~~~lp~l~~l~~~   66 (434)
T PRK11192         19 KGYTRPTAIQAEAIPPAL----DGRDVLGSAPTGTGKTAAFLLPALQHLLDF   66 (434)
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHHhhc
Confidence            5677 9999999887753    678899999999999999999999988653

>PTZ00424 helicase 45; Provisional

Probab=98.63  E-value=5.5e-08  Score=78.56  Aligned_cols=48  Identities=21%  Similarity=0.324  Sum_probs=41.1

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..++|. |++.|.+.+..+    .++..+++.||||+|||++|++|++..+..
T Consensus        44 ~~~~~~~~~~~Q~~ai~~i----~~~~d~ii~apTGsGKT~~~~l~~l~~~~~   92 (401)
T PTZ00424         44 YSYGFEKPSAIQQRGIKPI----LDGYDTIGQAQSGTGKTATFVIAALQLIDY   92 (401)
T ss_pred             HHcCCCCCCHHHHHHHHHH----hCCCCEEEECCCCChHHHHHHHHHHHHhcC
Confidence            346777 999999988875    478889999999999999999999988753

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=98.58  E-value=9.5e-08  Score=79.58  Aligned_cols=48  Identities=21%  Similarity=0.244  Sum_probs=41.3

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ..+|. |+|.|.+.+..+    .+++.+|+.||||||||++|++|++..+...
T Consensus        21 ~~g~~~~t~iQ~~ai~~~----l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~   69 (460)
T PRK11776         21 ELGYTEMTPIQAQSLPAI----LAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK   69 (460)
T ss_pred             HCCCCCCCHHHHHHHHHH----hcCCCEEEECCCCCcHHHHHHHHHHHHhhhc
Confidence            36777 999999988865    4788999999999999999999999888654

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.58  E-value=1e-07  Score=79.97  Aligned_cols=47  Identities=21%  Similarity=0.252  Sum_probs=40.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++|. +++.|.+.+..+    .+|+++|+.+|||||||++|++|++.-+...
T Consensus       105 ~g~~~~~~iQ~~ai~~~----~~G~dvi~~apTGSGKTlay~lpil~~l~~~  152 (475)
T PRK01297        105 LGFPYCTPIQAQVLGYT----LAGHDAIGRAQTGTGKTAAFLISIINQLLQT  152 (475)
T ss_pred             CCCCCCCHHHHHHHHHH----hCCCCEEEECCCCChHHHHHHHHHHHHHHhc
Confidence            6677 899999987754    5789999999999999999999999877654

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.58  E-value=7.5e-08  Score=82.98  Aligned_cols=45  Identities=24%  Similarity=0.274  Sum_probs=39.1

Q ss_pred             cccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         24 EFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        24 ~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      .-.|+|+ +||.|.+.+..+    .+|+.+++.||||+|||++|++|++.
T Consensus         6 ~~~fg~~~fr~~Q~~~i~~i----l~g~dvlv~~PTG~GKTl~y~lpal~   51 (591)
T TIGR01389         6 KRTFGYDDFRPGQEEIISHV----LDGRDVLVVMPTGGGKSLCYQVPALL   51 (591)
T ss_pred             HHhcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCccHhHHHHHHHHH
Confidence            3469999 899999988765    46789999999999999999999873

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.

>PTZ00110 helicase; Provisional

Probab=98.55  E-value=1.2e-07  Score=81.69  Aligned_cols=46  Identities=20%  Similarity=0.098  Sum_probs=39.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..|. |++.|.+.+..+    .+|+.+|+.||||||||++|++|++..+..
T Consensus       148 ~g~~~pt~iQ~~aip~~----l~G~dvI~~ApTGSGKTlaylLP~l~~i~~  194 (545)
T PTZ00110        148 AGFTEPTPIQVQGWPIA----LSGRDMIGIAETGSGKTLAFLLPAIVHINA  194 (545)
T ss_pred             CCCCCCCHHHHHHHHHH----hcCCCEEEEeCCCChHHHHHHHHHHHHHHh
Confidence            4577 999999987764    578899999999999999999999887754

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.54  E-value=1e-07  Score=82.97  Aligned_cols=46  Identities=22%  Similarity=0.211  Sum_probs=39.3

Q ss_pred             ccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         23 SEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        23 ~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      ..-.|+|+ +||.|.+.++.+    .+++.+++.+|||+|||++|++|++.
T Consensus        17 l~~~fG~~~~r~~Q~~ai~~i----l~g~dvlv~apTGsGKTl~y~lpal~   63 (607)
T PRK11057         17 LQETFGYQQFRPGQQEIIDAV----LSGRDCLVVMPTGGGKSLCYQIPALV   63 (607)
T ss_pred             HHHHcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCchHHHHHHHHHHH
Confidence            33468998 999999988865    47889999999999999999999773

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.54  E-value=1.4e-07  Score=81.80  Aligned_cols=47  Identities=19%  Similarity=0.164  Sum_probs=41.0

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+.|. |+|+|.+.+..+    .+++.+|+.||||||||++|++|++..+..
T Consensus        26 ~~g~~~ptpiQ~~~ip~~----l~G~Dvi~~ApTGSGKTlafllpil~~l~~   73 (572)
T PRK04537         26 SAGFTRCTPIQALTLPVA----LPGGDVAGQAQTGTGKTLAFLVAVMNRLLS   73 (572)
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEEcCCCCcHHHHHHHHHHHHHHh
Confidence            46777 999999988864    578999999999999999999999987754

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

Probab=98.52  E-value=1.7e-07  Score=83.84  Aligned_cols=47  Identities=17%  Similarity=0.200  Sum_probs=40.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ..|. ||+.|.+.+..+    .+|+++|+.+|||||||++|++|++..+...
T Consensus        32 ~g~~~p~~~Q~~ai~~i----l~G~nvvv~apTGSGKTla~~LPiL~~l~~~   79 (742)
T TIGR03817        32 AGIHRPWQHQARAAELA----HAGRHVVVATGTASGKSLAYQLPVLSALADD   79 (742)
T ss_pred             cCCCcCCHHHHHHHHHH----HCCCCEEEECCCCCcHHHHHHHHHHHHHhhC
Confidence            4565 999999988764    6889999999999999999999999988654

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.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.45  E-value=3.6e-07  Score=80.71  Aligned_cols=52  Identities=15%  Similarity=0.263  Sum_probs=45.8

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      -.|||++++.|.+.+..|..-+.++  ...++.||||||||++|++|++..+..
T Consensus       256 ~~l~f~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~  309 (681)
T PRK10917        256 ASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA  309 (681)
T ss_pred             HhCCCCCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            4589999999999999998887655  478999999999999999999887754

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=98.38  E-value=6e-07  Score=79.03  Aligned_cols=48  Identities=19%  Similarity=0.243  Sum_probs=40.9

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .++|. |+|.|.+.+..+    .+++.+|+.||||||||++|++|++..+...
T Consensus        23 ~~G~~~ptpiQ~~ai~~l----l~g~dvl~~ApTGsGKT~af~lpll~~l~~~   71 (629)
T PRK11634         23 DLGYEKPSPIQAECIPHL----LNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE   71 (629)
T ss_pred             HCCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc
Confidence            35777 999999988765    4678999999999999999999999877543

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

Probab=98.37  E-value=4.7e-07  Score=84.79  Aligned_cols=46  Identities=22%  Similarity=0.094  Sum_probs=39.7

Q ss_pred             ccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         23 SEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        23 ~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      ....|+|. +||.|.+.+..+    .+|+.+|+.+|||+|||++|++|++.
T Consensus       452 lk~~FG~~sFRp~Q~eaI~ai----L~GrDVLVimPTGSGKSLcYQLPAL~  498 (1195)
T PLN03137        452 NKKVFGNHSFRPNQREIINAT----MSGYDVFVLMPTGGGKSLTYQLPALI  498 (1195)
T ss_pred             HHHHcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCccHHHHHHHHHHH
Confidence            44578888 999999987764    57899999999999999999999864

>KOG0348|consensus

Probab=98.36  E-value=1.3e-07  Score=83.30  Aligned_cols=55  Identities=15%  Similarity=0.199  Sum_probs=47.4

Q ss_pred             ccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         23 SEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        23 ~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.-.+.+. |..+|.+.|..|.    +|+.+++.|+||||||||||+|+++.++....++
T Consensus       151 L~~~m~i~~pTsVQkq~IP~lL----~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki  206 (708)
T KOG0348|consen  151 LNTKMKISAPTSVQKQAIPVLL----EGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKI  206 (708)
T ss_pred             HHHHhccCccchHhhcchhhhh----cCcceEEEcCCCCcccHHHHHHHHHHHHhcCccc
Confidence            33445666 8899999999864    5999999999999999999999999999988776

>KOG0345|consensus

Probab=98.36  E-value=6e-07  Score=78.01  Aligned_cols=49  Identities=22%  Similarity=0.284  Sum_probs=42.0

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++|+ ..|+|...+..+    .+++.++++|||||||||||++|++.-+....
T Consensus        23 ~~GF~~mTpVQa~tIPll----l~~KDVvveavTGSGKTlAFllP~le~i~rr~   72 (567)
T KOG0345|consen   23 ESGFEKMTPVQAATIPLL----LKNKDVVVEAVTGSGKTLAFLLPMLEIIYRRE   72 (567)
T ss_pred             hcCCcccCHHHHhhhHHH----hcCCceEEEcCCCCCchhhHHHHHHHHHHhhc
Confidence            35677 889999999874    67889999999999999999999999884443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.36  E-value=8.8e-07  Score=77.49  Aligned_cols=52  Identities=19%  Similarity=0.314  Sum_probs=44.9

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..+||.+++.|.+.+..|..-+...  .+.++.||||||||++|+.|++..+..
T Consensus       230 ~~lpf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~  283 (630)
T TIGR00643       230 ASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA  283 (630)
T ss_pred             HhCCCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            3689999999999999998877554  468999999999999999998877654

>PRK13767 ATP-dependent helicase; Provisional

Probab=98.34  E-value=8.2e-07  Score=80.60  Aligned_cols=44  Identities=25%  Similarity=0.290  Sum_probs=38.5

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        29 f~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      |. ++|.|.+.+..+    .+|+++++.||||||||++|++|++..+..
T Consensus        30 ~~~~tpiQ~~Ai~~i----l~g~nvli~APTGSGKTlaa~Lpil~~l~~   74 (876)
T PRK13767         30 FGTFTPPQRYAIPLI----HEGKNVLISSPTGSGKTLAAFLAIIDELFR   74 (876)
T ss_pred             cCCCCHHHHHHHHHH----HcCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            44 999999988765    578899999999999999999999987764

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

Probab=98.31  E-value=1e-06  Score=80.11  Aligned_cols=45  Identities=16%  Similarity=0.203  Sum_probs=41.4

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        29 f~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      |. |+|.|.+++..|    .+|.++++.||||+|||+|+++|++.-+...
T Consensus        20 ~~~~t~~Q~~a~~~i----~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~   65 (814)
T COG1201          20 FTSLTPPQRYAIPEI----HSGENVLIIAPTGSGKTEAAFLPVINELLSL   65 (814)
T ss_pred             cCCCCHHHHHHHHHH----hCCCceEEEcCCCCChHHHHHHHHHHHHHhc
Confidence            55 999999999886    4899999999999999999999999998887

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.30  E-value=1.3e-06  Score=80.21  Aligned_cols=52  Identities=17%  Similarity=0.209  Sum_probs=45.8

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .|||++++.|.+.++.|.+-+.++  ..++++||||+|||.+++.|++..+...
T Consensus       447 ~~~f~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g  500 (926)
T TIGR00580       447 SFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG  500 (926)
T ss_pred             hCCCCCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhC
Confidence            589999999999999998888765  5789999999999999999988777553

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.30  E-value=1.3e-06  Score=61.18  Aligned_cols=46  Identities=22%  Similarity=0.231  Sum_probs=38.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++.+++.|.+++..+.    +. +.+++.+|||+|||.+++.+++..+...
T Consensus         6 ~~~~~~~Q~~~~~~~~----~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~   52 (201)
T smart00487        6 FEPLRPYQKEAIEALL----SGLRDVILAAPTGSGKTLAALLPALEALKRG   52 (201)
T ss_pred             CCCCCHHHHHHHHHHH----cCCCcEEEECCCCCchhHHHHHHHHHHhccc
Confidence            4559999999888764    44 7899999999999999999888777664

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

Probab=98.29  E-value=1.2e-06  Score=75.21  Aligned_cols=46  Identities=20%  Similarity=0.217  Sum_probs=40.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..|. |.|+|...+..+    ..|+.++..|+||||||+||++|++..+..
T Consensus        47 ~gf~~pt~IQ~~~IP~~----l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~   93 (513)
T COG0513          47 LGFEEPTPIQLAAIPLI----LAGRDVLGQAQTGTGKTAAFLLPLLQKILK   93 (513)
T ss_pred             cCCCCCCHHHHHHHHHH----hCCCCEEEECCCCChHHHHHHHHHHHHHhc
Confidence            4677 999999998875    467999999999999999999999999873

>PRK01172 ski2-like helicase; Provisional

Probab=98.28  E-value=1.3e-06  Score=76.44  Aligned_cols=48  Identities=25%  Similarity=0.312  Sum_probs=40.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .+|++|+.|.+.++.+    .+++++++.||||+|||++++.+++..+...+
T Consensus        19 ~~~~l~~~Q~~ai~~l----~~~~nvlv~apTGSGKTl~a~lail~~l~~~~   66 (674)
T PRK01172         19 NDFELYDHQRMAIEQL----RKGENVIVSVPTAAGKTLIAYSAIYETFLAGL   66 (674)
T ss_pred             CCCCCCHHHHHHHHHH----hcCCcEEEECCCCchHHHHHHHHHHHHHHhCC
Confidence            4678999999988764    67889999999999999999999887765543

>PRK02362 ski2-like helicase; Provisional

Probab=98.20  E-value=2.1e-06  Score=76.09  Aligned_cols=49  Identities=22%  Similarity=0.196  Sum_probs=40.2

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      +|. +||.|.+.+..   .+.+++++|+.||||+|||++|++|++..+...++
T Consensus        20 g~~~l~p~Q~~ai~~---~~~~g~nvlv~APTGSGKTlia~lail~~l~~~~k   69 (737)
T PRK02362         20 GIEELYPPQAEAVEA---GLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGK   69 (737)
T ss_pred             CCCcCCHHHHHHHHH---HHhCCCcEEEECCCcchHHHHHHHHHHHHHhcCCc
Confidence            455 99999998765   35678999999999999999999998887754333

>PRK00254 ski2-like helicase; Provisional

Probab=98.16  E-value=3.1e-06  Score=74.83  Aligned_cols=49  Identities=18%  Similarity=0.173  Sum_probs=40.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .+|. ++|.|.+.+..   .+.+++++++.||||+|||+++.+|++..+...+
T Consensus        19 ~g~~~l~~~Q~~ai~~---~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~~   68 (720)
T PRK00254         19 RGIEELYPPQAEALKS---GVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREG   68 (720)
T ss_pred             CCCCCCCHHHHHHHHH---HHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhcC
Confidence            4565 89999997764   3568899999999999999999999887765444

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

Probab=98.09  E-value=5.1e-06  Score=75.76  Aligned_cols=47  Identities=21%  Similarity=0.289  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+|..|.+.++.+    .+|+++|+..|||||||.+|++|++.-+...+..
T Consensus        70 ~lY~HQ~~A~~~~----~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a  116 (851)
T COG1205          70 RLYSHQVDALRLI----REGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA  116 (851)
T ss_pred             cccHHHHHHHHHH----HCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc
Confidence            3899999987764    6889999999999999999999999888776665

>KOG0335|consensus

Probab=97.96  E-value=2.7e-06  Score=73.58  Aligned_cols=47  Identities=15%  Similarity=0.241  Sum_probs=39.3

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        29 f~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      |. |.|+|+..+..|    ..|..++.+|+||+|||.+||+|++.++.+.+.
T Consensus        94 ~~~ptpvQk~sip~i----~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~  141 (482)
T KOG0335|consen   94 YTKPTPVQKYSIPII----SGGRDLMACAQTGSGKTAAFLIPIISYLLDEGP  141 (482)
T ss_pred             ccCCCcceeecccee----ecCCceEEEccCCCcchHHHHHHHHHHHHhcCc
Confidence            44 777787776653    678889999999999999999999999988744

>KOG0331|consensus

Probab=97.96  E-value=4.5e-06  Score=72.82  Aligned_cols=46  Identities=17%  Similarity=0.123  Sum_probs=40.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      -.|+ |.|+|.+....+    ..|+.+|.-|-|||||||||++|++.++..
T Consensus       109 ~g~~~PtpIQaq~wp~~----l~GrD~v~iA~TGSGKTLay~lP~i~~l~~  155 (519)
T KOG0331|consen  109 QGFEKPTPIQAQGWPIA----LSGRDLVGIARTGSGKTLAYLLPAIVHLNN  155 (519)
T ss_pred             cCCCCCchhhhccccee----ccCCceEEEeccCCcchhhhhhHHHHHHHh
Confidence            4567 889999977754    588999999999999999999999999987

>PRK10689 transcription-repair coupling factor; Provisional

Probab=97.95  E-value=1.7e-05  Score=74.28  Aligned_cols=51  Identities=14%  Similarity=0.126  Sum_probs=43.4

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      -.|||++.+.|.+.++.|..-+.+.  ..++++||||+|||..++.++...+.
T Consensus       595 ~~~~~~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~  647 (1147)
T PRK10689        595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE  647 (1147)
T ss_pred             HhCCCCCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH
Confidence            4699999999999999988777654  67999999999999999888766554

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.93  E-value=1.4e-05  Score=73.80  Aligned_cols=48  Identities=19%  Similarity=0.169  Sum_probs=38.4

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..||+.+|.|.+.+..+    ..+..+|.+|+||+|||++|++|++.-+..
T Consensus        87 ~~~p~~~tp~qvQ~I~~i----~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~  134 (970)
T PRK12899         87 YHQQWDMVPYDVQILGAI----AMHKGFITEMQTGEGKTLTAVMPLYLNALT  134 (970)
T ss_pred             ccCCCCCChHHHHHhhhh----hcCCCeEEEeCCCCChHHHHHHHHHHHHhh
Confidence            455666689999988765    346679999999999999999999866643

>KOG0344|consensus

Probab=97.93  E-value=9.3e-06  Score=71.59  Aligned_cols=47  Identities=28%  Similarity=0.339  Sum_probs=39.4

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +|. |.|.|.+.+..    +..+..++.+||||+||||+|++|++.-+....
T Consensus       155 ~F~~Pt~iq~~aipv----fl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~  202 (593)
T KOG0344|consen  155 GFDEPTPIQKQAIPV----FLEKRDVLACAPTGSGKTLAFNLPILQHLKDLS  202 (593)
T ss_pred             CCCCCCcccchhhhh----hhcccceEEeccCCCcchhhhhhHHHHHHHHhh
Confidence            466 77888876553    457789999999999999999999999998876

>KOG0350|consensus

Probab=97.89  E-value=9e-06  Score=71.34  Aligned_cols=50  Identities=20%  Similarity=0.379  Sum_probs=40.5

Q ss_pred             CCHHHHHHHHHHHHHHhc-----CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~-----~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+|+|...+.-+...+..     .+.+++.|||||||||||.+|+++.+-...-+
T Consensus       160 ~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~  214 (620)
T KOG0350|consen  160 LFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVK  214 (620)
T ss_pred             ccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCcc
Confidence            457888888887777752     36789999999999999999999999776433

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

Probab=97.87  E-value=3.1e-05  Score=72.53  Aligned_cols=50  Identities=14%  Similarity=0.187  Sum_probs=39.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +.+.+|+.|.+.++.+.+++.++ +.+++.+|||||||++.+..+..++..
T Consensus       410 ~~~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai~li~~L~~~  460 (1123)
T PRK11448        410 YGLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKA  460 (1123)
T ss_pred             cCCCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            34569999999999999998765 578999999999999866655454443

>KOG0330|consensus

Probab=97.80  E-value=1.7e-05  Score=67.89  Aligned_cols=49  Identities=20%  Similarity=0.108  Sum_probs=43.5

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+. |.++|.+.|..+    ..|+++|.-|.||||||.+|++|+++.+..+++.
T Consensus        80 ~~~~PT~IQ~~aiP~~----L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~  129 (476)
T KOG0330|consen   80 GWKKPTKIQSEAIPVA----LGGRDVIGLAETGSGKTGAFALPILQRLLQEPKL  129 (476)
T ss_pred             CcCCCchhhhhhcchh----hCCCcEEEEeccCCCchhhhHHHHHHHHHcCCCC
Confidence            355 899999999875    5889999999999999999999999999887765

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

Probab=97.79  E-value=2e-05  Score=69.78  Aligned_cols=47  Identities=26%  Similarity=0.208  Sum_probs=40.5

Q ss_pred             ccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         23 SEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        23 ~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ....|+|+ .|++|.+.++.    +.+++++++-+|||.|||++|.+|++-.
T Consensus         9 L~~~fGy~~FR~gQ~evI~~----~l~g~d~lvvmPTGgGKSlCyQiPAll~   56 (590)
T COG0514           9 LKQVFGYASFRPGQQEIIDA----LLSGKDTLVVMPTGGGKSLCYQIPALLL   56 (590)
T ss_pred             HHHHhCccccCCCHHHHHHH----HHcCCcEEEEccCCCCcchHhhhHHHhc
Confidence            45679999 89999986665    4678999999999999999999998866

>PRK09694 helicase Cas3; Provisional

Probab=97.79  E-value=3.2e-05  Score=70.97  Aligned_cols=45  Identities=18%  Similarity=0.245  Sum_probs=35.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .|.|||.|..+...    ..+.+..||+||||+|||.++|..+...+..
T Consensus       284 ~~~p~p~Q~~~~~~----~~~pgl~ileApTGsGKTEAAL~~A~~l~~~  328 (878)
T PRK09694        284 GYQPRQLQTLVDAL----PLQPGLTIIEAPTGSGKTEAALAYAWRLIDQ  328 (878)
T ss_pred             CCCChHHHHHHHhh----ccCCCeEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            46799999987432    1356789999999999999999887765543

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

Probab=97.77  E-value=4.3e-05  Score=64.56  Aligned_cols=45  Identities=22%  Similarity=0.352  Sum_probs=38.6

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      +.+.+.+|+.|.+.++.+.+...++..+++.+|||+|||+..+..
T Consensus        31 ~~~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~   75 (442)
T COG1061          31 VAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEA   75 (442)
T ss_pred             cccCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHH
Confidence            667788999999999988877776889999999999999876554

>PRK09401 reverse gyrase; Reviewed

Probab=97.71  E-value=5.6e-05  Score=71.10  Aligned_cols=48  Identities=17%  Similarity=0.158  Sum_probs=36.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++|+|++.|...+..+    ..|.++++.||||+|||+ ++++++.++...+
T Consensus        76 ~~G~~pt~iQ~~~i~~i----l~g~dv~i~ApTGsGKT~-f~l~~~~~l~~~g  123 (1176)
T PRK09401         76 KTGSKPWSLQRTWAKRL----LLGESFAIIAPTGVGKTT-FGLVMSLYLAKKG  123 (1176)
T ss_pred             hcCCCCcHHHHHHHHHH----HCCCcEEEEcCCCCCHHH-HHHHHHHHHHhcC
Confidence            46788999999977764    478899999999999996 4455555554433

>COG1204 Superfamily II helicase [General function prediction only]

Probab=97.70  E-value=3.6e-05  Score=69.68  Aligned_cols=48  Identities=21%  Similarity=0.259  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +.++.|++   +|+..+..++++|+++|||+|||+.++++++.-+.+.+.+
T Consensus        31 el~~~qq~---av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~~k   78 (766)
T COG1204          31 ELFNPQQE---AVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGGK   78 (766)
T ss_pred             HhhHHHHH---HhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcCCc
Confidence            57888888   5555666789999999999999999999999999886444

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

Probab=97.67  E-value=4.9e-05  Score=69.59  Aligned_cols=41  Identities=17%  Similarity=0.281  Sum_probs=31.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCC-cEEEecCCCCCchHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~-~~iiEaPTGtGKTls~L~~al   71 (115)
                      .+|+|+|+|.+.+..+    .+|+ .+++.+|||||||.++.+..+
T Consensus        12 ~G~~PtpiQ~~~i~~i----l~G~~~v~~~apTGSGKTaa~aafll   53 (844)
T TIGR02621        12 HGYSPFPWQLSLAERF----VAGQPPESCSTPTGLGKTSIIAAWLL   53 (844)
T ss_pred             hCCCCCHHHHHHHHHH----HcCCCcceEecCCCCcccHHHHHhhc
Confidence            3577999999988875    3565 688899999999987654444

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.

>KOG0346|consensus

Probab=97.67  E-value=4.3e-05  Score=66.48  Aligned_cols=50  Identities=20%  Similarity=0.181  Sum_probs=41.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+|+ |.-+|...|..+    .+|+.+|.-|-||||||++||+|.++.+...++.
T Consensus        37 lG~ekpTlIQs~aIpla----LEgKDvvarArTGSGKT~AYliPllqkll~~k~t   87 (569)
T KOG0346|consen   37 LGWEKPTLIQSSAIPLA----LEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKT   87 (569)
T ss_pred             hCcCCcchhhhcccchh----hcCcceeeeeccCCCchHHHHHHHHHHHHHhhhc
Confidence            4566 777888877753    4678999999999999999999999999887766

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.65  E-value=8.9e-05  Score=65.88  Aligned_cols=50  Identities=14%  Similarity=0.064  Sum_probs=40.3

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..|+.+++.|.+.++.|...+ .....++.||||+|||.+|+.++...+..
T Consensus       140 ~~~~~Lt~~Q~~ai~~i~~~~-~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~  189 (679)
T PRK05580        140 FEPPTLNPEQAAAVEAIRAAA-GFSPFLLDGVTGSGKTEVYLQAIAEVLAQ  189 (679)
T ss_pred             cCCCCCCHHHHHHHHHHHhcc-CCCcEEEECCCCChHHHHHHHHHHHHHHc
Confidence            456778999999888876544 45679999999999999999887766654

>PRK14701 reverse gyrase; Provisional

Probab=97.61  E-value=8.2e-05  Score=72.02  Aligned_cols=45  Identities=27%  Similarity=0.172  Sum_probs=37.1

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .++|+|++.|.+.+..+    .+|+.+++.||||+|||+.++.+++..+
T Consensus        75 ~~G~~pt~iQ~~~i~~i----l~G~d~li~APTGsGKTl~~~~~al~~~  119 (1638)
T PRK14701         75 ITGFEFWSIQKTWAKRI----LRGKSFSIVAPTGMGKSTFGAFIALFLA  119 (1638)
T ss_pred             hhCCCCCHHHHHHHHHH----HcCCCEEEEEcCCCCHHHHHHHHHHHHH
Confidence            47889999999988765    4688999999999999997676666543

>PHA02653 RNA helicase NPH-II; Provisional

Probab=97.58  E-value=0.00012  Score=65.56  Aligned_cols=45  Identities=16%  Similarity=0.201  Sum_probs=38.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH---------HHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS---------LICGILKWYS   75 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls---------~L~~al~~l~   75 (115)
                      .++.|.++-+.+...+.+++.+|+.|+||||||.+         |+.|++..+.
T Consensus       161 l~~~~~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~  214 (675)
T PHA02653        161 LASLQPDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLD  214 (675)
T ss_pred             CCchhHHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhh
Confidence            66888888888888899999999999999999997         5667777664

>PHA02558 uvsW UvsW helicase; Provisional

Probab=97.57  E-value=0.00013  Score=62.27  Aligned_cols=38  Identities=21%  Similarity=0.134  Sum_probs=29.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .+.||+.|.+.+..+   + .+..+++.+|||+|||+.++..
T Consensus       112 ~~~~r~~Q~~av~~~---l-~~~~~il~apTGsGKT~i~~~l  149 (501)
T PHA02558        112 KIEPHWYQYDAVYEG---L-KNNRRLLNLPTSAGKSLIQYLL  149 (501)
T ss_pred             cCCCCHHHHHHHHHH---H-hcCceEEEeCCCCCHHHHHHHH
Confidence            367999999966543   4 3567899999999999976543

>KOG0338|consensus

Probab=97.57  E-value=3.7e-05  Score=67.96  Aligned_cols=51  Identities=18%  Similarity=0.034  Sum_probs=43.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+|. |.|+|...|...    .-|+.++.+|.||||||.+|.+|+|.-+...++++
T Consensus       199 lGy~~PTpIQ~a~IPva----llgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~  250 (691)
T KOG0338|consen  199 LGYKKPTPIQVATIPVA----LLGKDICACAATGSGKTAAFALPILERLLYRPKKV  250 (691)
T ss_pred             cCCCCCCchhhhcccHH----hhcchhhheecccCCchhhhHHHHHHHHhcCcccC
Confidence            5677 889999988843    24788999999999999999999999999888875

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

Probab=97.53  E-value=0.00014  Score=64.43  Aligned_cols=45  Identities=18%  Similarity=0.271  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHHHHhc------CCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDN------SKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~------~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +|..|...++.+...+.+      ++.+++.+|||||||++.+..+...+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~  289 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALE  289 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHh
Confidence            889999999999999876      357999999999999998877665553

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

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=97.52  E-value=0.00011  Score=60.14  Aligned_cols=34  Identities=26%  Similarity=0.438  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHH
Q psy14273         35 QSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        35 Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      |.+.++.+    .++  ..+++.||||+|||+++++|++.
T Consensus         2 Q~~~~~~~----~~~~~~~~~i~apTGsGKT~~~~~~~l~   37 (357)
T TIGR03158         2 QVATFEAL----QSKDADIIFNTAPTGAGKTLAWLTPLLH   37 (357)
T ss_pred             HHHHHHHH----HcCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            56655554    444  35889999999999999998774

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.

>TIGR01054 rgy reverse gyrase

Probab=97.52  E-value=0.00015  Score=68.21  Aligned_cols=49  Identities=16%  Similarity=0.188  Sum_probs=37.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ..+.|++.|...+..+    ..|+.+++.||||+|||+ +++|++.++...+.+
T Consensus        75 ~g~~p~~iQ~~~i~~i----l~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~g~~  123 (1171)
T TIGR01054        75 VGSEPWSIQKMWAKRV----LRGDSFAIIAPTGVGKTT-FGLAMSLFLAKKGKR  123 (1171)
T ss_pred             cCCCCcHHHHHHHHHH----hCCCeEEEECCCCCCHHH-HHHHHHHHHHhcCCe
Confidence            4567999999977754    478899999999999997 556666666544433

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.

>KOG0354|consensus

Probab=97.46  E-value=0.00017  Score=65.38  Aligned_cols=48  Identities=19%  Similarity=0.241  Sum_probs=41.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      -++..|.+|.++..   .+|  ++++|+.+|||+|||+.+..-++.|+...++
T Consensus        59 ~~~~lR~YQ~eivq---~AL--gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~  106 (746)
T KOG0354|consen   59 TNLELRNYQEELVQ---PAL--GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK  106 (746)
T ss_pred             CcccccHHHHHHhH---Hhh--cCCeEEEeecCCCccchHHHHHHHHHhcCCc
Confidence            34669999999655   466  9999999999999999999999999988766

>KOG0342|consensus

Probab=97.46  E-value=5.6e-05  Score=65.98  Aligned_cols=50  Identities=22%  Similarity=0.295  Sum_probs=40.6

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      ..+|+ ..++|...+..+    ..|+.++.-|-||||||+|+|+|++.++...+.
T Consensus        99 ~~GF~~MT~VQ~~ti~pl----l~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~  149 (543)
T KOG0342|consen   99 EMGFETMTPVQQKTIPPL----LEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKF  149 (543)
T ss_pred             hcCccchhHHHHhhcCcc----CCCccceeeeccCCCceeeehhHHHHHHHhccc
Confidence            45676 778888766653    567899999999999999999999999987543

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.44  E-value=0.00016  Score=47.55  Aligned_cols=27  Identities=30%  Similarity=0.536  Sum_probs=22.8

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +++++.+|||+|||..++..+...+..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~   27 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS   27 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc
Confidence            368999999999999999887776654

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

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

Probab=97.43  E-value=0.00024  Score=66.34  Aligned_cols=70  Identities=16%  Similarity=0.221  Sum_probs=50.1

Q ss_pred             CCchHHHhhcCCCCCCccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273          7 NEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|...--++..........|||++.+.|++.+.    +|.++..++++||||+|||+..-++ +.++..++.++
T Consensus        96 ~~~~~~~a~~~~~~~~~~~~~~F~LD~fQ~~a~~----~Ler~esVlV~ApTssGKTvVaeyA-i~~al~~~qrv  165 (1041)
T COG4581          96 DYDMVPDAESPFDLAPPAREYPFELDPFQQEAIA----ILERGESVLVCAPTSSGKTVVAEYA-IALALRDGQRV  165 (1041)
T ss_pred             hhcccchhhcccccCcHHHhCCCCcCHHHHHHHH----HHhCCCcEEEEccCCCCcchHHHHH-HHHHHHcCCce
Confidence            3333333343333555666799999999999655    5689999999999999999988777 45555555555

>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=97.43  E-value=0.00026  Score=55.12  Aligned_cols=42  Identities=24%  Similarity=0.398  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ..|..+++.+.    +...+++.||.|||||+-.++.++..+....
T Consensus         7 ~~Q~~~~~al~----~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~   48 (205)
T PF02562_consen    7 EEQKFALDALL----NNDLVIVNGPAGTGKTFLALAAALELVKEGE   48 (205)
T ss_dssp             HHHHHHHHHHH----H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHH----hCCeEEEECCCCCcHHHHHHHHHHHHHHhCC
Confidence            78999988875    6779999999999999999999999887743

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

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=97.41  E-value=0.00022  Score=64.91  Aligned_cols=38  Identities=26%  Similarity=0.347  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..+..|.+++.+++.+|+.||||||||.+|..+++...
T Consensus         8 ~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~   45 (812)
T PRK11664          8 AVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHG   45 (812)
T ss_pred             HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcC
Confidence            35668888899999999999999999999998887643

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=97.40  E-value=0.00014  Score=58.25  Aligned_cols=25  Identities=28%  Similarity=0.339  Sum_probs=22.0

Q ss_pred             EEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         52 GIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        52 ~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +|+.||||+|||++++.+++..+..
T Consensus         2 vvi~apTGsGKT~~~~~~~l~~~~~   26 (358)
T TIGR01587         2 LVIEAPTGYGKTEAALLWALHSIKS   26 (358)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhh
Confidence            7899999999999999999876643

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>PRK13766 Hef nuclease; Provisional

Probab=97.40  E-value=0.00025  Score=62.78  Aligned_cols=50  Identities=20%  Similarity=0.149  Sum_probs=37.7

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +-.+++|+.|.++...+   +..  ++++.+|||+|||+.+++++...+...+.+
T Consensus        11 ~~~~~~r~yQ~~~~~~~---l~~--n~lv~~ptG~GKT~~a~~~i~~~l~~~~~~   60 (773)
T PRK13766         11 PNTIEARLYQQLLAATA---LKK--NTLVVLPTGLGKTAIALLVIAERLHKKGGK   60 (773)
T ss_pred             cCcCCccHHHHHHHHHH---hcC--CeEEEcCCCccHHHHHHHHHHHHHHhCCCe
Confidence            34577999999977654   433  799999999999999998877776433333

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=97.37  E-value=0.00021  Score=64.94  Aligned_cols=41  Identities=20%  Similarity=0.263  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ||.|.+++..+  .+.+|  .|++++||+|||+++++|++..+..
T Consensus        70 rpydVQlig~l--~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~  110 (762)
T TIGR03714        70 FPYDVQVLGAI--VLHQG--NIAEMKTGEGKTLTATMPLYLNALT  110 (762)
T ss_pred             CccHHHHHHHH--HhcCC--ceeEecCCcchHHHHHHHHHHHhhc
Confidence            44444455544  23334  6999999999999999997654443

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=97.35  E-value=0.00045  Score=62.55  Aligned_cols=45  Identities=22%  Similarity=0.287  Sum_probs=34.3

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al   71 (115)
                      .+.+.+.+||.|.+.++.   ++.++  ..+|+.+|||+|||+..+..+.
T Consensus       249 ~L~~~~~LRpYQ~eAl~~---~~~~gr~r~GIIvLPtGaGKTlvai~aa~  295 (732)
T TIGR00603       249 DLKPTTQIRPYQEKSLSK---MFGNGRARSGIIVLPCGAGKSLVGVTAAC  295 (732)
T ss_pred             ccccCCCcCHHHHHHHHH---HHhcCCCCCcEEEeCCCCChHHHHHHHHH
Confidence            334457799999996654   45555  4799999999999999886643

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).

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

Probab=97.35  E-value=0.00021  Score=52.13  Aligned_cols=38  Identities=24%  Similarity=0.434  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +.|.+.+   ..++.+....+|.||.|||||.++ +.++..+
T Consensus         4 ~~Q~~Ai---~~~~~~~~~~~i~GpPGTGKT~~l-~~~i~~~   41 (236)
T PF13086_consen    4 ESQREAI---QSALSSNGITLIQGPPGTGKTTTL-ASIIAQL   41 (236)
T ss_dssp             HHHHHHH---HHHCTSSE-EEEE-STTSSHHHHH-HHHHHHH
T ss_pred             HHHHHHH---HHHHcCCCCEEEECCCCCChHHHH-HHHHHHh
Confidence            5777754   445555555999999999999544 4445444

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=97.33  E-value=0.00032  Score=62.84  Aligned_cols=48  Identities=21%  Similarity=0.054  Sum_probs=38.4

Q ss_pred             ccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        23 ~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ....++..||++|......+    .+|.  |.+|.||+|||+++++|++..+..
T Consensus        96 ~~R~lg~~p~~VQ~~~~~~l----l~G~--Iae~~TGeGKTla~~lp~~~~al~  143 (656)
T PRK12898         96 SGRVLGQRHFDVQLMGGLAL----LSGR--LAEMQTGEGKTLTATLPAGTAALA  143 (656)
T ss_pred             HHHHhCCCCChHHHHHHHHH----hCCC--eeeeeCCCCcHHHHHHHHHHHhhc
Confidence            34456788999999977765    3555  899999999999999998876643

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.29  E-value=0.00061  Score=53.54  Aligned_cols=38  Identities=18%  Similarity=0.141  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHH
Q psy14273         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L   67 (115)
                      -..+.+.++.+.+..++..+.+++++||+|||||....
T Consensus         2 ~~t~~~~~l~~~~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640         2 IETDAVKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            35678889999999999999999999999999997644

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).

>PF13245 AAA_19: Part of AAA domain

Probab=97.27  E-value=0.00045  Score=45.57  Aligned_cols=35  Identities=26%  Similarity=0.398  Sum_probs=25.5

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .|..++..+..+++.||.|||||..++--+..++.
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~   36 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLA   36 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHH
Confidence            35556764566778999999999877666666553

>KOG0334|consensus

Probab=97.26  E-value=0.00015  Score=67.27  Aligned_cols=48  Identities=19%  Similarity=0.301  Sum_probs=41.4

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      -.+.|. |+++|.+++..|    ..|..+|..|-||+|||++|++|.+.....
T Consensus       381 kkl~y~k~~~IQ~qAiP~I----msGrdvIgvakTgSGKT~af~LPmirhi~d  429 (997)
T KOG0334|consen  381 KKLGYEKPTPIQAQAIPAI----MSGRDVIGVAKTGSGKTLAFLLPMIRHIKD  429 (997)
T ss_pred             HHhcCCCCcchhhhhcchh----ccCcceEEeeccCCccchhhhcchhhhhhc
Confidence            457788 999999999976    689999999999999999999998854443

>KOG0340|consensus

Probab=97.26  E-value=0.0002  Score=61.00  Aligned_cols=49  Identities=20%  Similarity=0.159  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|.|+|..++..|    .+|..||-+|-||||||.+|-+|.+.-+.+.+.-+
T Consensus        28 ~~pTpiQ~~cIpkI----LeGrdcig~AkTGsGKT~AFaLPil~rLsedP~gi   76 (442)
T KOG0340|consen   28 KKPTPIQQACIPKI----LEGRDCIGCAKTGSGKTAAFALPILNRLSEDPYGI   76 (442)
T ss_pred             CCCCchHhhhhHHH----hcccccccccccCCCcchhhhHHHHHhhccCCCcc
Confidence            34899999999986    58999999999999999999999999888776554

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=97.25  E-value=0.00044  Score=63.12  Aligned_cols=38  Identities=24%  Similarity=0.297  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+...|.+++.++..+|+.||||||||..+..+++...
T Consensus         5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~   42 (819)
T TIGR01970         5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAP   42 (819)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhh
Confidence            35567888899999999999999999999999988654

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.

>KOG0952|consensus

Probab=97.17  E-value=0.00041  Score=65.08  Aligned_cols=53  Identities=26%  Similarity=0.329  Sum_probs=44.1

Q ss_pred             CCccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         21 VPSEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        21 ~~~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+.+-+|+|. .-..|.+..+.++   ..+.+++|+||||+|||.-+++.+|..+..
T Consensus       100 ~~rk~~f~f~~fN~iQS~vFp~aY---~SneNMLIcAPTGsGKT~la~L~ILr~ik~  153 (1230)
T KOG0952|consen  100 VGRKGFFSFEEFNRIQSEVFPVAY---KSNENMLICAPTGSGKTVLAELCILRTIKE  153 (1230)
T ss_pred             hhhhhcccHHHHHHHHHHhhhhhh---cCCCCEEEECCCCCCchHHHHHHHHHHHHh
Confidence            3345678888 5689999888654   678899999999999999999999988876

>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=97.08  E-value=0.0011  Score=43.95  Aligned_cols=32  Identities=28%  Similarity=0.288  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHhc--CCcEEEecCCCCCchHH
Q psy14273         34 IQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls   65 (115)
                      .|...+..+...+..  +.++++.||+|+|||..
T Consensus         2 ~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l   35 (151)
T cd00009           2 GQEEAIEALREALELPPPKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             chHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHH
Confidence            355667777777776  67899999999999953

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.

>KOG0352|consensus

Probab=97.08  E-value=0.00062  Score=59.59  Aligned_cols=45  Identities=22%  Similarity=0.203  Sum_probs=35.7

Q ss_pred             cccCCCC--CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHH
Q psy14273         24 EFPFPFD--AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        24 ~~~fpf~--~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      +-.|+|.  -.+-|.+   ++.-++..++.+.+++|||+||||+|-+|+|
T Consensus        12 KK~FGh~kFKs~LQE~---A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL   58 (641)
T KOG0352|consen   12 KKLFGHKKFKSRLQEQ---AINCIVKRKCDVYVSMPTGAGKSLCYQLPAL   58 (641)
T ss_pred             HHHhCchhhcChHHHH---HHHHHHhccCcEEEeccCCCchhhhhhchHH
Confidence            4457777  4488888   4445567788999999999999999998875

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=97.05  E-value=0.00091  Score=61.08  Aligned_cols=44  Identities=25%  Similarity=0.213  Sum_probs=32.3

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .++..||++|.-..-.    +.+|.  |.||.||+|||+++++|++..+.
T Consensus        74 ~~g~~p~~vQl~~~~~----l~~G~--Iaem~TGeGKTL~a~lp~~l~al  117 (790)
T PRK09200         74 VLGMRPYDVQLIGALV----LHEGN--IAEMQTGEGKTLTATMPLYLNAL  117 (790)
T ss_pred             HhCCCCchHHHHhHHH----HcCCc--eeeecCCCcchHHHHHHHHHHHH
Confidence            4566688888765433    33454  99999999999999999874443

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

Probab=97.02  E-value=0.001  Score=61.18  Aligned_cols=47  Identities=17%  Similarity=0.147  Sum_probs=40.1

Q ss_pred             CCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +|..|...++.|.+++.+| ..+++.|.||||||.+++.-+-..++..
T Consensus       166 ~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~~  213 (875)
T COG4096         166 PRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKSG  213 (875)
T ss_pred             chHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhcc
Confidence            8999999999999999988 4599999999999999877655555444

>KOG0333|consensus

Probab=97.01  E-value=0.0005  Score=61.03  Aligned_cols=48  Identities=21%  Similarity=0.219  Sum_probs=41.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ..|. |.|+|+..+..    ..+...+|.-|-||||||+++++|++.|+...+
T Consensus       263 ~~y~eptpIqR~aipl----~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP  311 (673)
T KOG0333|consen  263 PGYKEPTPIQRQAIPL----GLQNRDPIGVAETGSGKTAAFLIPLLIWISSLP  311 (673)
T ss_pred             cCCCCCchHHHhhccc----hhccCCeeeEEeccCCccccchhhHHHHHHcCC
Confidence            4566 89999998884    457778888999999999999999999998877

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

Probab=96.93  E-value=0.0013  Score=49.41  Aligned_cols=48  Identities=19%  Similarity=0.160  Sum_probs=24.5

Q ss_pred             HHHHHHHHHH--HHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNL--YYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I--~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+...+..+  ..++.++..+++.||+|+|||.-+.+-+-..+. ++..+
T Consensus        29 ~~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~-~g~~v   78 (178)
T PF01695_consen   29 GIDKAQIAQLAALEFIENGENLILYGPPGTGKTHLAVAIANEAIR-KGYSV   78 (178)
T ss_dssp             -----HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHHHHHHHH-TT--E
T ss_pred             hHHHHHHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHHHHHhcc-CCcce
Confidence            3334444433  334566788999999999999765555444444 55554

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.

>KOG0343|consensus

Probab=96.86  E-value=0.00042  Score=61.90  Aligned_cols=43  Identities=19%  Similarity=0.187  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +.++|.+.|...    ..|..++--|-||||||||||+|+|..+...
T Consensus        92 ~teiQ~~~Ip~a----L~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~  134 (758)
T KOG0343|consen   92 MTEIQRDTIPMA----LQGHDVLGAAKTGSGKTLAFLVPVLEALYRL  134 (758)
T ss_pred             HHHHHHhhcchh----ccCcccccccccCCCceeeehHHHHHHHHHc
Confidence            557777765542    3678899999999999999999999877654

>PHA02244 ATPase-like protein

Probab=96.85  E-value=0.004  Score=52.87  Aligned_cols=43  Identities=9%  Similarity=-0.028  Sum_probs=33.0

Q ss_pred             ccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         23 SEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        23 ~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      ..+.++|. .-+.+......+.+++..+..++|.||||||||..
T Consensus        92 ~~~d~~~ig~sp~~~~~~~ri~r~l~~~~PVLL~GppGtGKTtL  135 (383)
T PHA02244         92 SGIDTTKIASNPTFHYETADIAKIVNANIPVFLKGGAGSGKNHI  135 (383)
T ss_pred             hhCCCcccCCCHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHH
Confidence            44556665 44555555667789999999999999999999954

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=96.82  E-value=0.0014  Score=59.65  Aligned_cols=45  Identities=24%  Similarity=0.205  Sum_probs=32.4

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHH-HHHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL-KWYS   75 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al-~~l~   75 (115)
                      ..++..||+.|.-..-.    +..|.  |.+++||+|||+++++|++ ..+.
T Consensus        51 R~lg~~p~~vQlig~~~----l~~G~--Iaem~TGeGKTLva~lpa~l~aL~   96 (745)
T TIGR00963        51 RVLGMRPFDVQLIGGIA----LHKGK--IAEMKTGEGKTLTATLPAYLNALT   96 (745)
T ss_pred             HHhCCCccchHHhhhhh----hcCCc--eeeecCCCccHHHHHHHHHHHHHh
Confidence            34566788888765443    33443  8999999999999999984 4443

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.81  E-value=0.0019  Score=53.13  Aligned_cols=40  Identities=20%  Similarity=0.074  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         36 SNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        36 ~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..+...+..++..+.+++|.||||||||.. |-+.+.++..
T Consensus       147 ~~~~~~L~~~v~~~~nili~G~tgSGKTTl-l~aL~~~ip~  186 (332)
T PRK13900        147 KKIKEFLEHAVISKKNIIISGGTSTGKTTF-TNAALREIPA  186 (332)
T ss_pred             HHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHhhCCC
Confidence            345566777888899999999999999964 4555666644

>PRK10536 hypothetical protein; Provisional

Probab=96.79  E-value=0.0033  Score=50.93  Aligned_cols=42  Identities=14%  Similarity=0.228  Sum_probs=32.7

Q ss_pred             CC-HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AY-DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r-~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      |+ ..|..++..+    .++..+++.||+|||||+-.++.++..+..
T Consensus        59 p~n~~Q~~~l~al----~~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         59 ARNEAQAHYLKAI----ESKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             CCCHHHHHHHHHH----hcCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            44 7788877754    557799999999999999888887765533

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.76  E-value=0.0021  Score=50.60  Aligned_cols=36  Identities=19%  Similarity=0.328  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L~~   69 (115)
                      +|.+..+.+.+++.++.  +++|.||+|||||..+..-
T Consensus        19 g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~   56 (337)
T PRK12402         19 GQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRAL   56 (337)
T ss_pred             CCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHH
Confidence            56778888888888876  8999999999999765443

>KOG0989|consensus

Probab=96.76  E-value=0.0026  Score=53.30  Aligned_cols=46  Identities=24%  Similarity=0.255  Sum_probs=37.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      |+---+|......+.+++...  .+.+|.||.|||||.++++-+-+..
T Consensus        35 ~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~   82 (346)
T KOG0989|consen   35 FDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALN   82 (346)
T ss_pred             HHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhc
Confidence            445578999999999999773  7899999999999999887765544

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

Probab=96.75  E-value=0.0031  Score=58.86  Aligned_cols=54  Identities=11%  Similarity=0.061  Sum_probs=41.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhc----------------------------------CCcEEEecCCCCCchHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDN----------------------------------SKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~----------------------------------~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      |-|+--|.|.+++.+|..++..                                  ...+.|+|+||||||.+||..++.
T Consensus         3 ~~~e~l~hQ~~av~ai~~~F~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~~~~~~~n~~~~M~TGtGKT~~~~~~i~~   82 (986)
T PRK15483          3 ILLEELPHQEQALAAILAAFTGIDIASADPNHYANPLIKLRYENGIPGRSRTRIDDKANIDIKMETGTGKTYVYTRLMYE   82 (986)
T ss_pred             cccccChhHHHHHHHHHHHhcCCCccCCccccccCcccccchhhccccccccccCccceEEEEeCCCCCHHHHHHHHHHH
Confidence            3455458888888888877742                                  136789999999999999999888


Q ss_pred             HHHhhhhh
Q psy14273         73 WYSDHKIA   80 (115)
Q Consensus        73 ~l~~~~~~   80 (115)
                      ....++..
T Consensus        83 l~~~~~~~   90 (986)
T PRK15483         83 LHQKYGLF   90 (986)
T ss_pred             HHHHcCCc
Confidence            87776544

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.75  E-value=0.0032  Score=51.89  Aligned_cols=51  Identities=20%  Similarity=0.173  Sum_probs=32.4

Q ss_pred             CCCHHHHHHHHHHHHHHh----cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         30 DAYDIQSNFMKNLYYTLD----NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~----~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .||..+..++..+...+.    .+..++|.||||+|||.-..+- ...+...+..|
T Consensus       160 ~~~~~~~~~~~~~~~f~~~f~~~~~~Lll~G~~GtGKThLa~aI-a~~l~~~g~~V  214 (329)
T PRK06835        160 SPRKNMEKILEKCKNFIENFDKNNENLLFYGNTGTGKTFLSNCI-AKELLDRGKSV  214 (329)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHH-HHHHHHCCCeE
Confidence            355666666665555555    4578999999999999744443 33344444444

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=96.74  E-value=0.0026  Score=57.14  Aligned_cols=47  Identities=21%  Similarity=0.342  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .++.|...++.+.+--..+..++++||||.|||.+.+.+++.-+...
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~  242 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK  242 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc
Confidence            57888888877665544444899999999999999999998888773

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.72  E-value=0.0029  Score=51.91  Aligned_cols=34  Identities=18%  Similarity=0.284  Sum_probs=25.8

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +.+..++..+.++++.||||+||| +++-+++.++
T Consensus       139 ~~L~~~v~~~~~ilI~G~tGSGKT-Tll~aL~~~~  172 (319)
T PRK13894        139 EAIIAAVRAHRNILVIGGTGSGKT-TLVNAIINEM  172 (319)
T ss_pred             HHHHHHHHcCCeEEEECCCCCCHH-HHHHHHHHhh
Confidence            345567778899999999999999 5555555554

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.66  E-value=0.0037  Score=50.56  Aligned_cols=37  Identities=19%  Similarity=0.082  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        39 m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ...+..++..++.+++.||||+|||.. +-+++.++..
T Consensus       122 ~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~al~~~i~~  158 (299)
T TIGR02782       122 RDVLREAVLARKNILVVGGTGSGKTTL-ANALLAEIAK  158 (299)
T ss_pred             HHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHhhc
Confidence            345666777888999999999999964 3444555543

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.

>KOG0351|consensus

Probab=96.65  E-value=0.00074  Score=62.66  Aligned_cols=47  Identities=23%  Similarity=0.083  Sum_probs=39.2

Q ss_pred             ccccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         23 SEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        23 ~~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ....|.+. .|+.|.+++.    +...|+.+++.+|||.||+|+|-+||+-+
T Consensus       256 l~~~Fg~~~FR~~Q~eaI~----~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~  303 (941)
T KOG0351|consen  256 LKEVFGHKGFRPNQLEAIN----ATLSGKDCFVLMPTGGGKSLCYQLPALLL  303 (941)
T ss_pred             HHHHhccccCChhHHHHHH----HHHcCCceEEEeecCCceeeEeecccccc
Confidence            45578888 8999999665    45689999999999999999999987643

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.64  E-value=0.0037  Score=51.57  Aligned_cols=34  Identities=15%  Similarity=0.160  Sum_probs=25.5

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +.+..++..+.++||.||||||||.. |-+.+.++
T Consensus       135 ~~L~~~v~~~~nilI~G~tGSGKTTl-l~aL~~~i  168 (323)
T PRK13833        135 SVIRSAIDSRLNIVISGGTGSGKTTL-ANAVIAEI  168 (323)
T ss_pred             HHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHH
Confidence            34556778889999999999999964 34455555

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

Probab=96.63  E-value=0.0023  Score=55.94  Aligned_cols=48  Identities=17%  Similarity=0.203  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHHHHHhc-CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhhH
Q psy14273         31 AYDIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYSDHKIAGL   82 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~-~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~   82 (115)
                      ..+.|...+..   .+.. .+.+++.||||||||.+ |.+++.++.....++.
T Consensus       242 ~~~~~~~~~~~---~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~~~nI~  290 (500)
T COG2804         242 MSPFQLARLLR---LLNRPQGLILVTGPTGSGKTTT-LYAALSELNTPERNII  290 (500)
T ss_pred             CCHHHHHHHHH---HHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCCCceEE
Confidence            34666654443   3333 36788999999999987 5566888887777653

>KOG0336|consensus

Probab=96.62  E-value=0.0004  Score=60.49  Aligned_cols=49  Identities=24%  Similarity=0.114  Sum_probs=36.6

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +|. |.|.|.++-..    +.+|..++.-|.||+||||+||.|.+..+......
T Consensus       239 GFqKPtPIqSQaWPI----~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~  288 (629)
T KOG0336|consen  239 GFQKPTPIQSQAWPI----LLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKR  288 (629)
T ss_pred             cCCCCCcchhcccce----eecCcceEEEEecCCCcCHHHhccceeeeeccchh
Confidence            444 66666665443    45788899999999999999999988777665443

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

Probab=96.61  E-value=0.0047  Score=46.65  Aligned_cols=46  Identities=15%  Similarity=0.285  Sum_probs=31.8

Q ss_pred             CHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         32 YDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -+.|.++++.+   +.++ +..++.||.|||||.+ |..+...+...+.+|
T Consensus         3 ~~~Q~~a~~~~---l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~g~~v   49 (196)
T PF13604_consen    3 NEEQREAVRAI---LTSGDRVSVLQGPAGTGKTTL-LKALAEALEAAGKRV   49 (196)
T ss_dssp             -HHHHHHHHHH---HHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHTT--E
T ss_pred             CHHHHHHHHHH---HhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhCCCeE
Confidence            37899987775   3444 6788999999999975 455666666666554

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=96.48  E-value=0.0024  Score=52.84  Aligned_cols=42  Identities=31%  Similarity=0.351  Sum_probs=33.2

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHH-hcC-CcEEEecCCCCCchHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTL-DNS-KFGIFESPTGTGKSLS   65 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l-~~~-~~~iiEaPTGtGKTls   65 (115)
                      +.+|||...-+|.+..+.+.-++ ..+ .+++++||.|+|||..
T Consensus         2 ~~~~~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~l   45 (334)
T PRK13407          2 KKPFPFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTA   45 (334)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHH
Confidence            46778886678999988777544 355 7999999999999954

>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=96.45  E-value=0.0046  Score=47.28  Aligned_cols=39  Identities=18%  Similarity=0.250  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +.|.++++.      .++.++|.|+.|||||.+++.=++..+...
T Consensus         3 ~eQ~~~i~~------~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~   41 (315)
T PF00580_consen    3 DEQRRIIRS------TEGPLLVNAGAGSGKTTTLLERIAYLLYEG   41 (315)
T ss_dssp             HHHHHHHHS-------SSEEEEEE-TTSSHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHhC------CCCCEEEEeCCCCCchHHHHHHHHHhhccc
Confidence            567776552      467899999999999998877766666554

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 ....

>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=96.43  E-value=0.0035  Score=48.65  Aligned_cols=41  Identities=20%  Similarity=0.204  Sum_probs=29.3

Q ss_pred             HHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        39 m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+.+..++..++.++|.||||||||..+ ..++.++.....+
T Consensus       117 ~~~l~~~v~~~~~ili~G~tGSGKTT~l-~all~~i~~~~~~  157 (270)
T PF00437_consen  117 AEFLRSAVRGRGNILISGPTGSGKTTLL-NALLEEIPPEDER  157 (270)
T ss_dssp             HHHHHHCHHTTEEEEEEESTTSSHHHHH-HHHHHHCHTTTSE
T ss_pred             HHHHhhccccceEEEEECCCccccchHH-HHHhhhccccccc
Confidence            3344455567889999999999999654 6667777666333

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 ....

>PRK08181 transposase; Validated

Probab=96.42  E-value=0.013  Score=47.14  Aligned_cols=48  Identities=15%  Similarity=-0.103  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|...+..+.+++..+.+++|.||+|+|||.-+.+- ...+...+..+
T Consensus        90 ~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa~Ai-a~~a~~~g~~v  137 (269)
T PRK08181         90 KAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLAAAI-GLALIENGWRV  137 (269)
T ss_pred             HHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHHHHH-HHHHHHcCCce
Confidence            5666666666578888899999999999999543322 22333444443

>PLN03025 replication factor C subunit; Provisional

Probab=96.38  E-value=0.0049  Score=49.50  Aligned_cols=36  Identities=22%  Similarity=0.272  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      +|.+.+..+..++.++  .+++|.||.|+|||..+.+-
T Consensus        17 g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~l   54 (319)
T PLN03025         17 GNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILAL   54 (319)
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHH
Confidence            5677777887777765  57999999999999765554

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.37  E-value=0.0035  Score=40.80  Aligned_cols=21  Identities=19%  Similarity=0.251  Sum_probs=16.7

Q ss_pred             CCcEEEecCCCCCchHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~   69 (115)
                      +.+++|.||+|||||.....-
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l   22 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARAL   22 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHH
Confidence            467899999999999765443

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.36  E-value=0.003  Score=55.19  Aligned_cols=34  Identities=18%  Similarity=0.108  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~   66 (115)
                      -+|.+.++.+..++..+.+++++||+|||||+.+
T Consensus        23 ~gre~vI~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         23 YERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             cCcHHHHHHHHHHHccCCCEEEECCCChhHHHHH
Confidence            4677889999999999999999999999999754

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

Probab=96.26  E-value=0.0058  Score=51.27  Aligned_cols=54  Identities=17%  Similarity=0.264  Sum_probs=34.7

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhc-CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~-~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      -.|.. |.-.|..+=+.+...+.. .+.+++.||||||||.+ |++.+.|+..+...
T Consensus       100 ~Ip~~i~~~e~LglP~i~~~~~~~~~GLILVTGpTGSGKSTT-lAamId~iN~~~~~  155 (353)
T COG2805         100 LIPSKIPTLEELGLPPIVRELAESPRGLILVTGPTGSGKSTT-LAAMIDYINKHKAK  155 (353)
T ss_pred             ccCccCCCHHHcCCCHHHHHHHhCCCceEEEeCCCCCcHHHH-HHHHHHHHhccCCc
Confidence            34544 444454444444443333 36788999999999976 56678888776544

>KOG0326|consensus

Probab=96.20  E-value=0.00035  Score=59.23  Aligned_cols=52  Identities=17%  Similarity=0.095  Sum_probs=43.6

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .-+|+ |.|.|.+.+..+    ..|+.++.-|-+|||||.||++|.|.-+......+
T Consensus       102 e~G~ekPSPiQeesIPia----LtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~I  154 (459)
T KOG0326|consen  102 EKGFEKPSPIQEESIPIA----LTGRDILARAKNGTGKTAAYCIPVLEKIDPKKNVI  154 (459)
T ss_pred             HhccCCCCCcccccccee----ecchhhhhhccCCCCCccceechhhhhcCccccce
Confidence            44677 889999977753    47889999999999999999999999988776664

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

Probab=96.20  E-value=0.007  Score=44.95  Aligned_cols=30  Identities=23%  Similarity=0.449  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.|.++   +..++..+..++|.||||+|||..
T Consensus        12 ~~~~~~---l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130          12 PLQAAY---LWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             HHHHHH---HHHHHhCCCEEEEECCCCCCHHHH
Confidence            455554   445678899999999999999964

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.

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.18  E-value=0.0058  Score=56.68  Aligned_cols=45  Identities=22%  Similarity=0.237  Sum_probs=30.7

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..+..||++|.-  -.+  +|.+|  -|.+|+||+|||+++++|++..+..
T Consensus        78 ~lg~~~ydvQli--Gg~--~Lh~G--~Iaem~TGeGKTL~a~Lpa~~~al~  122 (896)
T PRK13104         78 TLGLRHFDVQLI--GGM--VLHEG--NIAEMRTGEGKTLVATLPAYLNAIS  122 (896)
T ss_pred             HcCCCcchHHHh--hhh--hhccC--ccccccCCCCchHHHHHHHHHHHhc
Confidence            345557777654  222  23333  4679999999999999998865543

>KOG0327|consensus

Probab=96.16  E-value=0.0035  Score=53.37  Aligned_cols=49  Identities=20%  Similarity=0.348  Sum_probs=40.0

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +.|+|+ |..+|...+--   ++ .|.++++.+++|||||.+++++++.-+.-.
T Consensus        42 y~yGFekPSaIQqraI~p---~i-~G~dv~~qaqsgTgKt~af~i~iLq~iD~~   91 (397)
T KOG0327|consen   42 YAYGFEKPSAIQQRAILP---CI-KGHDVIAQAQSGTGKTAAFLISILQQIDMS   91 (397)
T ss_pred             HhhccCCchHHHhccccc---cc-cCCceeEeeeccccchhhhHHHHHhhcCcc
Confidence            468899 99999885443   33 678999999999999999999999886443

>KOG0337|consensus

Probab=96.16  E-value=0.0025  Score=55.42  Aligned_cols=47  Identities=17%  Similarity=0.243  Sum_probs=40.1

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .|. |.|+|+.-|..|    .++..++--|-||+|||.||++|+++.+..+.
T Consensus        40 g~~~ptpiqRKTipli----Le~~dvv~martgsgktaaf~ipm~e~Lk~~s   87 (529)
T KOG0337|consen   40 GFNTPTPIQRKTIPLI----LEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS   87 (529)
T ss_pred             hcCCCCchhcccccce----eeccccceeeecCCcchhhHHHHHHHHHhhcc
Confidence            355 778888877754    57788899999999999999999999998877

>PRK10436 hypothetical protein; Provisional

Probab=96.15  E-value=0.0075  Score=51.92  Aligned_cols=33  Identities=24%  Similarity=0.381  Sum_probs=25.4

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .++.+++.||||||||.++ .+++.++.....++
T Consensus       217 ~~GliLvtGpTGSGKTTtL-~a~l~~~~~~~~~i  249 (462)
T PRK10436        217 PQGLILVTGPTGSGKTVTL-YSALQTLNTAQINI  249 (462)
T ss_pred             cCCeEEEECCCCCChHHHH-HHHHHhhCCCCCEE
Confidence            4578999999999999876 55677776555554

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=96.15  E-value=0.006  Score=49.17  Aligned_cols=42  Identities=19%  Similarity=0.225  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      -++.+.+..+..++..+.+++++||+|+|||+  |+-.++....
T Consensus        27 ~g~~~~~~~~l~a~~~~~~vll~G~PG~gKT~--la~~lA~~l~   68 (329)
T COG0714          27 VGDEEVIELALLALLAGGHVLLEGPPGVGKTL--LARALARALG   68 (329)
T ss_pred             eccHHHHHHHHHHHHcCCCEEEECCCCccHHH--HHHHHHHHhC
Confidence            33888888999999999999999999999995  3444444433

>PRK06526 transposase; Provisional

Probab=96.07  E-value=0.013  Score=46.39  Aligned_cols=37  Identities=19%  Similarity=0.111  Sum_probs=25.5

Q ss_pred             HHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        44 ~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .++..+.++++.||+|+|||....+-+.. +...+.++
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa~al~~~-a~~~g~~v  129 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLAIGLGIR-ACQAGHRV  129 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHHHHHHHH-HHHCCCch
Confidence            46677789999999999999755444333 33344454

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

Probab=96.02  E-value=0.024  Score=44.85  Aligned_cols=47  Identities=15%  Similarity=0.065  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         34 IQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+.........++.++..++|.||+|+|||.-+.+-+...+ ..+..|
T Consensus        90 ~~l~~~~~~~~~~~~~~nl~l~G~~G~GKThLa~Ai~~~l~-~~g~sv  136 (254)
T COG1484          90 KALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELL-KAGISV  136 (254)
T ss_pred             HHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHH-HcCCeE
Confidence            33334444455677788999999999999965444444444 444444

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=96.02  E-value=0.0034  Score=60.75  Aligned_cols=23  Identities=30%  Similarity=0.384  Sum_probs=20.4

Q ss_pred             EecCCCCCchHHHHHHHHHHHHh
Q psy14273         54 FESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        54 iEaPTGtGKTls~L~~al~~l~~   76 (115)
                      |.||||||||++|++|+|.-+..
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~   23 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFR   23 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHh
Confidence            47999999999999999987764

>KOG0991|consensus

Probab=96.01  E-value=0.014  Score=48.04  Aligned_cols=40  Identities=23%  Similarity=0.346  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         36 SNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        36 ~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .+.++.+.-...+|  +++|+.||.|+|||.|.+|-|-..+=
T Consensus        33 e~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG   74 (333)
T KOG0991|consen   33 EDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLG   74 (333)
T ss_pred             HHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhC
Confidence            35566666556666  78999999999999999998877664

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.01  E-value=0.0098  Score=51.99  Aligned_cols=46  Identities=20%  Similarity=0.266  Sum_probs=30.2

Q ss_pred             CHHHHHHHHHHHHHHh-cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         32 YDIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~-~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+.|.+.+.   +.+. .++.+++.||||||||.++ .+++.++.....++
T Consensus       301 ~~~~~~~l~---~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~~~~~~i  347 (564)
T TIGR02538       301 EPDQKALFL---EAIHKPQGMVLVTGPTGSGKTVSL-YTALNILNTEEVNI  347 (564)
T ss_pred             CHHHHHHHH---HHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhCCCCceE
Confidence            355555443   3343 4578899999999999875 56677775444444

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.

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=96.00  E-value=0.0059  Score=56.67  Aligned_cols=44  Identities=25%  Similarity=0.240  Sum_probs=30.7

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .+...||++|.-  -.+  +|  +.--|.|++||.||||++.+|++..+.
T Consensus        78 ~lgm~~ydVQli--Ggl--~L--~~G~IaEm~TGEGKTL~a~lp~~l~al  121 (908)
T PRK13107         78 VFEMRHFDVQLL--GGM--VL--DSNRIAEMRTGEGKTLTATLPAYLNAL  121 (908)
T ss_pred             HhCCCcCchHHh--cch--Hh--cCCccccccCCCCchHHHHHHHHHHHh
Confidence            456667788763  222  12  233577999999999999999875554

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

Probab=95.95  E-value=0.011  Score=46.86  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHh-cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~-~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|.+.+   .+.+. .+..++|.||||+|||..+ ..++.++.....++
T Consensus        66 ~~~~~~l---~~~~~~~~GlilisG~tGSGKTT~l-~all~~i~~~~~~i  111 (264)
T cd01129          66 PENLEIF---RKLLEKPHGIILVTGPTGSGKTTTL-YSALSELNTPEKNI  111 (264)
T ss_pred             HHHHHHH---HHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhhCCCCCeE
Confidence            4555544   34444 3467999999999999764 44566665433333

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.

>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=95.87  E-value=0.013  Score=46.74  Aligned_cols=35  Identities=23%  Similarity=0.215  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      |...-..+...+...+.++..+++.||+|||||..
T Consensus        15 pT~dt~r~~~ll~~l~~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   15 PTVDTVRYSYLLDLLLSNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             --HHHHHHHHHHHHHHHCTEEEEEESSTTSSHHHH
T ss_pred             CcHHHHHHHHHHHHHHHcCCcEEEECCCCCchhHH
Confidence            55555555666667788899999999999999975

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=95.85  E-value=0.014  Score=45.54  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      -+|.+.++.+..++..+  .+++|.||.|+|||..+.+
T Consensus        20 ~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~   57 (319)
T PRK00440         20 VGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALA   57 (319)
T ss_pred             cCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHH
Confidence            36778888998888776  4689999999999976544

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=95.84  E-value=0.011  Score=49.17  Aligned_cols=38  Identities=16%  Similarity=0.101  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +...+..++..+++++|.||||||||.. +-+++.++..
T Consensus       151 ~~~~l~~~v~~~~nilI~G~tGSGKTTl-l~aLl~~i~~  188 (344)
T PRK13851        151 LEAFLHACVVGRLTMLLCGPTGSGKTTM-SKTLISAIPP  188 (344)
T ss_pred             HHHHHHHHHHcCCeEEEECCCCccHHHH-HHHHHcccCC
Confidence            4456667788899999999999999954 4444555433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.82  E-value=0.013  Score=51.02  Aligned_cols=39  Identities=26%  Similarity=0.170  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~al   71 (115)
                      -+|..+++.+..++.+++   ..+|.||.|+|||.++.+-+-
T Consensus        24 iGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk   65 (507)
T PRK06645         24 QGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAK   65 (507)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            489999999999888875   688999999999977655433

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=95.78  E-value=0.0082  Score=55.30  Aligned_cols=45  Identities=22%  Similarity=0.239  Sum_probs=31.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHH-HHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL-KWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al-~~l~~   76 (115)
                      ..+..||++|.--  .+  +|.+|  -|.|+.||+|||+++.+|++ ..+..
T Consensus        77 ~lg~~~~dvQlig--~l--~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~G  122 (830)
T PRK12904         77 VLGMRHFDVQLIG--GM--VLHEG--KIAEMKTGEGKTLVATLPAYLNALTG  122 (830)
T ss_pred             HhCCCCCccHHHh--hH--HhcCC--chhhhhcCCCcHHHHHHHHHHHHHcC
Confidence            3566677777543  33  34444  48899999999999999985 55543

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.76  E-value=0.017  Score=47.10  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=30.1

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -++.++.+++.+++.||||+|||. +|-+++.++-...+-+
T Consensus       135 yL~~~ie~~~siii~G~t~sGKTt-~lnall~~Ip~~~riv  174 (312)
T COG0630         135 YLWLAIEARKSIIICGGTASGKTT-LLNALLDFIPPEERIV  174 (312)
T ss_pred             HHHHHHHcCCcEEEECCCCCCHHH-HHHHHHHhCCchhcEE
Confidence            477889999999999999999995 4555566664444433

>TIGR00376 DNA helicase, putative

Probab=95.73  E-value=0.024  Score=50.38  Aligned_cols=47  Identities=19%  Similarity=0.299  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .-+.|.+.+.   .++.+....+|.||+|||||.++..-+..++ ..+.+|
T Consensus       158 ln~~Q~~Av~---~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~-~~g~~V  204 (637)
T TIGR00376       158 LNESQKEAVS---FALSSKDLFLIHGPPGTGKTRTLVELIRQLV-KRGLRV  204 (637)
T ss_pred             CCHHHHHHHH---HHhcCCCeEEEEcCCCCCHHHHHHHHHHHHH-HcCCCE
Confidence            4688998554   4566667899999999999976655444444 334444

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.

>KOG1803|consensus

Probab=95.73  E-value=0.015  Score=52.12  Aligned_cols=55  Identities=22%  Similarity=0.244  Sum_probs=38.7

Q ss_pred             ccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        23 ~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..-+||...-+.|...+.   -++.+....++.||+|||||.++.--+.+.++ .+++|
T Consensus       178 ~~~~~~~~ln~SQk~Av~---~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk-~~k~V  232 (649)
T KOG1803|consen  178 KITFFNKNLNSSQKAAVS---FAINNKDLLIIHGPPGTGKTRTLVEIISQLVK-QKKRV  232 (649)
T ss_pred             ccccCCccccHHHHHHHH---HHhccCCceEeeCCCCCCceeeHHHHHHHHHH-cCCeE
Confidence            344677777788988544   45556678999999999999986655555554 44554

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

Probab=95.63  E-value=0.024  Score=47.41  Aligned_cols=42  Identities=19%  Similarity=0.181  Sum_probs=29.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~~a   70 (115)
                      +.-|+.|.+-+..+......+   .++++.||||||||.+.-.-+
T Consensus        19 l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~   63 (366)
T COG1474          19 LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVM   63 (366)
T ss_pred             ccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHH
Confidence            346788877655555444444   459999999999998755543

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.62  E-value=0.018  Score=47.32  Aligned_cols=37  Identities=14%  Similarity=0.071  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      -+|.+.++.+.+++..++  | .+|.||.|+|||..+.+-
T Consensus        19 iGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~l   58 (363)
T PRK14961         19 IGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLL   58 (363)
T ss_pred             cChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHH
Confidence            489999999999998873  4 489999999999765544

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.58  E-value=0.04  Score=44.85  Aligned_cols=46  Identities=15%  Similarity=0.018  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHhc------CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         34 IQSNFMKNLYYTLDN------SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~------~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+..++..+..++.+      ++.++|.||+|+|||.-+.+.+ ..+...+..
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia-~~l~~~g~~  186 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIA-NELAKKGVS  186 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHH-HHHHHcCCC
Confidence            566666666666663      3578899999999996433333 333343443

>KOG0353|consensus

Probab=95.57  E-value=0.01  Score=51.68  Aligned_cols=45  Identities=22%  Similarity=0.187  Sum_probs=35.9

Q ss_pred             cccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         24 EFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        24 ~~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      +..|-.+ .||-|...+..+    ..+..+++-.|||-||+|+|-+|+|+
T Consensus        87 k~~f~lekfrplq~~ain~~----ma~ed~~lil~tgggkslcyqlpal~  132 (695)
T KOG0353|consen   87 KEQFHLEKFRPLQLAAINAT----MAGEDAFLILPTGGGKSLCYQLPALC  132 (695)
T ss_pred             HHHhhHHhcChhHHHHhhhh----hccCceEEEEeCCCccchhhhhhHHh
Confidence            3445556 789998866653    57888999999999999999999875

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.56  E-value=0.018  Score=47.88  Aligned_cols=42  Identities=19%  Similarity=0.222  Sum_probs=33.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~a   70 (115)
                      |+---+|....+.+.+++.++  .| .||+||.|+|||..+.+-+
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a   59 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFA   59 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHH
Confidence            443348999999999999887  34 7899999999997765543

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=95.53  E-value=0.022  Score=47.88  Aligned_cols=29  Identities=24%  Similarity=0.398  Sum_probs=21.8

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..++.+++.||||||||..+ .+++.++..
T Consensus       147 ~~~GlilI~G~TGSGKTT~l-~al~~~i~~  175 (372)
T TIGR02525       147 PAAGLGLICGETGSGKSTLA-ASIYQHCGE  175 (372)
T ss_pred             hcCCEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            34578899999999999764 556676653

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).

>COG4889 Predicted helicase [General function prediction only]

Probab=95.52  E-value=0.011  Score=55.65  Aligned_cols=46  Identities=15%  Similarity=0.143  Sum_probs=39.1

Q ss_pred             ccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHH
Q psy14273         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        23 ~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~   68 (115)
                      +...-|+.|||.|...++...+.+..+..+=+-+.+|||||++.|=
T Consensus       154 l~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsLk  199 (1518)
T COG4889         154 LPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSLK  199 (1518)
T ss_pred             cccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHHH
Confidence            4455688899999999999999998887777788999999998654

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=95.51  E-value=0.029  Score=42.87  Aligned_cols=37  Identities=22%  Similarity=0.290  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHHHHHhcCC-cEEEecCCCCCchHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~-~~iiEaPTGtGKTls~L   67 (115)
                      +.+.+.+.+..+...+..+. .+++.||+|+|||...-
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            34666777777777776654 68899999999996543

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=95.50  E-value=0.021  Score=54.74  Aligned_cols=33  Identities=15%  Similarity=0.199  Sum_probs=27.1

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..|..+|.+++.+||.|+||||||.  .+|.+.+-
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~lle  105 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTT--QLPKICLE  105 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHHH
Confidence            5777888889999999999999998  46866554

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.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=95.47  E-value=0.028  Score=54.05  Aligned_cols=33  Identities=15%  Similarity=0.217  Sum_probs=26.4

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +.|..++.+++.+|+.|+||||||.  .+|.+.+.
T Consensus        80 ~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle  112 (1294)
T PRK11131         80 QDILEAIRDHQVVIVAGETGSGKTT--QLPKICLE  112 (1294)
T ss_pred             HHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHH
Confidence            3666777889999999999999998  47855554

>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=95.47  E-value=0.015  Score=45.48  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .+|.+.-+++.-+...+.++++.||.|||||+.
T Consensus         6 ~GQe~aKrAL~iAAaG~h~lLl~GppGtGKTml   38 (206)
T PF01078_consen    6 VGQEEAKRALEIAAAGGHHLLLIGPPGTGKTML   38 (206)
T ss_dssp             SSTHHHHHHHHHHHHCC--EEEES-CCCTHHHH
T ss_pred             cCcHHHHHHHHHHHcCCCCeEEECCCCCCHHHH
Confidence            467788888888888888999999999999965

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.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.40  E-value=0.028  Score=41.88  Aligned_cols=35  Identities=20%  Similarity=0.220  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~L   67 (115)
                      +.+.+.++.+.+++..  +..++|.||+|||||..+.
T Consensus        20 ~~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        20 GGNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHH
Confidence            3567788888877533  3679999999999996543

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.

>KOG0347|consensus

Probab=95.40  E-value=0.0072  Score=54.22  Aligned_cols=47  Identities=21%  Similarity=0.217  Sum_probs=36.8

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ..+|. |.++|.-.+..+   +.....++--|-|||||||||=+|++.-+.
T Consensus       198 ~~gFs~Pt~IQsl~lp~a---i~gk~DIlGaAeTGSGKTLAFGIPiv~~l~  245 (731)
T KOG0347|consen  198 NLGFSRPTEIQSLVLPAA---IRGKVDILGAAETGSGKTLAFGIPIVERLL  245 (731)
T ss_pred             hcCCCCCccchhhcccHh---hccchhcccccccCCCceeeecchhhhhhh
Confidence            35677 889998876654   444477888999999999999999998443

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

Probab=95.38  E-value=0.021  Score=50.33  Aligned_cols=48  Identities=21%  Similarity=0.061  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +++|.+|..+...   ++.  ++.++..|||-|||+.+.+-+..++..++.++
T Consensus        14 ie~R~YQ~~i~a~---al~--~NtLvvlPTGLGKT~IA~~V~~~~l~~~~~kv   61 (542)
T COG1111          14 IEPRLYQLNIAAK---ALF--KNTLVVLPTGLGKTFIAAMVIANRLRWFGGKV   61 (542)
T ss_pred             ccHHHHHHHHHHH---Hhh--cCeEEEecCCccHHHHHHHHHHHHHHhcCCeE
Confidence            5699999996554   453  47888999999999998888888998887743

>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=95.36  E-value=0.018  Score=45.86  Aligned_cols=51  Identities=14%  Similarity=0.137  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +-.|+.|.++..++.+. .++.+.|...-.|-|||. .++|+++++.+.+.++
T Consensus        22 iliR~~Q~~ia~~mi~~-~~~~n~v~QlnMGeGKTs-VI~Pmla~~LAdg~~L   72 (229)
T PF12340_consen   22 ILIRPVQVEIAREMISP-PSGKNSVMQLNMGEGKTS-VIVPMLALALADGSRL   72 (229)
T ss_pred             ceeeHHHHHHHHHHhCC-CCCCCeEeeecccCCccc-hHHHHHHHHHcCCCcE
Confidence            33899999999888753 467889999999999995 6889999998888764

There are two conserved sequence motifs: LLE and NMG.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=95.36  E-value=0.032  Score=46.23  Aligned_cols=40  Identities=28%  Similarity=0.284  Sum_probs=33.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      |||..--+|.++...+.-++-+  ..+++|+|++|+|||..+
T Consensus         1 ~pf~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~   42 (337)
T TIGR02030         1 FPFTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAV   42 (337)
T ss_pred             CCccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHH
Confidence            7888667999999887666666  578999999999999653

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=95.32  E-value=0.02  Score=49.42  Aligned_cols=45  Identities=16%  Similarity=0.155  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHhc-CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~-~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|.+.+.   +.+.. ++.+++.||||||||.++ .+++..+.....++
T Consensus       228 ~~~~~~l~---~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~~~~~~i  273 (486)
T TIGR02533       228 PELLSRFE---RLIRRPHGIILVTGPTGSGKTTTL-YAALSRLNTPERNI  273 (486)
T ss_pred             HHHHHHHH---HHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccCCCCCcE
Confidence            55555433   34443 357889999999999775 44566665444443

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.

>PRK08116 hypothetical protein; Validated

Probab=95.32  E-value=0.054  Score=43.09  Aligned_cols=51  Identities=16%  Similarity=0.074  Sum_probs=30.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhc-------CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~-------~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      |...+.|..++..+.+.+.+       +..++|.|++|||||.-+.+ +...+...+..
T Consensus        87 f~~~~~~~~a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThLa~a-ia~~l~~~~~~  144 (268)
T PRK08116         87 FLFDKGSEKAYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYLAAC-IANELIEKGVP  144 (268)
T ss_pred             ccCChHHHHHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHH-HHHHHHHcCCe
Confidence            33557777666665544442       23488999999999964332 33444433443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=95.31  E-value=0.024  Score=52.04  Aligned_cols=46  Identities=22%  Similarity=0.221  Sum_probs=32.5

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..+++.||+.|.--  .+  +|.+|.  |.|+.||.|||++..+|++..+..
T Consensus        75 R~~g~~~~dvQlig--~l--~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~  120 (796)
T PRK12906         75 RVLGLRPFDVQIIG--GI--VLHEGN--IAEMKTGEGKTLTATLPVYLNALT  120 (796)
T ss_pred             HHhCCCCchhHHHH--HH--HHhcCC--cccccCCCCCcHHHHHHHHHHHHc
Confidence            34667788888653  33  344453  889999999999988886655543

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=95.29  E-value=0.032  Score=43.77  Aligned_cols=34  Identities=18%  Similarity=0.211  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHhc-----C--CcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDN-----S--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~-----~--~~~iiEaPTGtGKTls~L   67 (115)
                      +|.+..+.+..++..     +  .+++|.||.|+|||....
T Consensus         8 G~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~   48 (305)
T TIGR00635         8 GQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAH   48 (305)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            566666667666652     2  469999999999996543

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.

>PF12846 AAA_10: AAA-like domain

Probab=95.28  E-value=0.021  Score=43.34  Aligned_cols=32  Identities=19%  Similarity=0.178  Sum_probs=22.7

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|+++-|+||+|||..+. .++..+...+..+
T Consensus         1 n~h~~i~G~tGsGKT~~~~-~l~~~~~~~g~~~   32 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK-NLLEQLIRRGPRV   32 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHcCCCE
Confidence            3689999999999998777 4444444555443

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

Probab=95.28  E-value=0.011  Score=40.22  Aligned_cols=19  Identities=21%  Similarity=0.555  Sum_probs=12.4

Q ss_pred             cCCcEEEecCCCCCchHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~   66 (115)
                      ++.++++.||+|+|||...
T Consensus         3 ~~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ----EEEEE-TTSSHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHH
Confidence            4578999999999999653

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=95.27  E-value=0.029  Score=46.72  Aligned_cols=32  Identities=22%  Similarity=0.316  Sum_probs=23.1

Q ss_pred             HHHHh-cCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         43 YYTLD-NSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        43 ~~~l~-~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .+.+. .++.++|.||||||||.++ .+++.++.
T Consensus       127 ~~~~~~~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       127 IDAIAPQEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             HHHHhccCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            33443 5688999999999999764 55566664

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.23  E-value=0.043  Score=43.50  Aligned_cols=48  Identities=19%  Similarity=0.068  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHhc---C-CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNLYYTLDN---S-KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~---~-~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|...+..+.+...+   + ..+++.||+|||||.-+.+ +..++...+..+
T Consensus        79 ~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~a-ia~~l~~~g~~v  130 (244)
T PRK07952         79 EGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAA-ICNELLLRGKSV  130 (244)
T ss_pred             chHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHHHHH-HHHHHHhcCCeE
Confidence            5777777777766643   1 4689999999999964433 334444444443

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.21  E-value=0.025  Score=50.12  Aligned_cols=40  Identities=25%  Similarity=0.219  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~al~   72 (115)
                      -+|....+.+.+++.++  .| .+|+||.|+|||.++.+-+-.
T Consensus        16 vGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~   58 (584)
T PRK14952         16 VGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARS   58 (584)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            47999999999999987  45 589999999999876665433

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=95.18  E-value=0.023  Score=42.29  Aligned_cols=30  Identities=23%  Similarity=0.217  Sum_probs=21.3

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ....|+++.|+||+|||..+..-+..++..
T Consensus        36 ~~~~h~li~G~tgsGKS~~l~~ll~~l~~~   65 (205)
T PF01580_consen   36 KKNPHLLIAGATGSGKSTLLRTLLLSLALT   65 (205)
T ss_dssp             GGS-SEEEE--TTSSHHHHHHHHHHHHHTT
T ss_pred             CCCceEEEEcCCCCCccHHHHHHHHHHHHH
Confidence            345699999999999999887766666653

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=95.14  E-value=0.037  Score=41.22  Aligned_cols=33  Identities=18%  Similarity=0.146  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++++.+.++......++|+|++||||++.
T Consensus         6 ~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~l   38 (168)
T PF00158_consen    6 PAMKRLREQAKRAASSDLPVLITGETGTGKELL   38 (168)
T ss_dssp             HHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHH
Confidence            455677778888888889999999999999964

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

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

Probab=95.13  E-value=0.011  Score=42.00  Aligned_cols=47  Identities=15%  Similarity=0.280  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHHHHHHHHh--cCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         29 FDAYDIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~--~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      |--|..|.+.+.....+..  .+..++|.|+.|+|||.-+ -.++..+..
T Consensus         2 fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll-~~~~~~~~~   50 (185)
T PF13191_consen    2 FVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLL-RALLDRLAE   50 (185)
T ss_dssp             -TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHH-HHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            3346666664444433222  2367999999999999542 223444433

>KOG0328|consensus

Probab=95.13  E-value=0.0031  Score=52.87  Aligned_cols=51  Identities=18%  Similarity=0.281  Sum_probs=42.4

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      ..++|+ |...|...+..|    .+|..+|..|..|||||.+|-|++++-+.-..+
T Consensus        43 Y~yGfekPS~IQqrAi~~I----lkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r   94 (400)
T KOG0328|consen   43 YAYGFEKPSAIQQRAIPQI----LKGRDVIAQAQSGTGKTATFSISVLQSLDISVR   94 (400)
T ss_pred             HHhccCCchHHHhhhhhhh----hcccceEEEecCCCCceEEEEeeeeeecccccc
Confidence            457888 999999977765    478899999999999999999998877765544

>PRK09183 transposase/IS protein; Provisional

Probab=95.13  E-value=0.027  Score=44.55  Aligned_cols=23  Identities=22%  Similarity=0.387  Sum_probs=18.8

Q ss_pred             HHhcCCcEEEecCCCCCchHHHH
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L   67 (115)
                      ++.++.+++|-||+|+|||.-..
T Consensus        98 ~i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         98 FIERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             chhcCCeEEEEeCCCCCHHHHHH
Confidence            36778899999999999995433

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

Probab=95.09  E-value=0.032  Score=45.92  Aligned_cols=48  Identities=17%  Similarity=0.261  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHh--cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~--~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|++.++.|.+++.  .+.++++.||-|||||.-+ =.+..++...++.+
T Consensus         4 ~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~-~~i~~~~~~~~~~~   53 (364)
T PF05970_consen    4 EEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLI-KAIIDYLRSRGKKV   53 (364)
T ss_pred             HHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHH-HHHHHHhccccceE
Confidence            679999999988885  4467889999999999643 22345555544554

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

>PRK06921 hypothetical protein; Provisional

Probab=95.07  E-value=0.073  Score=42.36  Aligned_cols=21  Identities=19%  Similarity=0.191  Sum_probs=16.5

Q ss_pred             cCCcEEEecCCCCCchHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~   68 (115)
                      .+..++|.||+|+|||.-+.+
T Consensus       116 ~~~~l~l~G~~G~GKThLa~a  136 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTA  136 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHH
Confidence            356799999999999964433

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.07  E-value=0.057  Score=43.11  Aligned_cols=32  Identities=22%  Similarity=0.224  Sum_probs=20.8

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhh-hhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHK-IAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~-~~v   81 (115)
                      ..++|.||||+|||.+..--+..+...++ .+|
T Consensus       195 ~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V  227 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTLAKLAARFVLEHGNKKV  227 (282)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeE
Confidence            46788999999999875544444443323 444

>PRK13764 ATPase; Provisional

Probab=95.06  E-value=0.03  Score=49.94  Aligned_cols=34  Identities=18%  Similarity=0.237  Sum_probs=24.6

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..++.+++.||||||||.. +.+++.++...+..+
T Consensus       255 ~~~~~ILIsG~TGSGKTTl-l~AL~~~i~~~~riV  288 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTF-AQALAEFYADMGKIV  288 (602)
T ss_pred             hcCCEEEEECCCCCCHHHH-HHHHHHHHhhCCCEE
Confidence            4567899999999999974 455666766554444

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.04  E-value=0.042  Score=43.99  Aligned_cols=36  Identities=25%  Similarity=0.116  Sum_probs=23.1

Q ss_pred             CCHHHHHHHHHH-HHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         31 AYDIQSNFMKNL-YYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        31 ~r~~Q~e~m~~I-~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      -|..|.+-+... ..++..+  ..++|.||+|||||...
T Consensus        19 gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~   57 (365)
T TIGR02928        19 HRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVT   57 (365)
T ss_pred             CcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHH
Confidence            466666543333 3333322  57999999999999664

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.02  E-value=0.034  Score=47.91  Aligned_cols=41  Identities=27%  Similarity=0.284  Sum_probs=31.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCc---EEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~---~iiEaPTGtGKTls~L~~   69 (115)
                      |+-.-+|.+....+.+++.++..   .+|.||.|+|||..+.+-
T Consensus        13 ~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~l   56 (472)
T PRK14962         13 FSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARIL   56 (472)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            33335788888899999988743   689999999999765443

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.01  E-value=0.031  Score=45.03  Aligned_cols=36  Identities=22%  Similarity=0.213  Sum_probs=25.4

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +.+.+.-++..+.++++.||||+|||..+ ..++.++
T Consensus       133 ~~~~l~~~v~~~~~ili~G~tGsGKTTll-~al~~~~  168 (308)
T TIGR02788       133 IKEFLRLAIASRKNIIISGGTGSGKTTFL-KSLVDEI  168 (308)
T ss_pred             HHHHHHHHhhCCCEEEEECCCCCCHHHHH-HHHHccC
Confidence            33445567788899999999999999643 3334444

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.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=94.99  E-value=0.033  Score=48.32  Aligned_cols=29  Identities=24%  Similarity=0.379  Sum_probs=24.0

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls~   66 (115)
                      ..+.+..++..++++++.||+|||||..+
T Consensus       183 ~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        183 TIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            44566777888999999999999999654

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

Probab=94.95  E-value=0.022  Score=43.44  Aligned_cols=30  Identities=17%  Similarity=0.088  Sum_probs=19.9

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++-||||+|||.+..=-|..+... +++|
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v   32 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLK-GKKV   32 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT-T--E
T ss_pred             EEEEECCCCCchHhHHHHHHHHHhhc-cccc
Confidence            57889999999998855444444444 6665

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 ....

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=94.93  E-value=0.038  Score=50.59  Aligned_cols=46  Identities=22%  Similarity=0.211  Sum_probs=34.9

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ...++..||+.|.--+-.+    .+|  -|.|+.||.|||++..+|+...+.
T Consensus        72 ~R~lg~r~ydvQlig~l~L----l~G--~VaEM~TGEGKTLvA~l~a~l~AL  117 (764)
T PRK12326         72 ERTLGLRPFDVQLLGALRL----LAG--DVIEMATGEGKTLAGAIAAAGYAL  117 (764)
T ss_pred             HHHcCCCcchHHHHHHHHH----hCC--CcccccCCCCHHHHHHHHHHHHHH
Confidence            3456777899998877654    344  477999999999999999776553

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.91  E-value=0.024  Score=47.79  Aligned_cols=32  Identities=16%  Similarity=0.121  Sum_probs=23.3

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++..++|-||||+|||.+..--+..+...++
T Consensus       135 ~~g~ii~lvGptGvGKTTtiakLA~~~~~~~G  166 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTAKLAARCVMRFG  166 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHhcC
Confidence            34678999999999999886655555554443

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.88  E-value=0.034  Score=48.32  Aligned_cols=40  Identities=20%  Similarity=0.143  Sum_probs=32.0

Q ss_pred             CHHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~al   71 (115)
                      --+|...++.+.+++.++  .| .+|.||.|+|||..+.+-+-
T Consensus        18 ivGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk   60 (509)
T PRK14958         18 VIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAK   60 (509)
T ss_pred             hcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHH
Confidence            348999999999999887  34 58999999999976555433

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=94.86  E-value=0.024  Score=42.84  Aligned_cols=37  Identities=11%  Similarity=-0.017  Sum_probs=27.6

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -+..|...+|.|++|+|||.-.+--+..++...+.++
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~v   45 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPV   45 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCce
Confidence            4556778999999999999766656667776645554

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.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=94.79  E-value=0.011  Score=49.30  Aligned_cols=22  Identities=32%  Similarity=0.475  Sum_probs=20.2

Q ss_pred             CcEEEecCCCCCchHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al   71 (115)
                      .|+++-||||+|||.++++|.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~l   66 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNL   66 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHH
Confidence            4899999999999999999965

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

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=94.74  E-value=0.057  Score=44.92  Aligned_cols=28  Identities=21%  Similarity=0.204  Sum_probs=23.7

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      ....|..++..+++++++||+|+|||..
T Consensus        53 ~~~~vl~~l~~~~~ilL~G~pGtGKTtl   80 (327)
T TIGR01650        53 TTKAICAGFAYDRRVMVQGYHGTGKSTH   80 (327)
T ss_pred             HHHHHHHHHhcCCcEEEEeCCCChHHHH
Confidence            4456778888899999999999999964

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=94.73  E-value=0.028  Score=42.33  Aligned_cols=26  Identities=27%  Similarity=0.600  Sum_probs=19.0

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +.++|.||||+|||..+ ..++.++..
T Consensus         2 GlilI~GptGSGKTTll-~~ll~~~~~   27 (198)
T cd01131           2 GLVLVTGPTGSGKSTTL-AAMIDYINK   27 (198)
T ss_pred             cEEEEECCCCCCHHHHH-HHHHHHhhh
Confidence            46889999999999775 334555543

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.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=94.71  E-value=0.03  Score=46.69  Aligned_cols=36  Identities=22%  Similarity=0.194  Sum_probs=27.5

Q ss_pred             CHHHHHHHHH---HHHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         32 YDIQSNFMKN---LYYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        32 r~~Q~e~m~~---I~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      .-+|.+++..   +.+++.++  .+++|.||+|||||..+-
T Consensus        14 ~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         14 VVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLAR   54 (413)
T ss_pred             hcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHH
Confidence            4467777665   77888776  479999999999996543

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

Probab=94.69  E-value=0.049  Score=50.40  Aligned_cols=33  Identities=15%  Similarity=0.248  Sum_probs=26.1

Q ss_pred             HHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        39 m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ..+|..++.+++.+||.||||+|||.-  +|-..+
T Consensus        55 ~~~i~~ai~~~~vvii~getGsGKTTq--lP~~ll   87 (845)
T COG1643          55 RDEILKAIEQNQVVIIVGETGSGKTTQ--LPQFLL   87 (845)
T ss_pred             HHHHHHHHHhCCEEEEeCCCCCChHHH--HHHHHH
Confidence            346777889999999999999999965  564433

>TIGR00595 priA primosomal protein N'

Probab=94.68  E-value=0.016  Score=50.05  Aligned_cols=27  Identities=22%  Similarity=0.199  Sum_probs=19.6

Q ss_pred             EEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         53 IFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        53 iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ++.||||+|||..|+..+...+ ..++.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l-~~g~~   27 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVL-ALGKS   27 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHH-HcCCe
Confidence            4689999999999987754444 33444

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).

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.67  E-value=0.046  Score=47.73  Aligned_cols=39  Identities=26%  Similarity=0.166  Sum_probs=31.7

Q ss_pred             CHHHHHHHHHHHHHHhcCCc---EEEecCCCCCchHHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~---~iiEaPTGtGKTls~L~~a   70 (115)
                      --+|...+..+..++.+++.   .+|.||.|+|||..+.+-+
T Consensus        20 vVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLA   61 (484)
T PRK14956         20 VIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILA   61 (484)
T ss_pred             HhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            35899999999999998853   6999999999997655443

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=94.57  E-value=0.032  Score=47.34  Aligned_cols=33  Identities=27%  Similarity=0.204  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHh------------------cCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLD------------------NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~------------------~~~~~iiEaPTGtGKTls   65 (115)
                      -+|.+..+.+..++.                  ...+++|.||||||||+.
T Consensus        74 iGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~l  124 (412)
T PRK05342         74 IGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLL  124 (412)
T ss_pred             eChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHH
Confidence            467777776654442                  135799999999999965

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=94.54  E-value=0.0083  Score=49.16  Aligned_cols=22  Identities=23%  Similarity=0.323  Sum_probs=19.2

Q ss_pred             cEEEecCCCCCchHHHHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~   72 (115)
                      |+++.||||+|||.++++|.+-
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll   22 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLL   22 (384)
T ss_pred             CeeEecCCCCCCccEEEccchh
Confidence            5789999999999999988553

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=94.50  E-value=0.049  Score=43.82  Aligned_cols=38  Identities=21%  Similarity=0.265  Sum_probs=25.8

Q ss_pred             CCCHHHHHHHHHHHHHHhc----C---CcEEEecCCCCCchHHHH
Q psy14273         30 DAYDIQSNFMKNLYYTLDN----S---KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~----~---~~~iiEaPTGtGKTls~L   67 (115)
                      +-+-+|.+.++.+...+..    +   .+++|.||+|+|||..+.
T Consensus        25 ~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         25 DEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHH
Confidence            3344666666666555542    2   579999999999997654

>KOG0951|consensus

Probab=94.49  E-value=0.053  Score=52.53  Aligned_cols=53  Identities=25%  Similarity=0.251  Sum_probs=38.6

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+|.+. .-++|-.+-..   ++....+++++||||+|||-..+..+|.-+..+.+.
T Consensus       303 aF~g~~sLNrIQS~v~da---Al~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~  356 (1674)
T KOG0951|consen  303 AFFGKQSLNRIQSKVYDA---ALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLRE  356 (1674)
T ss_pred             hcccchhhhHHHHHHHHH---HhcCcCcEEEeccCCCCchHHHHHHHHHHHhccccc
Confidence            344454 34566654443   455668999999999999999999999988776653

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.38  E-value=0.065  Score=46.70  Aligned_cols=39  Identities=15%  Similarity=0.065  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~~al   71 (115)
                      -+|..+.+.+.+++..+   ...+|.||.|+|||.++.+-+.
T Consensus        16 iGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk   57 (491)
T PRK14964         16 VGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISL   57 (491)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHH
Confidence            47889999999999887   3588999999999976655443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=94.37  E-value=0.07  Score=43.23  Aligned_cols=39  Identities=23%  Similarity=0.154  Sum_probs=24.7

Q ss_pred             CCHHHHH-HHHHHHHHHhcC--CcEEEecCCCCCchHHHHHH
Q psy14273         31 AYDIQSN-FMKNLYYTLDNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        31 ~r~~Q~e-~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      -|..|.+ +...+..++..+  ..++|.||+|+|||..+-.-
T Consensus        34 ~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v   75 (394)
T PRK00411         34 HREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKV   75 (394)
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHH
Confidence            3555544 344444545432  57999999999999865444

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

Probab=94.35  E-value=0.038  Score=49.49  Aligned_cols=42  Identities=24%  Similarity=0.374  Sum_probs=36.3

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLS   65 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls   65 (115)
                      .+.-+|.|---|-+.|+.+...+.+| ++-++-|-||||||++
T Consensus         6 ~l~s~f~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT   48 (663)
T COG0556           6 KLHSPFKPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFT   48 (663)
T ss_pred             EeccCCCCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhH
Confidence            34567889889999999999999988 6778889999999987

>PRK12377 putative replication protein; Provisional

Probab=94.31  E-value=0.14  Score=40.73  Aligned_cols=48  Identities=17%  Similarity=0.003  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHh---c-CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         33 DIQSNFMKNLYYTLD---N-SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~---~-~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|..++..+.....   . ...++|.||+|||||.-+.+- ...+...+..+
T Consensus        81 ~~~~~a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThLa~AI-a~~l~~~g~~v  132 (248)
T PRK12377         81 DGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHLAAAI-GNRLLAKGRSV  132 (248)
T ss_pred             hhHHHHHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHH-HHHHHHcCCCe
Confidence            677766665554433   2 357899999999999643333 33444444443

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=94.31  E-value=0.036  Score=46.36  Aligned_cols=42  Identities=26%  Similarity=0.235  Sum_probs=34.5

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls   65 (115)
                      ...|||..--+|.++...+..++.+.  ..++|.||+|||||..
T Consensus        11 ~~~~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~   54 (350)
T CHL00081         11 RPVFPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTT   54 (350)
T ss_pred             CCCCCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHH
Confidence            55799997789999999888777664  4688999999999954

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=94.30  E-value=0.036  Score=45.36  Aligned_cols=28  Identities=25%  Similarity=0.529  Sum_probs=20.9

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++.++|.||||+|||..+ ..++.++..
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~  148 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINK  148 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCc
Confidence            4678999999999999765 344555543

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.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.30  E-value=0.058  Score=46.86  Aligned_cols=37  Identities=22%  Similarity=0.281  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHhcCC--cE-EEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--FG-IFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~~-iiEaPTGtGKTls~L~~   69 (115)
                      -+|.+..+.+.+++.++.  |. +|.||.|+|||..+.+-
T Consensus        17 vGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~l   56 (504)
T PRK14963         17 VGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLI   56 (504)
T ss_pred             cChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            578888999999998874  44 99999999999876544

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.29  E-value=0.062  Score=46.78  Aligned_cols=37  Identities=19%  Similarity=0.215  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      -+|...++.+.+++.+++  | .||.||.|+|||..+.+-
T Consensus        19 vGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~l   58 (527)
T PRK14969         19 VGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARIL   58 (527)
T ss_pred             cCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHH
Confidence            378899999999998873  4 489999999999765544

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=94.23  E-value=0.096  Score=36.88  Aligned_cols=33  Identities=24%  Similarity=0.220  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++.+.+.+....+..++|.|+.||||++.
T Consensus         5 ~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~   37 (138)
T PF14532_consen    5 PAMRRLRRQLERLAKSSSPVLITGEPGTGKSLL   37 (138)
T ss_dssp             HHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHH
Confidence            344556666666667778999999999999964

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=94.18  E-value=0.059  Score=45.99  Aligned_cols=34  Identities=26%  Similarity=0.153  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHh-------c-------------CCcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLD-------N-------------SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~-------~-------------~~~~iiEaPTGtGKTls~   66 (115)
                      -+|.+..+.+..++.       .             +.+++|.||||+|||...
T Consensus        80 iGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lA  133 (413)
T TIGR00382        80 IGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLA  133 (413)
T ss_pred             cCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHH
Confidence            578888777766551       1             247999999999999653

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.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.18  E-value=0.067  Score=46.33  Aligned_cols=33  Identities=33%  Similarity=0.274  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHhcC----------------CcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNS----------------KFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~----------------~~~iiEaPTGtGKTls   65 (115)
                      -+|.+..+.+.-++.++                .++++.||||+|||..
T Consensus        15 iGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~l   63 (441)
T TIGR00390        15 IGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEI   63 (441)
T ss_pred             cCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHH
Confidence            56778777777777653                6899999999999954

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.

>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=94.18  E-value=0.029  Score=38.95  Aligned_cols=15  Identities=33%  Similarity=0.465  Sum_probs=12.9

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      ++++.||+|+|||..
T Consensus         1 ~vlL~G~~G~GKt~l   15 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTL   15 (139)
T ss_dssp             EEEEEESSSSSHHHH
T ss_pred             CEEEECCCCCCHHHH
Confidence            478999999999954

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.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=94.18  E-value=0.076  Score=47.09  Aligned_cols=38  Identities=16%  Similarity=0.120  Sum_probs=32.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~   66 (115)
                      ++.--+|.+++..+..++.++.++++.||+|+|||...
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~~~ll~G~pG~GKT~la   54 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKRNVLLIGEPGVGKSMLA   54 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHH
Confidence            33446889999999999999999999999999999653

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=94.16  E-value=0.065  Score=47.61  Aligned_cols=41  Identities=12%  Similarity=0.088  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      -+|..+++.+.+++.+++   ..||.||.|+|||.+..+-+-..
T Consensus        27 iGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L   70 (598)
T PRK09111         27 IGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARAL   70 (598)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhh
Confidence            479999999999999884   48899999999998766554433

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.15  E-value=0.063  Score=47.96  Aligned_cols=42  Identities=19%  Similarity=0.236  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~a   70 (115)
                      |+---+|..++..+.+++.++.  | .||+||.|+|||..+.+-+
T Consensus        15 f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lA   59 (620)
T PRK14954         15 FADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFA   59 (620)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHH
Confidence            4433489999999999998873  3 7899999999997765543

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

Probab=94.10  E-value=0.069  Score=48.42  Aligned_cols=52  Identities=17%  Similarity=0.335  Sum_probs=45.4

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      -..||+....|...+++|..=+.+.  .+=++.|--|||||+.++++++..+..
T Consensus       257 ~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~  310 (677)
T COG1200         257 AALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA  310 (677)
T ss_pred             HhCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc
Confidence            4689999999999999999888777  456789999999999999998877755

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=94.07  E-value=0.057  Score=46.94  Aligned_cols=35  Identities=26%  Similarity=0.211  Sum_probs=28.3

Q ss_pred             CHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      --+|...|+.+..++...  .+++|.||+|||||..+
T Consensus        67 iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lA  103 (531)
T TIGR02902        67 IIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAA  103 (531)
T ss_pred             eeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHH
Confidence            457888888888777554  78999999999999653

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=94.07  E-value=0.1  Score=39.39  Aligned_cols=29  Identities=17%  Similarity=0.219  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHh---cCCcEEEecCCCCCchHH
Q psy14273         37 NFMKNLYYTLD---NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        37 e~m~~I~~~l~---~~~~~iiEaPTGtGKTls   65 (115)
                      ..+..+..+..   .+..++|.||+|||||.-
T Consensus        27 ~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~L   58 (227)
T PRK08903         27 ELVARLRELAAGPVADRFFYLWGEAGSGRSHL   58 (227)
T ss_pred             HHHHHHHHHHhccCCCCeEEEECCCCCCHHHH
Confidence            34555555544   346799999999999953

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.01  E-value=0.049  Score=46.25  Aligned_cols=33  Identities=21%  Similarity=0.140  Sum_probs=22.2

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHH-Hhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWY-SDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l-~~~~~~v   81 (115)
                      +..++|-||||+|||.+...-+..+. ...+.+|
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V  254 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKV  254 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeE
Confidence            45678899999999987665554444 3334444

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.01  E-value=0.065  Score=47.02  Aligned_cols=41  Identities=20%  Similarity=0.299  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      |+-.-+|...+..+.+++.++.  + .||.||.|+|||..+.+-
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~l   58 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARIL   58 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHH
Confidence            3333578999999999998873  3 489999999999776554

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=93.98  E-value=0.094  Score=38.39  Aligned_cols=32  Identities=28%  Similarity=0.277  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHhcC---CcEE--EecCCCCCchHH
Q psy14273         34 IQSNFMKNLYYTLDNS---KFGI--FESPTGTGKSLS   65 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~---~~~i--iEaPTGtGKTls   65 (115)
                      .+..++++|...+.+.   +.+|  +.||||||||..
T Consensus        33 a~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v   69 (127)
T PF06309_consen   33 AVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFV   69 (127)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHH
Confidence            3445556666665543   3344  799999999965

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

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.92  E-value=0.064  Score=47.77  Aligned_cols=39  Identities=26%  Similarity=0.187  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~al   71 (115)
                      -+|.++...+.+++..++   ..+|.||.|+|||..+.+-+-
T Consensus        19 iGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk   60 (620)
T PRK14948         19 VGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAK   60 (620)
T ss_pred             cChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHH
Confidence            478888999999998874   468999999999977655433

>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=93.92  E-value=0.058  Score=36.18  Aligned_cols=14  Identities=36%  Similarity=0.615  Sum_probs=12.3

Q ss_pred             EEEecCCCCCchHH
Q psy14273         52 GIFESPTGTGKSLS   65 (115)
Q Consensus        52 ~iiEaPTGtGKTls   65 (115)
                      +++.||.|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            57899999999965

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 ....

>PF13476 AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V_A 3QG5_B 3QF7_A 3THO_A

Probab=93.89  E-value=0.054  Score=38.72  Aligned_cols=26  Identities=19%  Similarity=0.374  Sum_probs=19.5

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +..||.||+|+|||..  +-++.|+...
T Consensus        20 g~~vi~G~Ng~GKSti--l~ai~~~L~~   45 (202)
T PF13476_consen   20 GLNVIYGPNGSGKSTI--LEAIRYALGG   45 (202)
T ss_dssp             EEEEEEESTTSSHHHH--HHHHHHHHHS
T ss_pred             CcEEEECCCCCCHHHH--HHHHHHHHcC
Confidence            5678899999999954  4666777643

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.82  E-value=0.075  Score=49.75  Aligned_cols=38  Identities=21%  Similarity=0.192  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHhcC--CcE-EEecCCCCCchHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KFG-IFESPTGTGKSLSLICGI   70 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~~-iiEaPTGtGKTls~L~~a   70 (115)
                      =+|..+++.+.+++.++  .|+ ||.||.|+|||..+.+-+
T Consensus        19 IGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLA   59 (944)
T PRK14949         19 VGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFA   59 (944)
T ss_pred             cCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            38899999999999887  455 899999999997655543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=93.78  E-value=0.088  Score=41.89  Aligned_cols=38  Identities=24%  Similarity=0.253  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~   69 (115)
                      .-+|.+.++.+.+++.++.   ..+|.||.|+|||....+-
T Consensus        16 iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~l   56 (355)
T TIGR02397        16 VIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIF   56 (355)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            3578888889999998874   3689999999999665433

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup

Probab=93.76  E-value=0.034  Score=45.63  Aligned_cols=45  Identities=20%  Similarity=0.335  Sum_probs=29.5

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHHH----HhcC--CcEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYYT----LDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~~----l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+-..|.++.+.+..-    +-+|  ..++..|+||||||.+.+
T Consensus        55 ~~f~Fd~vf~~~~tq~~vy~~~~~p~v~~~l~G~n~ti~aYGqtGSGKTyTm~  107 (345)
T cd01368          55 TKFSFSKVFGPNTTQKEFFEGTALPLVQDLLKGKNSLLFTYGVTNSGKTYTMQ  107 (345)
T ss_pred             eEeecCeEECCCCCHHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCCeEEec
Confidence            344444  33556787777765432    2344  457779999999999974

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

>PRK04195 replication factor C large subunit; Provisional

Probab=93.75  E-value=0.079  Score=45.15  Aligned_cols=34  Identities=18%  Similarity=0.148  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHhc------CCcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDN------SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~------~~~~iiEaPTGtGKTls~L   67 (115)
                      +|.+..+.+..++.+      ...++|.||+|+|||..+-
T Consensus        18 g~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~   57 (482)
T PRK04195         18 GNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAH   57 (482)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            445555566666543      3679999999999996543

>cd01373 KISc_KLP2_like Kinesin motor domain, KLP2-like subgroup

Probab=93.74  E-value=0.031  Score=45.61  Aligned_cols=46  Identities=17%  Similarity=0.188  Sum_probs=31.1

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      ..|.|.  |.+...|.++.+.+..    .+-+|  ..++..|+||||||.+.+-
T Consensus        41 ~~f~FD~vf~~~~~q~~vy~~~~~p~v~~~~~G~n~ti~aYGqTGSGKTyTm~G   94 (337)
T cd01373          41 RMFTFDHVADSNTNQEDVFQSVGKPLVEDCLSGYNGSIFAYGQTGSGKTYTMMG   94 (337)
T ss_pred             cEEeCCeEeCCCCCHHHHHHHHHHHHHHHHhCCCceeEEEeCCCCCCceEEecC
Confidence            445555  4466778887776643    23344  4577799999999988754

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

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=93.74  E-value=0.13  Score=37.67  Aligned_cols=41  Identities=17%  Similarity=0.220  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +|.+..+.+.+.+.++  .+ .+|+||.|+||+..++.-+-..+
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll   44 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALL   44 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHc
Confidence            4788889999999888  34 69999999999866555443333

...

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=93.73  E-value=0.058  Score=41.59  Aligned_cols=37  Identities=24%  Similarity=0.250  Sum_probs=26.5

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -+..+..++|.||+|+|||.-.+--+..++..++..|
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~v   62 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRV   62 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceE
Confidence            4556788999999999999765555556655545454

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>cd01375 KISc_KIF9_like Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling

Probab=93.71  E-value=0.044  Score=44.64  Aligned_cols=44  Identities=18%  Similarity=0.240  Sum_probs=29.9

Q ss_pred             cccCC--CCCCHHHHHHHHHHHHH----HhcC--CcEEEecCCCCCchHHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLYYT----LDNS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~~~----l~~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      .|.|.  |++ ..|.++.+.+..-    +-+|  ..++..|+||||||.+.+-
T Consensus        49 ~f~FD~vf~~-~~q~~vy~~~~~p~v~~~~~G~n~~i~ayG~tgSGKTyTm~G  100 (334)
T cd01375          49 SFKFDGVFHN-ASQEEVYETVAKPVVDSALDGYNGTIFAYGQTGAGKTFTMTG  100 (334)
T ss_pred             EEEcCcccCC-CCHHHHHHHHHHHHHHHHhCCCccceeeecCCCCCCeEEccC
Confidence            34454  446 7888887765432    2344  4677899999999988754

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

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.70  E-value=0.097  Score=46.15  Aligned_cols=42  Identities=21%  Similarity=0.207  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~a   70 (115)
                      |+-.-+|...+..+.+++.+++  + .||.||.|+|||..+.+-+
T Consensus        15 f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lA   59 (546)
T PRK14957         15 FAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLA   59 (546)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            3333488999999999998864  3 6899999999997655443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=93.68  E-value=0.12  Score=40.09  Aligned_cols=26  Identities=19%  Similarity=0.271  Sum_probs=20.5

Q ss_pred             CCc-EEEecCCCCCchHHHHHHHHHHH
Q psy14273         49 SKF-GIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        49 ~~~-~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..+ .+|.||.|+|||.++++-+-...
T Consensus        23 ~~halL~~Gp~G~Gktt~a~~lA~~l~   49 (325)
T COG0470          23 LPHALLFYGPPGVGKTTAALALAKELL   49 (325)
T ss_pred             CCceeeeeCCCCCCHHHHHHHHHHHHh
Confidence            367 99999999999988777655444

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane

Probab=93.66  E-value=0.13  Score=41.61  Aligned_cols=49  Identities=20%  Similarity=0.125  Sum_probs=30.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||+.|.-..-.    |..|.  |+|+.||=|||++..+|+...+.. ++.|
T Consensus        73 ~~g~~p~~vQll~~l~----L~~G~--laEm~TGEGKTli~~l~a~~~AL~-G~~V  121 (266)
T PF07517_consen   73 TLGLRPYDVQLLGALA----LHKGR--LAEMKTGEGKTLIAALPAALNALQ-GKGV  121 (266)
T ss_dssp             HTS----HHHHHHHHH----HHTTS--EEEESTTSHHHHHHHHHHHHHHTT-SS-E
T ss_pred             HcCCcccHHHHhhhhh----cccce--eEEecCCCCcHHHHHHHHHHHHHh-cCCc
Confidence            5677788888764432    34443  889999999999988886655543 4443

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=93.62  E-value=0.088  Score=46.07  Aligned_cols=33  Identities=15%  Similarity=0.349  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHhc-------CCcEEEecCCCCCchHHHHH
Q psy14273         36 SNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        36 ~e~m~~I~~~l~~-------~~~~iiEaPTGtGKTls~L~   68 (115)
                      ..=+++|..||.+       .+.+|+.||+|+|||.+.-+
T Consensus        25 kkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~   64 (519)
T PF03215_consen   25 KKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKV   64 (519)
T ss_pred             HHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHH
Confidence            4445678888865       24688999999999976544

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

Probab=93.61  E-value=0.073  Score=46.64  Aligned_cols=37  Identities=22%  Similarity=0.273  Sum_probs=30.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      |.--.+|.+.=+.+.-+...+.++++.||.|||||+.
T Consensus       178 ~~DV~GQ~~AKrAleiAAAGgHnLl~~GpPGtGKTml  214 (490)
T COG0606         178 FKDVKGQEQAKRALEIAAAGGHNLLLVGPPGTGKTML  214 (490)
T ss_pred             hhhhcCcHHHHHHHHHHHhcCCcEEEecCCCCchHHh
Confidence            3333678888888888887889999999999999964

>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup

Probab=93.60  E-value=0.032  Score=45.60  Aligned_cols=45  Identities=22%  Similarity=0.312  Sum_probs=29.6

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+...|.++.+.+..    .+-+|  ..++..|+||||||.+.+
T Consensus        54 ~~f~Fd~vf~~~~~q~~vf~~~~~plv~~~~~G~n~~i~ayGqtGSGKTyTm~  106 (338)
T cd01370          54 LKYSFDRVFDETSTQEEVYENTTKPLVDGVLNGYNATVFAYGATGAGKTHTML  106 (338)
T ss_pred             eEEEeccccCCCCCHHHHHHHHHHHHHHHHHCCCCceEEeeCCCCCCCeEEEc
Confidence            344444  3355668887776653    22345  457779999999999973

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

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=93.59  E-value=0.072  Score=38.69  Aligned_cols=28  Identities=14%  Similarity=0.260  Sum_probs=24.1

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .|...+|.||+|+|||...+--+..++.
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~   58 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALAT   58 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            5678999999999999988887777775

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=93.58  E-value=0.097  Score=48.19  Aligned_cols=42  Identities=24%  Similarity=0.195  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      -+|...++.|.+++.++  .| .||+||.|+|||.+.++-+-.++
T Consensus        18 iGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~   62 (824)
T PRK07764         18 IGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLN   62 (824)
T ss_pred             cCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhC
Confidence            47888999999999887  35 68999999999988777654443

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=93.57  E-value=0.081  Score=45.85  Aligned_cols=32  Identities=28%  Similarity=0.274  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHhc----------------CCcEEEecCCCCCchH
Q psy14273         33 DIQSNFMKNLYYTLDN----------------SKFGIFESPTGTGKSL   64 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~----------------~~~~iiEaPTGtGKTl   64 (115)
                      -+|.+..+.+..++.+                ..++++.||||+|||.
T Consensus        18 iGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~   65 (443)
T PRK05201         18 IGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTE   65 (443)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHH
Confidence            5788888888877754                3689999999999993

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=93.51  E-value=0.091  Score=44.41  Aligned_cols=46  Identities=11%  Similarity=0.090  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhhHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLE   83 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~~   83 (115)
                      +.|..   .+..++....++++.|+||||||.. |-+...+..... ++..
T Consensus       160 ~~~a~---~L~~av~~r~NILisGGTGSGKTTl-LNal~~~i~~~e-RvIt  205 (355)
T COG4962         160 RRAAK---FLRRAVGIRCNILISGGTGSGKTTL-LNALSGFIDSDE-RVIT  205 (355)
T ss_pred             HHHHH---HHHHHHhhceeEEEeCCCCCCHHHH-HHHHHhcCCCcc-cEEE
Confidence            45555   4445566668999999999999953 444445554434 5543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.50  E-value=0.11  Score=47.41  Aligned_cols=41  Identities=17%  Similarity=0.121  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~al~~   73 (115)
                      -+|....+.+.+++.+++  + .||.||.|+|||..+.+-|-..
T Consensus        18 IGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~L   61 (702)
T PRK14960         18 VGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCL   61 (702)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            478889999999998884  3 4999999999997765554443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.50  E-value=0.11  Score=42.20  Aligned_cols=41  Identities=27%  Similarity=0.328  Sum_probs=31.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~   69 (115)
                      |+..-+|...++.+.+.+.++.   +.+|.||.|+|||.....-
T Consensus        16 ~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~l   59 (367)
T PRK14970         16 FDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARIL   59 (367)
T ss_pred             HHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            4434588888999999998873   6889999999999654433

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=93.47  E-value=0.063  Score=41.86  Aligned_cols=20  Identities=30%  Similarity=0.253  Sum_probs=15.9

Q ss_pred             CcEEEecCCCCCchHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~   69 (115)
                      .+++|.||+|||||..+-+-
T Consensus        43 ~~vll~GppGtGKTtlA~~i   62 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVARIL   62 (261)
T ss_pred             ceEEEEcCCCCCHHHHHHHH
Confidence            47899999999999765333

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.

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=93.46  E-value=0.17  Score=45.62  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=33.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +++...+.|.+.++.+    .+++..++.|+.|||||..+ ..++..+...+
T Consensus       320 ~~~~l~~~Q~~Ai~~~----~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~  366 (720)
T TIGR01448       320 LRKGLSEEQKQALDTA----IQHKVVILTGGPGTGKTTIT-RAIIELAEELG  366 (720)
T ss_pred             cCCCCCHHHHHHHHHH----HhCCeEEEECCCCCCHHHHH-HHHHHHHHHcC
Confidence            4566779999977765    35679999999999999643 34444444443

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=93.43  E-value=0.13  Score=40.44  Aligned_cols=33  Identities=12%  Similarity=0.194  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHhcCC--cEEE-ecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK--FGIF-ESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~--~~ii-EaPTGtGKTls~   66 (115)
                      +|.+....+..++.++.  ++++ .||+|+|||...
T Consensus        25 ~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la   60 (316)
T PHA02544         25 LPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVA   60 (316)
T ss_pred             CcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHH
Confidence            67777778888887773  4554 999999999654

>KOG0947|consensus

Probab=93.43  E-value=0.14  Score=48.64  Aligned_cols=59  Identities=14%  Similarity=0.166  Sum_probs=47.2

Q ss_pred             CCCCCccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         18 LAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        18 ~~~~~~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.++...+.|||++-.-|++.+-    +|..|..+++-|+|-+|||+.+=++ ++.++.|..+.
T Consensus       285 ~lVpe~a~~~pFelD~FQk~Ai~----~lerg~SVFVAAHTSAGKTvVAEYA-ialaq~h~TR~  343 (1248)
T KOG0947|consen  285 QLVPEMALIYPFELDTFQKEAIY----HLERGDSVFVAAHTSAGKTVVAEYA-IALAQKHMTRT  343 (1248)
T ss_pred             HhchhHHhhCCCCccHHHHHHHH----HHHcCCeEEEEecCCCCcchHHHHH-HHHHHhhccce
Confidence            35666788999999999999655    5688999999999999999987665 56666666554

>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=93.40  E-value=0.2  Score=38.12  Aligned_cols=38  Identities=18%  Similarity=0.218  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHH---------hcCCcEEEecCCCCCchHHHHHHHH
Q psy14273         34 IQSNFMKNLYYTL---------DNSKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        34 ~Q~e~m~~I~~~l---------~~~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      .|.+.+.-+....         .....+|+....|+|||+..+.-+.
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~   47 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALIS   47 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhh
Confidence            4777777777666         4557799999999999988776654

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.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=93.40  E-value=0.14  Score=42.27  Aligned_cols=37  Identities=16%  Similarity=0.178  Sum_probs=25.4

Q ss_pred             HHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        39 m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+.+..++..+.++++.|+||+|||.. |..++.++..
T Consensus       168 ~~~L~~~v~~~~~ili~G~tGsGKTTl-l~al~~~i~~  204 (340)
T TIGR03819       168 ARLLRAIVAARLAFLISGGTGSGKTTL-LSALLALVAP  204 (340)
T ss_pred             HHHHHHHHhCCCeEEEECCCCCCHHHH-HHHHHccCCC
Confidence            344555677789999999999999853 3334445443

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.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=93.39  E-value=0.21  Score=43.46  Aligned_cols=36  Identities=22%  Similarity=0.127  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~   68 (115)
                      ..+...+..+..++.++.++|+-||+|||||..+..
T Consensus       193 r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~  228 (449)
T TIGR02688       193 RQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNN  228 (449)
T ss_pred             HHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHH
Confidence            455555566667888999999999999999955443

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.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=93.34  E-value=0.12  Score=46.42  Aligned_cols=39  Identities=18%  Similarity=0.152  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L   67 (115)
                      ++...+|.+.+..+..++.++.++++.+|+|+|||...-
T Consensus        30 ~~~vigq~~a~~~L~~~~~~~~~~l~~G~~G~GKttla~   68 (637)
T PRK13765         30 IDQVIGQEHAVEVIKKAAKQRRHVMMIGSPGTGKSMLAK   68 (637)
T ss_pred             HHHcCChHHHHHHHHHHHHhCCeEEEECCCCCcHHHHHH
Confidence            445578999999999999999999999999999996543

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=93.31  E-value=0.13  Score=44.08  Aligned_cols=33  Identities=21%  Similarity=0.228  Sum_probs=22.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHH-Hhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWY-SDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l-~~~~~~v   81 (115)
                      ++.+++-||||.|||.++-=-|..|. ....++|
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kV  236 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKV  236 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhccCcce
Confidence            67889999999999877544444454 3444444

>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=93.30  E-value=0.1  Score=37.54  Aligned_cols=29  Identities=17%  Similarity=0.173  Sum_probs=19.0

Q ss_pred             EEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         52 GIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        52 ~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .++.||+|+|||.-.+--+...+ ..+.++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~g~~v   30 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-ARGEPG   30 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HCCCcE
Confidence            68899999999975444344444 344443

A related protein is found in archaea.

>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup

Probab=93.30  E-value=0.05  Score=43.94  Aligned_cols=45  Identities=16%  Similarity=0.231  Sum_probs=29.3

Q ss_pred             ccccCC--CCCCHHHHHHHHHHH----HHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~----~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+...|.++.+.+.    ..+-+|  ..++..|+||||||.+++
T Consensus        47 ~~f~FD~vf~~~~~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKTyTm~   99 (319)
T cd01376          47 KKYQFDAFYGTECTQEDIFSREVKPIVPHLLSGQNATVFAYGSTGAGKTHTML   99 (319)
T ss_pred             cEEecCeEECCCCCHHHHHHHHHHHHHHHHhCCCceEEEEECCCCCCCcEEEe
Confidence            344455  446677888777632    223345  346678999999999873

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

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=93.28  E-value=0.12  Score=44.18  Aligned_cols=42  Identities=21%  Similarity=0.107  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~a   70 (115)
                      |+-.-+|...+..+.+++..+.   ..+|.||.|+|||..+.+-+
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lA   60 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFA   60 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHH
Confidence            4434588999999999998873   36899999999997655543

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=93.25  E-value=0.11  Score=35.44  Aligned_cols=23  Identities=26%  Similarity=0.291  Sum_probs=16.4

Q ss_pred             cEEEecCCCCCchHHHHHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      +++|.||+|+|||.-...-+...
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~   23 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNI   23 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHH
Confidence            36789999999997654443333

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=93.24  E-value=0.1  Score=46.92  Aligned_cols=32  Identities=28%  Similarity=0.351  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHH
Q psy14273         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLS   65 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls   65 (115)
                      +|.+.++.|.+++...           ...+|.||||+|||..
T Consensus       458 GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~l  500 (731)
T TIGR02639       458 GQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTEL  500 (731)
T ss_pred             CcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHH
Confidence            6777778777777631           2468999999999954

>PRK08727 hypothetical protein; Validated

Probab=93.23  E-value=0.19  Score=38.77  Aligned_cols=16  Identities=31%  Similarity=0.547  Sum_probs=13.6

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..+++.||+|+|||.-
T Consensus        42 ~~l~l~G~~G~GKThL   57 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL   57 (233)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999953

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=93.21  E-value=0.17  Score=45.77  Aligned_cols=50  Identities=12%  Similarity=0.147  Sum_probs=34.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++...+.|.+.+..+   +..++..+|.|+.|||||.. +-.++..+...+.+|
T Consensus       350 ~~~Ls~~Q~~Av~~i---~~s~~~~il~G~aGTGKTtl-l~~i~~~~~~~g~~V  399 (744)
T TIGR02768       350 HYRLSEEQYEAVRHV---TGSGDIAVVVGRAGTGKSTM-LKAAREAWEAAGYRV  399 (744)
T ss_pred             cCCCCHHHHHHHHHH---hcCCCEEEEEecCCCCHHHH-HHHHHHHHHhCCCeE
Confidence            455679999977665   44467899999999999864 344455555545544

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.

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

Probab=93.19  E-value=0.082  Score=45.03  Aligned_cols=25  Identities=28%  Similarity=0.397  Sum_probs=18.0

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++++-|||||||||  |+-.|+-+..
T Consensus        98 SNILLiGPTGsGKTl--LAqTLAk~Ln  122 (408)
T COG1219          98 SNILLIGPTGSGKTL--LAQTLAKILN  122 (408)
T ss_pred             ccEEEECCCCCcHHH--HHHHHHHHhC
Confidence            578999999999995  4444544433

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=93.17  E-value=0.037  Score=49.82  Aligned_cols=23  Identities=22%  Similarity=0.431  Sum_probs=20.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      ..|+++-||||+|||.++++|.+
T Consensus       139 ~~hvlviApTgSGKgvg~VIPnL  161 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPTL  161 (670)
T ss_pred             CceEEEEecCCCCceeeehHhHH
Confidence            46899999999999999999954

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=93.15  E-value=0.13  Score=46.99  Aligned_cols=39  Identities=21%  Similarity=0.166  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~al   71 (115)
                      -+|..+++.+.+++.+++  + +||.||.|+|||....+-+-
T Consensus        19 IGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk   60 (709)
T PRK08691         19 VGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAK   60 (709)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            579999999999998874  3 69999999999976655433

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.15  E-value=0.12  Score=46.20  Aligned_cols=42  Identities=19%  Similarity=0.212  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~a   70 (115)
                      |+-.-+|..+++.+.+++.+++  | .+|.||.|+|||....+-+
T Consensus        15 f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lA   59 (618)
T PRK14951         15 FSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILA   59 (618)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            4433479999999999998873  4 4899999999997765543

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=93.13  E-value=0.098  Score=41.82  Aligned_cols=17  Identities=29%  Similarity=0.313  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      .+++|.||+|||||..+
T Consensus        59 ~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        59 LHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            37999999999999754

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.

>KOG0341|consensus

Probab=93.07  E-value=0.015  Score=50.65  Aligned_cols=47  Identities=17%  Similarity=0.139  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |.|.|.+-+..+    .+|...|--|-||||||+.|.+|.+-++.+....+
T Consensus       193 PTpIQvQGlPvv----LsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~l  239 (610)
T KOG0341|consen  193 PTPIQVQGLPVV----LSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMML  239 (610)
T ss_pred             CCceeecCcceE----eecCceeeEEeecCCceEEEeHHHHHHHHHHHhcC
Confidence            455555555543    35677888899999999999999988877655443

>PF05729 NACHT: NACHT domain

Probab=93.04  E-value=0.13  Score=35.49  Aligned_cols=26  Identities=19%  Similarity=0.070  Sum_probs=17.6

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|.|+.|+|||..+---+..|...
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~   27 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEE   27 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhc
Confidence            57899999999997543333344433

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=93.04  E-value=0.032  Score=49.66  Aligned_cols=25  Identities=24%  Similarity=0.491  Sum_probs=21.7

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ..|+++-||||+|||.++++|.+..
T Consensus       158 ~~hvLviapTgSGKg~g~VIPnLL~  182 (606)
T PRK13897        158 FQHALLFAPTGSGKGVGFVIPNLLF  182 (606)
T ss_pred             CceEEEEcCCCCCcceEEehhhHHh
Confidence            4689999999999999999996543

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=93.03  E-value=0.1  Score=47.74  Aligned_cols=34  Identities=24%  Similarity=0.196  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls~   66 (115)
                      -+|.+.|+.|.+++...           ...+|.||||+|||..+
T Consensus       568 ~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA  612 (852)
T TIGR03346       568 VGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELA  612 (852)
T ss_pred             CCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHH
Confidence            57888888888888652           24789999999999653

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.03  E-value=0.24  Score=41.96  Aligned_cols=25  Identities=24%  Similarity=0.283  Sum_probs=18.8

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..+++-||||+|||.+..--|..+.
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~  199 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYG  199 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5688999999999988654444444

>TIGR00750 lao LAO/AO transport system ATPase

Probab=93.00  E-value=0.094  Score=42.04  Aligned_cols=44  Identities=11%  Similarity=0.045  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.+.........+.|.||+|+|||.- +.....++...+.++
T Consensus        22 ~~~~~~~~~~~~~~~i~i~G~~G~GKttl-~~~l~~~~~~~~~~v   65 (300)
T TIGR00750        22 QLLDRIMPYTGNAHRVGITGTPGAGKSTL-LEALGMELRRRGLKV   65 (300)
T ss_pred             HHHHhCCcccCCceEEEEECCCCCCHHHH-HHHHHHHHHHCCCeE
Confidence            34555544444567788899999999953 333344444444444

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>KOG0243|consensus

Probab=93.00  E-value=0.091  Score=49.60  Aligned_cols=42  Identities=21%  Similarity=0.240  Sum_probs=28.3

Q ss_pred             ccCCCC----CCHHHHHHHHHHHHHHh----cC--CcEEEecCCCCCchHHH
Q psy14273         25 FPFPFD----AYDIQSNFMKNLYYTLD----NS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        25 ~~fpf~----~r~~Q~e~m~~I~~~l~----~~--~~~iiEaPTGtGKTls~   66 (115)
                      ..|+|+    |-..|.++.+.+..-+-    .|  .-++..|+||||||.+.
T Consensus        95 k~ftFDkVFGpes~Q~d~Y~~~v~p~i~eVl~GyNCTIFAYGQTGTGKTyTM  146 (1041)
T KOG0243|consen   95 KTFTFDKVFGPESQQEDLYDQAVSPIIKEVLEGYNCTIFAYGQTGTGKTYTM  146 (1041)
T ss_pred             ceeecceeeCcchhHHHHHHHHHHHHHHHHhccCCceEEEecCCCCCceeee
Confidence            335555    66778877766544332    34  45778999999999874

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=92.98  E-value=0.13  Score=46.97  Aligned_cols=34  Identities=24%  Similarity=0.208  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHHHhc--------C---CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDN--------S---KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~--------~---~~~iiEaPTGtGKTls~   66 (115)
                      -+|.+.++.|..++..        +   ..++|.||||+|||...
T Consensus       461 iGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lA  505 (758)
T PRK11034        461 FGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVT  505 (758)
T ss_pred             eCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHH
Confidence            3678888888888762        1   35789999999999654

>PRK06620 hypothetical protein; Validated

Probab=92.97  E-value=0.21  Score=38.35  Aligned_cols=34  Identities=9%  Similarity=0.025  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHhc-C-----CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDN-S-----KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~-~-----~~~iiEaPTGtGKTls~   66 (115)
                      +........+.++... +     ..++|.||+|+|||.-+
T Consensus        22 ~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl   61 (214)
T PRK06620         22 SSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLT   61 (214)
T ss_pred             ccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHH
Confidence            4344455666655542 1     44899999999999643

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.96  E-value=0.14  Score=44.99  Aligned_cols=41  Identities=20%  Similarity=0.281  Sum_probs=32.4

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      |+---+|.+..+.+.+++.+++  | .||.||.|+|||....+-
T Consensus        15 f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~l   58 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARIL   58 (576)
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            4433588999999999998873  4 489999999999876554

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

Probab=92.94  E-value=0.098  Score=39.45  Aligned_cols=34  Identities=12%  Similarity=0.144  Sum_probs=21.3

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+..+++.||+|||||+=.+--+...+...+.++
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~v   51 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKV   51 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--E
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcE
Confidence            3568999999999999654433444444424443

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 ....

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=92.94  E-value=0.15  Score=44.80  Aligned_cols=45  Identities=22%  Similarity=0.241  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~al~~   73 (115)
                      |+---+|.+..+.+.+++.++  .| .+|.||.|+|||..+-+-+-.+
T Consensus        15 f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal   62 (559)
T PRK05563         15 FEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAV   62 (559)
T ss_pred             HHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            333358999999999999877  34 6789999999997765554443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=92.90  E-value=0.098  Score=48.06  Aligned_cols=36  Identities=22%  Similarity=0.176  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls~L~   68 (115)
                      -+|...|..|..++...           ..++|.||||+|||..+-+
T Consensus       571 iGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~a  617 (857)
T PRK10865        571 IGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKA  617 (857)
T ss_pred             eCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHH
Confidence            47888888888887632           2578999999999976533

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=92.90  E-value=0.18  Score=41.07  Aligned_cols=42  Identities=17%  Similarity=0.137  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .-+...++.+.+.++...+..++|.|.+||||++.  +-++...
T Consensus        11 ~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~l--A~~iH~~   52 (326)
T PRK11608         11 EANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELI--ASRLHYL   52 (326)
T ss_pred             CCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHH--HHHHHHh
Confidence            34667778888888888889999999999999954  4444433

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=92.89  E-value=0.17  Score=45.63  Aligned_cols=38  Identities=21%  Similarity=0.195  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHhcCCc---EEEecCCCCCchHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~---~iiEaPTGtGKTls~L~~a   70 (115)
                      -+|...+..+.+++.+++.   .||.||.|+|||....+-+
T Consensus        19 vGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lA   59 (647)
T PRK07994         19 VGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLA   59 (647)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            4899999999999998853   5899999999997655443

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=92.88  E-value=0.12  Score=45.78  Aligned_cols=39  Identities=26%  Similarity=0.272  Sum_probs=31.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls   65 (115)
                      |||..--+|..+...+..++.+.  ..++|.|+.|||||..
T Consensus         1 ~pf~~ivGq~~~~~al~~~av~~~~g~vli~G~~GtgKs~l   41 (633)
T TIGR02442         1 FPFTAIVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTA   41 (633)
T ss_pred             CCcchhcChHHHHHHHHHHhhCCCCCeEEEEcCCCCcHHHH
Confidence            78886678888888887777653  4699999999999965

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=92.83  E-value=0.16  Score=32.75  Aligned_cols=29  Identities=17%  Similarity=0.290  Sum_probs=21.1

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      +...+|.+|+|+|||.  |+=|++|+.--..
T Consensus        23 g~~tli~G~nGsGKST--llDAi~~~L~~~~   51 (62)
T PF13555_consen   23 GDVTLITGPNGSGKST--LLDAIQTVLYGNT   51 (62)
T ss_pred             CcEEEEECCCCCCHHH--HHHHHHHHHcCCc
Confidence            3478999999999995  4666777655433

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=92.83  E-value=0.14  Score=45.84  Aligned_cols=44  Identities=25%  Similarity=0.132  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--C-cEEEecCCCCCchHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--K-FGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~-~~iiEaPTGtGKTls~L~~al~   72 (115)
                      |+-.-+|...++.+.+++.++  . ..+|.||.|+|||..+.+-+-.
T Consensus        15 F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~   61 (605)
T PRK05896         15 FKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKA   61 (605)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            333348888999999999776  3 3779999999999776655433

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=92.80  E-value=0.25  Score=37.96  Aligned_cols=25  Identities=24%  Similarity=0.255  Sum_probs=18.5

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|.||+|+|||- +|.++...+..
T Consensus        36 ~l~l~G~~G~GKTH-LL~Ai~~~~~~   60 (219)
T PF00308_consen   36 PLFLYGPSGLGKTH-LLQAIANEAQK   60 (219)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHH-HHHHHHHHHHh
Confidence            48999999999998 55555554444

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=92.75  E-value=0.14  Score=47.85  Aligned_cols=42  Identities=26%  Similarity=0.245  Sum_probs=28.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+..||++|.-  -.+  +|.  .--|.|+.||.|||+++.+|++..+
T Consensus        79 lGm~~ydVQli--Gg~--~Lh--~G~iaEM~TGEGKTLvA~l~a~l~a  120 (913)
T PRK13103         79 MGMRHFDVQLI--GGM--TLH--EGKIAEMRTGEGKTLVGTLAVYLNA  120 (913)
T ss_pred             hCCCcchhHHH--hhh--Hhc--cCccccccCCCCChHHHHHHHHHHH
Confidence            35567788764  222  232  3367799999999999988876444

>CHL00095 clpC Clp protease ATP binding subunit

Probab=92.70  E-value=0.12  Score=47.00  Aligned_cols=33  Identities=21%  Similarity=0.209  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls   65 (115)
                      -+|.+.++.|.+++...           ...+|.||||+|||..
T Consensus       512 ~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~l  555 (821)
T CHL00095        512 IGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTEL  555 (821)
T ss_pred             cChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHH
Confidence            48999999998888632           1368999999999954

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=92.69  E-value=0.13  Score=47.57  Aligned_cols=37  Identities=22%  Similarity=0.210  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      =+|.++++.+.+++.+++  | .||.||.|+|||....+-
T Consensus        19 IGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriL   58 (830)
T PRK07003         19 VGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIF   58 (830)
T ss_pred             cCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            479999999999998873  4 589999999999765543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.69  E-value=0.16  Score=46.22  Aligned_cols=39  Identities=18%  Similarity=0.165  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~al   71 (115)
                      =+|.++++.+.+++.+++  | .||.||.|+|||....+-+-
T Consensus        19 IGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAk   60 (700)
T PRK12323         19 VGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK   60 (700)
T ss_pred             cCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            479999999999999884  4 58999999999976555433

>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group

Probab=92.68  E-value=0.052  Score=44.00  Aligned_cols=37  Identities=11%  Similarity=0.123  Sum_probs=25.4

Q ss_pred             CCHHHHHHHHHH----HHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         31 AYDIQSNFMKNL----YYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        31 ~r~~Q~e~m~~I----~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      +..-|.++.+.+    ...+-+|  ..++..|+||||||.+..
T Consensus        61 ~~~~q~~vf~~~~~plv~~~~~G~n~~i~ayGqtGSGKTyTm~  103 (322)
T cd01367          61 EAVTNEEVYRSTVKPLIPHVFEGGVATCFAYGQTGSGKTYTML  103 (322)
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCceEEEeccCCCCCCceEec
Confidence            555677777763    3333345  456679999999999875

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

>TIGR03263 guanyl_kin guanylate kinase

Probab=92.66  E-value=0.072  Score=38.46  Aligned_cols=16  Identities=31%  Similarity=0.561  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      |+.++|.||+|+|||.
T Consensus         1 g~ii~l~G~~GsGKsT   16 (180)
T TIGR03263         1 GLLIVISGPSGVGKST   16 (180)
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4578999999999995

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.58  E-value=0.18  Score=43.68  Aligned_cols=37  Identities=24%  Similarity=0.178  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      -+|...+..+.+++.++.  + .+|.||.|+|||....+-
T Consensus        19 iGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~l   58 (486)
T PRK14953         19 IGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARIL   58 (486)
T ss_pred             cChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            489999999999998873  4 478999999998765544

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=92.58  E-value=0.16  Score=46.12  Aligned_cols=36  Identities=19%  Similarity=0.190  Sum_probs=26.6

Q ss_pred             CHHHHHHHH---HHHHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         32 YDIQSNFMK---NLYYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        32 r~~Q~e~m~---~I~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      .-+|...+.   .+.+.+.++  .+++|.||+|||||..+-
T Consensus        30 ~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~   70 (725)
T PRK13341         30 FVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLAR   70 (725)
T ss_pred             hcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHH
Confidence            357777773   566667665  579999999999996543

>cd01365 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins

Probab=92.57  E-value=0.055  Score=44.37  Aligned_cols=35  Identities=20%  Similarity=0.195  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      --|.++.+.+..    .+-+|  ..++..|+||||||.+++
T Consensus        67 ~tq~~vf~~~~~p~v~~~l~G~n~~i~ayGqtGSGKT~Tm~  107 (356)
T cd01365          67 ASQEDVFEDLGRELLDHAFEGYNVCLFAYGQTGSGKSYTMM  107 (356)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCceEEEEecCCCCCCeEEec
Confidence            458887766533    33345  457779999999999875

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.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=92.56  E-value=0.28  Score=40.37  Aligned_cols=43  Identities=16%  Similarity=0.093  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~al~~   73 (115)
                      .||-|....+.+.+.+.+++  | .+|.||.|+||+..++.-+-..
T Consensus         5 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~L   50 (319)
T PRK08769          5 FSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHV   50 (319)
T ss_pred             ccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHH
Confidence            78899999999999998874  4 7899999999987655543333

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=92.51  E-value=0.3  Score=39.65  Aligned_cols=49  Identities=14%  Similarity=0.153  Sum_probs=33.4

Q ss_pred             CHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         32 YDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |+.=.++++.+.++-.+.  ...|+.|+.|||||.++ +-++.|+..++=-|
T Consensus         4 R~~t~el~~~l~~~~~~~~~~r~vL~G~~GsGKS~~L-~q~~~~A~~~~wiV   54 (309)
T PF10236_consen    4 RKPTLELINKLKEADKSSKNNRYVLTGERGSGKSVLL-AQAVHYARENGWIV   54 (309)
T ss_pred             chHHHHHHHHHHHhcccCCceEEEEECCCCCCHHHHH-HHHHHHHHhCCEEE
Confidence            444456666666663333  56899999999999864 45578887765444

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>KOG0349|consensus

Probab=92.49  E-value=0.04  Score=48.73  Aligned_cols=43  Identities=19%  Similarity=0.198  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      |.++|.+.|..|    ..|..+++-|-||||||=++.+|+++-..+.
T Consensus        25 ptdvqaeaipli----lgggdvlmaaetgsgktgaf~lpilqiv~et   67 (725)
T KOG0349|consen   25 PTDVQAEAIPLI----LGGGDVLMAAETGSGKTGAFCLPILQIVWET   67 (725)
T ss_pred             ccccccccccEE----ecCCcEEEEeccCCCCccceehhhHHHHHHH
Confidence            678899988865    4678999999999999999999999876553

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.43  E-value=0.25  Score=43.97  Aligned_cols=30  Identities=20%  Similarity=0.313  Sum_probs=20.7

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +..++.++|.||||+|||.....-+..+..
T Consensus       347 l~~G~vIaLVGPtGvGKTTtaakLAa~la~  376 (559)
T PRK12727        347 LERGGVIALVGPTGAGKTTTIAKLAQRFAA  376 (559)
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            445678889999999999765443333333

>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=92.39  E-value=0.089  Score=35.09  Aligned_cols=14  Identities=21%  Similarity=0.154  Sum_probs=11.9

Q ss_pred             EEEecCCCCCchHH
Q psy14273         52 GIFESPTGTGKSLS   65 (115)
Q Consensus        52 ~iiEaPTGtGKTls   65 (115)
                      ++|.|++|||||..
T Consensus         1 I~i~G~~GsGKtTi   14 (129)
T PF13238_consen    1 IGISGIPGSGKTTI   14 (129)
T ss_dssp             EEEEESTTSSHHHH
T ss_pred             CEEECCCCCCHHHH
Confidence            57899999999953

...

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=92.37  E-value=0.051  Score=48.91  Aligned_cols=25  Identities=24%  Similarity=0.369  Sum_probs=21.8

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      ...|+++-||||+|||.++++|.|.
T Consensus       143 g~~hvLviApTrSGKgvg~VIPnLL  167 (663)
T PRK13876        143 GPEHVLCFAPTRSGKGVGLVVPTLL  167 (663)
T ss_pred             CCceEEEEecCCCCcceeEehhhHH
Confidence            3479999999999999999999653

>CHL00181 cbbX CbbX; Provisional

Probab=92.35  E-value=0.12  Score=41.51  Aligned_cols=20  Identities=25%  Similarity=0.230  Sum_probs=16.1

Q ss_pred             CcEEEecCCCCCchHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~   69 (115)
                      .+++|.||+|||||..+-+-
T Consensus        60 ~~ill~G~pGtGKT~lAr~l   79 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALKM   79 (287)
T ss_pred             ceEEEECCCCCCHHHHHHHH
Confidence            46899999999999765444

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=92.33  E-value=0.033  Score=49.68  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=21.2

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      ..|+++.||||+|||.++++|.|.
T Consensus       175 ~~HvlviapTgSGKgvg~ViPnLL  198 (636)
T PRK13880        175 PEHVLTYAPTRSGKGVGLVVPTLL  198 (636)
T ss_pred             CceEEEEecCCCCCceEEEccchh
Confidence            368999999999999999999653

>cd01366 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins

Probab=92.31  E-value=0.084  Score=42.55  Aligned_cols=38  Identities=13%  Similarity=0.141  Sum_probs=24.8

Q ss_pred             CCHHHHHHHHHHHHHHh---cC--CcEEEecCCCCCchHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLD---NS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~---~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      +...|.++.+.|...+.   +|  ..++..|+||||||.+++-
T Consensus        55 ~~~~q~~v~~~v~p~v~~~~~G~~~~i~ayG~tgSGKT~tl~G   97 (329)
T cd01366          55 PDASQEDVFEEVSPLVQSALDGYNVCIFAYGQTGSGKTYTMEG   97 (329)
T ss_pred             CCCCHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCCcEEecC
Confidence            44456666555544333   34  3567799999999998744

Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport 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 this subgroup the motor domain is found at the C-terminus (C-type). 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 mi

>KOG1802|consensus

Probab=92.29  E-value=0.13  Score=47.37  Aligned_cols=48  Identities=23%  Similarity=0.285  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhhH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGL   82 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~   82 (115)
                      .-..|....+.|    .+...-+|.||.|||||++--.-+...+..+..+|+
T Consensus       411 LN~SQ~~AV~~V----L~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~~VL  458 (935)
T KOG1802|consen  411 LNASQSNAVKHV----LQRPLSLIQGPPGTGKTVTSATIVYHLARQHAGPVL  458 (935)
T ss_pred             hchHHHHHHHHH----HcCCceeeecCCCCCceehhHHHHHHHHHhcCCceE
Confidence            446777755543    467789999999999999854445555666666653

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=92.28  E-value=0.099  Score=45.99  Aligned_cols=36  Identities=25%  Similarity=0.250  Sum_probs=28.5

Q ss_pred             CCCHHHHHHHHHHHH---HHhcCCcEEEecCCCCCchHH
Q psy14273         30 DAYDIQSNFMKNLYY---TLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~---~l~~~~~~iiEaPTGtGKTls   65 (115)
                      --|++|.++...+..   .+..|..+++.||.|+|||.-
T Consensus        10 i~r~Ie~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKSTL   48 (504)
T TIGR03238        10 VKRKIQTDLERILVKFNKELPSSSLLFLCGSSGDGKSEI   48 (504)
T ss_pred             echHHHHHHHHHHhCCceeecCCCEEEEECCCCCCHHHH
Confidence            367999998777654   245688999999999999953

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=92.27  E-value=0.28  Score=46.23  Aligned_cols=49  Identities=16%  Similarity=0.159  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +...+.|.+.+..|   +..+..++|.|+.|||||.. |-.++..+...+.+|
T Consensus       345 ~~Ls~eQr~Av~~i---l~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~~G~~V  393 (988)
T PRK13889        345 LVLSGEQADALAHV---TDGRDLGVVVGYAGTGKSAM-LGVAREAWEAAGYEV  393 (988)
T ss_pred             CCCCHHHHHHHHHH---hcCCCeEEEEeCCCCCHHHH-HHHHHHHHHHcCCeE
Confidence            45678999976654   45456889999999999975 455555555555554

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=92.26  E-value=0.13  Score=45.41  Aligned_cols=32  Identities=25%  Similarity=0.483  Sum_probs=24.4

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+|+++.|+||||||. ++-..+.++..++.++
T Consensus       176 ~~h~li~G~tGsGKs~-~i~~ll~~~~~~g~~~  207 (566)
T TIGR02759       176 TQHILIHGTTGSGKSV-AIRKLLRWIRQRGDRA  207 (566)
T ss_pred             ccceEEEcCCCCCHHH-HHHHHHHHHHhcCCeE
Confidence            4689999999999996 4455778876666554

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).

>cd01372 KISc_KIF4 Kinesin motor domain, KIF4-like subfamily

Probab=92.25  E-value=0.082  Score=42.81  Aligned_cols=46  Identities=22%  Similarity=0.265  Sum_probs=29.7

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHHH----HhcC--CcEEEecCCCCCchHHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYYT----LDNS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~~----l~~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      ..|.|.  |.+-..|.++.+.+..-    +-+|  ..++..|+||||||.++.-
T Consensus        40 ~~f~FD~vf~~~~~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKT~Tm~G   93 (341)
T cd01372          40 KSFTFDYVFDPSTSQEEVYNTCVAPLVDGLFEGYNATVLAYGQTGSGKTYTMGT   93 (341)
T ss_pred             cEEeccccCCCCCCHHHHHHHHHHHHHHHHhCCCccceeeecCCCCCCcEEecC
Confidence            445555  33546677776665532    2344  4577899999999999643

Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during 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,

>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup

Probab=92.24  E-value=0.069  Score=43.04  Aligned_cols=44  Identities=20%  Similarity=0.268  Sum_probs=28.0

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      ..|.|.  |.+-.-|.++.+.+..    .+-.|  ..++..|+||||||.++
T Consensus        43 ~~f~FD~vf~~~~~q~~vy~~~~~~~v~~~~~G~n~~i~ayG~tgSGKT~Tm   94 (325)
T cd01369          43 KTFSFDRVFPPNTTQEDVYNFVAKPIVDDVLNGYNGTIFAYGQTGSGKTYTM   94 (325)
T ss_pred             eEEEcCeEECCCCCHHHHHHHHHHHHHHHHHcCccceEEEeCCCCCCceEEe
Confidence            344444  3355567777666532    22344  45778999999999985

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

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=92.24  E-value=0.23  Score=40.60  Aligned_cols=39  Identities=15%  Similarity=0.171  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      +.-.++.+.+.++...+..++|.|++||||++.  +-++..
T Consensus         6 ~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~l--Ar~iH~   44 (329)
T TIGR02974         6 NAFLEVLEQVSRLAPLDRPVLIIGERGTGKELI--AARLHY   44 (329)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCChHHHH--HHHHHH
Confidence            445566777777777788999999999999963  444443

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=92.22  E-value=0.14  Score=42.83  Aligned_cols=31  Identities=23%  Similarity=0.214  Sum_probs=22.5

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+|+++-|+||+|||.. +-.++.++...+..
T Consensus        42 ~~h~~i~g~tGsGKt~~-i~~l~~~~~~~~~~   72 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQ-IRELLASIRARGDR   72 (410)
T ss_pred             hccEEEEcCCCCCHHHH-HHHHHHHHHhcCCC
Confidence            46899999999999975 44456666555544

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=92.21  E-value=0.21  Score=42.88  Aligned_cols=35  Identities=14%  Similarity=0.167  Sum_probs=28.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .-+.-.++++.+.++...+..++|.|++||||++.
T Consensus       201 ~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~l  235 (534)
T TIGR01817       201 KSPAMRQVVDQARVVARSNSTVLLRGESGTGKELI  235 (534)
T ss_pred             CCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHH
Confidence            44666677777777777788999999999999964

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>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=92.17  E-value=0.12  Score=37.55  Aligned_cols=35  Identities=20%  Similarity=0.366  Sum_probs=23.6

Q ss_pred             HHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         39 MKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        39 m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ++.|.+++.++  .++++.||.|+|||. +|--++..+
T Consensus         8 l~~l~~~l~~~~~~~~~l~G~rg~GKTs-Ll~~~~~~~   44 (234)
T PF01637_consen    8 LEKLKELLESGPSQHILLYGPRGSGKTS-LLKEFINEL   44 (234)
T ss_dssp             HHHHHHCHHH--SSEEEEEESTTSSHHH-HHHHHHHHC
T ss_pred             HHHHHHHHHhhcCcEEEEEcCCcCCHHH-HHHHHHHHh
Confidence            34556666664  789999999999996 333444444

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=92.16  E-value=0.22  Score=44.26  Aligned_cols=41  Identities=17%  Similarity=0.181  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ..+.-..+.+.+..+...+..++|.|++|||||+.  +-++..
T Consensus       381 ~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~l--A~~ih~  421 (686)
T PRK15429        381 RSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELI--ARAIHN  421 (686)
T ss_pred             cCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHH--HHHHHH
Confidence            34556666666776667778999999999999963  444443

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

Probab=92.13  E-value=0.31  Score=44.63  Aligned_cols=49  Identities=16%  Similarity=0.135  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .-+.|....+.|...+......++.+.||+|||-.||-.+-..+.+ ++.
T Consensus       199 Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~-Gkq  247 (730)
T COG1198         199 LNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ-GKQ  247 (730)
T ss_pred             cCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc-CCE
Confidence            4589999999888777333678899999999999998887666655 444

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

Probab=92.12  E-value=0.27  Score=42.29  Aligned_cols=50  Identities=14%  Similarity=-0.028  Sum_probs=44.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..++|......+...++++...++-|-||+|||=. +..++.++...+.+|
T Consensus        98 Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~G~~v  147 (441)
T COG4098          98 LSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQGGRV  147 (441)
T ss_pred             cChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhcCCeE
Confidence            56899999999999999999999999999999975 567788888887775

>KOG1805|consensus

Probab=92.11  E-value=0.13  Score=48.57  Aligned_cols=46  Identities=22%  Similarity=0.247  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhhH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGL   82 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~   82 (115)
                      ..|++   ++.+++......+|.|-+|||||.+ ++.++.-+...+++|+
T Consensus       672 ~dQr~---A~~k~L~aedy~LI~GMPGTGKTTt-I~~LIkiL~~~gkkVL  717 (1100)
T KOG1805|consen  672 NDQRQ---ALLKALAAEDYALILGMPGTGKTTT-ISLLIKILVALGKKVL  717 (1100)
T ss_pred             HHHHH---HHHHHHhccchheeecCCCCCchhh-HHHHHHHHHHcCCeEE
Confidence            57888   5566788888999999999999965 5666777778888874

>KOG0922|consensus

Probab=92.04  E-value=0.16  Score=46.00  Aligned_cols=29  Identities=24%  Similarity=0.509  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      ++.+.|..++.+++.+|+-|.||+|||.=
T Consensus        54 ~~r~~il~~ve~nqvlIviGeTGsGKSTQ   82 (674)
T KOG0922|consen   54 KYRDQILYAVEDNQVLIVIGETGSGKSTQ   82 (674)
T ss_pred             HHHHHHHHHHHHCCEEEEEcCCCCCcccc
Confidence            45677888889999999999999999954

>cd01364 KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division

Probab=92.03  E-value=0.079  Score=43.24  Aligned_cols=46  Identities=17%  Similarity=0.143  Sum_probs=29.5

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHHH----HhcCC--cEEEecCCCCCchHHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYYT----LDNSK--FGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~~----l~~~~--~~iiEaPTGtGKTls~L~   68 (115)
                      ..|.|.  |.+-..|.++.+.+..-    +-+|.  .++..|+||||||.++.-
T Consensus        48 ~~f~Fd~vf~~~~~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKTyTl~G  101 (352)
T cd01364          48 KTYTFDKVFGPEADQIEVYSQVVSPILDEVLMGYNCTIFAYGQTGTGKTYTMEG  101 (352)
T ss_pred             eeEeccccCCCCCCHHHHHHHHHHHHHHHHhCCCeEEEEECCCCCCCCcEEecC
Confidence            345555  44556787777665433    23453  466789999999988643

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 d

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=91.98  E-value=0.12  Score=42.37  Aligned_cols=24  Identities=25%  Similarity=0.337  Sum_probs=17.8

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++.++|.||||||||.-    ++.+++.
T Consensus         4 ~~ii~I~GpTasGKS~L----Al~LA~~   27 (300)
T PRK14729          4 NKIVFIFGPTAVGKSNI----LFHFPKG   27 (300)
T ss_pred             CcEEEEECCCccCHHHH----HHHHHHh
Confidence            45789999999999953    3455555

>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=91.97  E-value=0.11  Score=35.02  Aligned_cols=14  Identities=43%  Similarity=0.660  Sum_probs=12.1

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|.||+|+|||.
T Consensus         1 vI~I~G~~gsGKST   14 (121)
T PF13207_consen    1 VIIISGPPGSGKST   14 (121)
T ss_dssp             EEEEEESTTSSHHH
T ss_pred             CEEEECCCCCCHHH
Confidence            36889999999994

...

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=91.96  E-value=0.19  Score=46.85  Aligned_cols=40  Identities=28%  Similarity=0.230  Sum_probs=28.2

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      ..++.||+.|.--.  +  ++  ..--|.|+.||-||||++.+|+.
T Consensus        72 ~lG~r~ydvQlig~--l--~L--~~G~IaEm~TGEGKTL~a~l~ay  111 (870)
T CHL00122         72 TLGLRHFDVQLIGG--L--VL--NDGKIAEMKTGEGKTLVATLPAY  111 (870)
T ss_pred             HhCCCCCchHhhhh--H--hh--cCCccccccCCCCchHHHHHHHH
Confidence            45566777775532  2  12  33477899999999999998874

>PRK08084 DNA replication initiation factor; Provisional

Probab=91.93  E-value=0.45  Score=36.78  Aligned_cols=33  Identities=24%  Similarity=0.273  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      .+...+..+.++...  +..+++.||+|+|||.-+
T Consensus        28 ~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl   62 (235)
T PRK08084         28 DNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLL   62 (235)
T ss_pred             ccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHH
Confidence            455566666665543  367999999999999543

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=91.91  E-value=0.4  Score=39.98  Aligned_cols=42  Identities=12%  Similarity=-0.020  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      -+|.+..+.+.+++.++  .| .+|.||.|+||+..++.-+-.++
T Consensus        22 iGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Ll   66 (365)
T PRK07471         22 FGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLL   66 (365)
T ss_pred             cChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHh
Confidence            58999999999999988  34 78999999999976655544443

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=91.87  E-value=0.28  Score=41.40  Aligned_cols=36  Identities=19%  Similarity=0.287  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHHHhcCC-----------c-EEEecCCCCCchHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK-----------F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~-----------~-~iiEaPTGtGKTls~L~~   69 (115)
                      +|....+.+.+++.++.           + .+|.||.|+|||.....-
T Consensus         9 Gq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~l   56 (394)
T PRK07940          9 GQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAF   56 (394)
T ss_pred             ChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHH
Confidence            78888888888888753           3 779999999998665544

>TIGR00763 lon ATP-dependent protease La

Probab=91.86  E-value=0.25  Score=44.74  Aligned_cols=33  Identities=15%  Similarity=0.132  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHh--------cCCcEEEecCCCCCchHHHH
Q psy14273         35 QSNFMKNLYYTLD--------NSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        35 Q~e~m~~I~~~l~--------~~~~~iiEaPTGtGKTls~L   67 (115)
                      |.+..+.|...+.        ++.+++|.||+|+|||..+-
T Consensus       325 ~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk  365 (775)
T TIGR00763       325 LKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGK  365 (775)
T ss_pred             hHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHH
Confidence            4555555555332        24579999999999996533

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.

>KOG0239|consensus

Probab=91.84  E-value=0.14  Score=46.25  Aligned_cols=45  Identities=18%  Similarity=0.273  Sum_probs=33.0

Q ss_pred             ccCC--CCCCHHHHHHHHHHHHHHhc---C--CcEEEecCCCCCchHHHHHH
Q psy14273         25 FPFP--FDAYDIQSNFMKNLYYTLDN---S--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        25 ~~fp--f~~r~~Q~e~m~~I~~~l~~---~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      |.|.  |.|-..|.+.+..+...+..   |  .+++..|.||+|||++.--|
T Consensus       362 f~fdkVf~p~~sQ~~VF~e~~~lv~S~lDGYnVCIFAYGQTGSGKTyTM~G~  413 (670)
T KOG0239|consen  362 FKFDKVFGPLASQDDVFEEVSPLVQSALDGYNVCIFAYGQTGSGKTYTMSGP  413 (670)
T ss_pred             ceeeeecCCcccHHHHHHHHHHHHHHHhcCcceeEEEecccCCCccccccCC
Confidence            4444  56888999988877665543   4  34556999999999987664

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=91.79  E-value=0.38  Score=39.96  Aligned_cols=37  Identities=22%  Similarity=0.116  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~   69 (115)
                      -+|.+....+..++.++.   ..+|.||.|+|||.....-
T Consensus        26 ~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~l   65 (351)
T PRK09112         26 FGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHL   65 (351)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHH
Confidence            578888899999998885   4889999999999665544

>PRK00300 gmk guanylate kinase; Provisional

Probab=91.79  E-value=0.11  Score=38.33  Aligned_cols=17  Identities=29%  Similarity=0.565  Sum_probs=15.0

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .+..++|.||+|+|||.
T Consensus         4 ~g~~i~i~G~sGsGKst   20 (205)
T PRK00300          4 RGLLIVLSGPSGAGKST   20 (205)
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            56789999999999994

>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis

Probab=91.75  E-value=0.095  Score=42.26  Aligned_cols=45  Identities=13%  Similarity=0.195  Sum_probs=28.4

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+-..|.++.+.+..    .+-+|  ..++..|+||||||.++.
T Consensus        40 ~~f~fd~vf~~~~~q~~vy~~~~~p~v~~~l~G~n~~i~ayG~tgSGKT~T~~   92 (321)
T cd01374          40 QSFTFDRVFGGESTNREVYERIAKPVVRSALEGYNGTIFAYGQTSSGKTFTMS   92 (321)
T ss_pred             eEEecCeEECCCCCHHHHHHHHHHHHHHHHHCCCceeEEeecCCCCCCceecc
Confidence            344444  3354567777665433    22345  356779999999999875

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

>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=91.73  E-value=0.38  Score=38.58  Aligned_cols=37  Identities=24%  Similarity=0.382  Sum_probs=25.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHh---c-C---CcEEEecCCCCCchH
Q psy14273         28 PFDAYDIQSNFMKNLYYTLD---N-S---KFGIFESPTGTGKSL   64 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~---~-~---~~~iiEaPTGtGKTl   64 (115)
                      -++-+-+|.++...+.-.+.   . +   .+++|.||.|+|||.
T Consensus        22 ~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTT   65 (233)
T PF05496_consen   22 SLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTT   65 (233)
T ss_dssp             SCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHH
T ss_pred             CHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhH
Confidence            46677899998887654443   1 2   489999999999984

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=91.73  E-value=0.49  Score=36.36  Aligned_cols=21  Identities=24%  Similarity=0.055  Sum_probs=15.5

Q ss_pred             CcEEEecCCCCCchHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~a   70 (115)
                      ..+++.||+|+|||.-+.+-+
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~   60 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVS   60 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            457899999999996444333

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=91.72  E-value=0.18  Score=43.91  Aligned_cols=30  Identities=20%  Similarity=0.163  Sum_probs=22.3

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +..++|-||||+|||.+...-+..+...++
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G  285 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHG  285 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcC
Confidence            457889999999999887666555554543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=91.71  E-value=0.2  Score=46.10  Aligned_cols=34  Identities=15%  Similarity=0.200  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHhc---C--------CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDN---S--------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~---~--------~~~iiEaPTGtGKTls~   66 (115)
                      -+|.+.+..|.+++..   |        ...+|.||||+|||...
T Consensus       569 ~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA  613 (852)
T TIGR03345       569 IGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETA  613 (852)
T ss_pred             cChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHH
Confidence            4788888888887743   1        24789999999999653

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

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

Probab=91.71  E-value=0.12  Score=42.69  Aligned_cols=29  Identities=17%  Similarity=0.163  Sum_probs=22.3

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhhH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAGL   82 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~   82 (115)
                      ..+||.|||++|||    .-+++.++..+-.|.
T Consensus         4 ~~i~I~GPTAsGKT----~lai~LAk~~~~eII   32 (308)
T COG0324           4 KLIVIAGPTASGKT----ALAIALAKRLGGEII   32 (308)
T ss_pred             cEEEEECCCCcCHH----HHHHHHHHHcCCcEE
Confidence            46889999999999    445677777776653

>PRK04296 thymidine kinase; Provisional

Probab=91.69  E-value=0.17  Score=37.97  Aligned_cols=32  Identities=16%  Similarity=0.247  Sum_probs=22.0

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |...++.||.|+|||..++--+..+. ..+.++
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~-~~g~~v   33 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYE-ERGMKV   33 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHH-HcCCeE
Confidence            34678999999999976665554444 345554

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=91.67  E-value=0.23  Score=45.35  Aligned_cols=38  Identities=21%  Similarity=0.241  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~a   70 (115)
                      -+|....+.+.+++.++  .| .+|.||.|+|||.++.+-|
T Consensus        21 iGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLA   61 (725)
T PRK07133         21 VGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFA   61 (725)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHH
Confidence            48899999999999887  34 4899999999997765543

>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=91.65  E-value=0.13  Score=41.32  Aligned_cols=27  Identities=22%  Similarity=0.218  Sum_probs=17.9

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+|-||||||||-    -++..++.++-.|
T Consensus         3 v~~i~GpT~tGKt~----~ai~lA~~~g~pv   29 (233)
T PF01745_consen    3 VYLIVGPTGTGKTA----LAIALAQKTGAPV   29 (233)
T ss_dssp             EEEEE-STTSSHHH----HHHHHHHHH--EE
T ss_pred             EEEEECCCCCChhH----HHHHHHHHhCCCE
Confidence            46789999999994    4566677766655

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

>smart00763 AAA_PrkA PrkA AAA domain

Probab=91.64  E-value=0.31  Score=41.20  Aligned_cols=35  Identities=17%  Similarity=0.208  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHHHHHHHh----cCCcEEEecCCCCCchHH
Q psy14273         31 AYDIQSNFMKNLYYTLD----NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~----~~~~~iiEaPTGtGKTls   65 (115)
                      ..+...+++..+..+..    ..+.++|.||+|+|||..
T Consensus        56 ~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStl   94 (361)
T smart00763       56 MEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSL   94 (361)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHH
Confidence            33445555555554443    136788999999999964

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=91.64  E-value=0.3  Score=43.57  Aligned_cols=39  Identities=13%  Similarity=0.029  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .-+.|.+.+..      .+++++|-|+.|||||.++..=+...+.
T Consensus         3 Ln~~Q~~av~~------~~g~~lV~AgpGSGKT~vL~~Ria~Li~   41 (672)
T PRK10919          3 LNPGQQQAVEF------VTGPCLVLAGAGSGKTRVITNKIAHLIR   41 (672)
T ss_pred             CCHHHHHHHhC------CCCCEEEEecCCCCHHHHHHHHHHHHHH
Confidence            34678775442      3567888899999999986666444443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=91.62  E-value=0.23  Score=43.82  Aligned_cols=39  Identities=26%  Similarity=0.282  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~al   71 (115)
                      -+|...+..+.+++.++.   ..+|.||.|+|||.++.+-+-
T Consensus        19 iGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk   60 (563)
T PRK06647         19 EGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFAR   60 (563)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            479999999999998873   368999999999987665433

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

Probab=91.57  E-value=0.37  Score=45.96  Aligned_cols=49  Identities=22%  Similarity=0.142  Sum_probs=35.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ++|+|...|+--.+.+    -.|+.--+-||||+|||.--++.++-++.. +++
T Consensus        79 ~G~~~ws~QR~WakR~----~rg~SFaiiAPTGvGKTTfg~~~sl~~a~k-gkr  127 (1187)
T COG1110          79 TGFRPWSAQRVWAKRL----VRGKSFAIIAPTGVGKTTFGLLMSLYLAKK-GKR  127 (1187)
T ss_pred             hCCCchHHHHHHHHHH----HcCCceEEEcCCCCchhHHHHHHHHHHHhc-CCe
Confidence            5678999999866654    467777778999999997766666655543 344

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=91.56  E-value=0.12  Score=43.32  Aligned_cols=16  Identities=44%  Similarity=0.704  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ++++|.||+|||||+.
T Consensus       152 knVLFyGppGTGKTm~  167 (368)
T COG1223         152 KNVLFYGPPGTGKTMM  167 (368)
T ss_pred             ceeEEECCCCccHHHH
Confidence            6899999999999964

>PLN03188 kinesin-12 family protein; Provisional

Probab=91.53  E-value=0.062  Score=51.60  Aligned_cols=51  Identities=18%  Similarity=0.136  Sum_probs=34.7

Q ss_pred             CCCCccccCC--CCCCHHHHHHHHHHHHHH----hcC--CcEEEecCCCCCchHHHHHH
Q psy14273         19 AEVPSEFPFP--FDAYDIQSNFMKNLYYTL----DNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        19 ~~~~~~~~fp--f~~r~~Q~e~m~~I~~~l----~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      .+.+..|.|.  |.+...|.++.+.+..-+    -+|  ..++..|.||||||.+..-+
T Consensus       128 ~I~~qtFtFD~VFdp~aTQedVFe~vv~PLV~svLdGyNaTIFAYGQTGSGKTYTM~G~  186 (1320)
T PLN03188        128 TINGQTFTFDSIADPESTQEDIFQLVGAPLVENCLAGFNSSVFAYGQTGSGKTYTMWGP  186 (1320)
T ss_pred             EEeCcEEeCCeeeCCCCCHHHHHHHHHHHHHHHHhcCCcceeecCCCCCCCCCEeeCCC
Confidence            3344556666  446677888887764432    344  45777999999999987653

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=91.48  E-value=0.078  Score=47.42  Aligned_cols=22  Identities=23%  Similarity=0.184  Sum_probs=20.3

Q ss_pred             CcEEEecCCCCCchHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al   71 (115)
                      .|+++-||||+|||.++.+|.+
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnL  233 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTA  233 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhh
Confidence            6999999999999999999953

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=91.47  E-value=0.21  Score=36.65  Aligned_cols=29  Identities=21%  Similarity=0.182  Sum_probs=19.5

Q ss_pred             EEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         52 GIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        52 ~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.|.|++|+|||. ++..++..+...+.++
T Consensus         2 i~i~G~~gsGKTt-l~~~l~~~l~~~G~~V   30 (155)
T TIGR00176         2 LQIVGPKNSGKTT-LIERLVKALKARGYRV   30 (155)
T ss_pred             EEEECCCCCCHHH-HHHHHHHHHHhcCCeE
Confidence            5678999999995 3444555555555454

This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=91.42  E-value=0.34  Score=42.50  Aligned_cols=39  Identities=13%  Similarity=0.065  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+.|.+.+.      ...+++++-|+.|||||.+++.=+...+..
T Consensus         3 n~~Q~~av~------~~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~   41 (664)
T TIGR01074         3 NPQQQEAVE------YVTGPCLVLAGAGSGKTRVITNKIAYLIQN   41 (664)
T ss_pred             CHHHHHHHh------CCCCCEEEEecCCCCHHHHHHHHHHHHHHh
Confidence            467777443      235789999999999999887776666643

Designed to identify rep members of the uvrD/rep subfamily.

>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins

Probab=91.39  E-value=0.11  Score=42.18  Aligned_cols=39  Identities=18%  Similarity=0.220  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      |.+-..|.++.+.+..    .+-+|  ..++..|+||||||.+++
T Consensus        56 f~~~~~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKTyTm~  100 (333)
T cd01371          56 YDPNSTQEDVYNETARPLVDSVLEGYNGTIFAYGQTGTGKTFTME  100 (333)
T ss_pred             cCCCccHHHHHHHHHHHHHHHHhCCCceeEEecCCCCCCCcEeec
Confidence            4455667777665432    33344  457779999999998853

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

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=91.39  E-value=0.34  Score=40.40  Aligned_cols=16  Identities=44%  Similarity=0.567  Sum_probs=13.9

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..+++.||+|||||+.
T Consensus       166 ~gvLL~GppGtGKT~l  181 (389)
T PRK03992        166 KGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CceEEECCCCCChHHH
Confidence            4589999999999965

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=91.37  E-value=0.15  Score=45.23  Aligned_cols=39  Identities=23%  Similarity=0.288  Sum_probs=28.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls   65 (115)
                      -.|+.--+|...|..+.+.+...  .+++|.||+|||||..
T Consensus       151 ~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTL  191 (615)
T TIGR02903       151 RAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTA  191 (615)
T ss_pred             CcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHH
Confidence            33443347777777777766544  5799999999999964

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=91.32  E-value=0.11  Score=35.78  Aligned_cols=13  Identities=46%  Similarity=0.652  Sum_probs=11.7

Q ss_pred             EEEecCCCCCchH
Q psy14273         52 GIFESPTGTGKSL   64 (115)
Q Consensus        52 ~iiEaPTGtGKTl   64 (115)
                      +++.||+|+|||.
T Consensus         2 ii~~G~pgsGKSt   14 (143)
T PF13671_consen    2 IILCGPPGSGKST   14 (143)
T ss_dssp             EEEEESTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            6899999999994

...

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=91.26  E-value=0.24  Score=36.18  Aligned_cols=28  Identities=25%  Similarity=0.353  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      ++-+.+.+.+..+..+++.|+-|+|||.
T Consensus        10 ~l~~~l~~~l~~~~~i~l~G~lGaGKTt   37 (133)
T TIGR00150        10 KFGKAFAKPLDFGTVVLLKGDLGAGKTT   37 (133)
T ss_pred             HHHHHHHHhCCCCCEEEEEcCCCCCHHH
Confidence            3455666677778899999999999984

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.

>KOG0339|consensus

Probab=91.22  E-value=0.074  Score=47.68  Aligned_cols=32  Identities=22%  Similarity=0.224  Sum_probs=26.5

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .+..++--|-||||||.+|+-|.+-.+.+.+.
T Consensus       259 sgrdvigIAktgSgktaAfi~pm~~himdq~e  290 (731)
T KOG0339|consen  259 SGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPE  290 (731)
T ss_pred             ccccchheeeccCcchhHHHHHHHHHhcchhh
Confidence            35677888999999999999999988776553

>KOG0332|consensus

Probab=91.21  E-value=0.09  Score=45.48  Aligned_cols=48  Identities=23%  Similarity=0.284  Sum_probs=35.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +.|+ |..+|...+..+..-  -.+++|..+..|||||.+|.+..|+-...
T Consensus       108 M~F~kPskIQe~aLPlll~~--Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~  156 (477)
T KOG0332|consen  108 MKFQKPSKIQETALPLLLAE--PPQNLIAQSQSGTGKTAAFVLTMLSRVDP  156 (477)
T ss_pred             hccCCcchHHHhhcchhhcC--CchhhhhhhcCCCchhHHHHHHHHHhcCc
Confidence            5566 778888877765311  13689999999999999999888866543

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=91.20  E-value=0.081  Score=47.41  Aligned_cols=23  Identities=22%  Similarity=0.236  Sum_probs=20.8

Q ss_pred             CCcEEEecCCCCCchHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      ..|+++-||||+|||.++++|.+
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnL  246 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTA  246 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhh
Confidence            36899999999999999999964

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=91.13  E-value=0.63  Score=37.60  Aligned_cols=59  Identities=17%  Similarity=0.174  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHHHHHHHHHHhhhhhhHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIK   90 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~~~~~~~~~   90 (115)
                      -++.|++.+..-...+.+|   .++++.|+-|||||...-. ++......+.++.+..+..+.
T Consensus        31 Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVka-ll~~y~~~GLRlIev~k~~L~   92 (249)
T PF05673_consen   31 GIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKA-LLNEYADQGLRLIEVSKEDLG   92 (249)
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHH-HHHHHhhcCceEEEECHHHhc
Confidence            3567777666555566566   6899999999999866555 344444556666444444443

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=91.13  E-value=0.38  Score=41.32  Aligned_cols=17  Identities=47%  Similarity=0.534  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||+.+
T Consensus       218 ~gVLL~GPPGTGKT~LA  234 (438)
T PTZ00361        218 KGVILYGPPGTGKTLLA  234 (438)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            46889999999999764

>KOG0743|consensus

Probab=91.11  E-value=0.31  Score=42.45  Aligned_cols=41  Identities=22%  Similarity=0.421  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..=.++|+.+.+.++.+           +-=++.||+|||||. +++++..++
T Consensus       208 ~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS-~IaAmAn~L  259 (457)
T KOG0743|consen  208 DLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSS-FIAAMANYL  259 (457)
T ss_pred             hHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHH-HHHHHHhhc
Confidence            34567788888777664           246789999999994 455544554

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=91.07  E-value=0.39  Score=39.26  Aligned_cols=17  Identities=41%  Similarity=0.511  Sum_probs=14.1

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..+++.||+|||||+..
T Consensus       157 ~gvLL~GppGtGKT~la  173 (364)
T TIGR01242       157 KGVLLYGPPGTGKTLLA  173 (364)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            35899999999999654

Many proteins may score above the trusted cutoff because an internal

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=91.07  E-value=0.53  Score=38.57  Aligned_cols=31  Identities=16%  Similarity=0.045  Sum_probs=20.5

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+++.||+|+|||.+...-+.. +...+.+|
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA~~-l~~~g~~V  145 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLAHK-YKAQGKKV  145 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH-HHhcCCeE
Confidence            46778899999999775544433 33444444

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=91.03  E-value=0.36  Score=43.30  Aligned_cols=41  Identities=24%  Similarity=0.350  Sum_probs=35.2

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLS   65 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls   65 (115)
                      +.-||.|.-.|-..+..+.+.+.++ +..++.|.||||||+.
T Consensus         4 ~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~   45 (655)
T TIGR00631         4 LHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFT   45 (655)
T ss_pred             eccCCCCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHH
Confidence            3568999999999999999999776 3567899999999976

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

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=91.01  E-value=0.26  Score=37.16  Aligned_cols=30  Identities=20%  Similarity=0.177  Sum_probs=20.8

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +..|..+++.||+|+|||.-.+.-+...+.
T Consensus        17 i~~G~~~~i~G~~G~GKT~l~~~~~~~~~~   46 (229)
T TIGR03881        17 IPRGFFVAVTGEPGTGKTIFCLHFAYKGLR   46 (229)
T ss_pred             CcCCeEEEEECCCCCChHHHHHHHHHHHHh
Confidence            345678999999999998655443344443

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.

>KOG1970|consensus

Probab=91.00  E-value=0.24  Score=44.46  Aligned_cols=31  Identities=23%  Similarity=0.369  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHh-----c----CCcEEEecCCCCCchHHHH
Q psy14273         37 NFMKNLYYTLD-----N----SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        37 e~m~~I~~~l~-----~----~~~~iiEaPTGtGKTls~L   67 (115)
                      .=+.+|..||.     .    +..+++.||+|+|||.++=
T Consensus        89 kKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvk  128 (634)
T KOG1970|consen   89 KKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVK  128 (634)
T ss_pred             HhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHH
Confidence            34678888887     2    3578999999999998753

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=90.99  E-value=0.57  Score=44.64  Aligned_cols=39  Identities=15%  Similarity=0.094  Sum_probs=25.2

Q ss_pred             CCHHHHHHHH-HHHHHHhcC--Cc-EEEecCCCCCchHHHHHH
Q psy14273         31 AYDIQSNFMK-NLYYTLDNS--KF-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        31 ~r~~Q~e~m~-~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~   69 (115)
                      -|+.|.+-+. .|..++...  .. +.|.|+||||||++...-
T Consensus       759 hREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~V  801 (1164)
T PTZ00112        759 CREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSV  801 (1164)
T ss_pred             ChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHH
Confidence            4666655444 444455432  23 459999999999987654

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=90.98  E-value=0.46  Score=38.77  Aligned_cols=38  Identities=24%  Similarity=0.347  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~~a   70 (115)
                      -+|.+..+.+.+++.++   ...+|.||.|+||+..+++-+
T Consensus         7 iGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a   47 (314)
T PRK07399          7 IGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFI   47 (314)
T ss_pred             CCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHH
Confidence            47888889999999888   458899999999997655443

>PRK14974 cell division protein FtsY; Provisional

Probab=90.94  E-value=0.53  Score=39.10  Aligned_cols=31  Identities=16%  Similarity=0.188  Sum_probs=21.5

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..++|.||+|+|||.+.---+ .++...+.++
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA-~~l~~~g~~V  171 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLA-YYLKKNGFSV  171 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHH-HHHHHcCCeE
Confidence            468899999999998754444 4455555454

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=90.89  E-value=0.22  Score=38.50  Aligned_cols=41  Identities=15%  Similarity=0.080  Sum_probs=30.2

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+..-+..+...+|-|+||.|||.-.+--+..++...+..|
T Consensus        11 ~~lgG~~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~~~~~v   51 (259)
T PF03796_consen   11 RLLGGLRPGELTVIAARPGVGKTAFALQIALNAALNGGYPV   51 (259)
T ss_dssp             HHHSSB-TT-EEEEEESTTSSHHHHHHHHHHHHHHTTSSEE
T ss_pred             HHhcCCCcCcEEEEEecccCCchHHHHHHHHHHHHhcCCeE
Confidence            33334456678999999999999988888888887765554

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=90.87  E-value=0.43  Score=42.90  Aligned_cols=41  Identities=12%  Similarity=0.025  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      ++|--+|.+.++.+...|..+  .++|+.||+|+|||...-.-
T Consensus       181 l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~GKT~l~~~l  223 (731)
T TIGR02639       181 IDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIAEGL  223 (731)
T ss_pred             CCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHH
Confidence            344456777777788777654  68999999999999764333

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=90.81  E-value=0.22  Score=37.10  Aligned_cols=14  Identities=29%  Similarity=0.503  Sum_probs=12.5

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .+++-||||+|||.
T Consensus         5 ~~ll~GpsGvGKT~   18 (171)
T PF07724_consen    5 NFLLAGPSGVGKTE   18 (171)
T ss_dssp             EEEEESSTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57899999999994

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 ....

>PRK00698 tmk thymidylate kinase; Validated

Probab=90.76  E-value=0.15  Score=37.33  Aligned_cols=16  Identities=38%  Similarity=0.443  Sum_probs=14.3

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..++||||.|+|||.
T Consensus         3 ~~~I~ieG~~gsGKsT   18 (205)
T PRK00698          3 GMFITIEGIDGAGKST   18 (205)
T ss_pred             ceEEEEECCCCCCHHH
Confidence            5679999999999995

>TIGR00368 Mg chelatase-related protein

Probab=90.76  E-value=0.15  Score=44.29  Aligned_cols=40  Identities=15%  Similarity=0.194  Sum_probs=32.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~   66 (115)
                      +.|.-..+|....+.+.-++..+.++++.+|+|+|||..+
T Consensus       189 ~d~~dv~Gq~~~~~al~~aa~~g~~vlliG~pGsGKTtla  228 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIAAAGGHNLLLFGPPGSGKTMLA  228 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhhccCCCEEEEEecCCCCHHHHH
Confidence            3455456788888888888888899999999999999753

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=90.74  E-value=0.12  Score=38.17  Aligned_cols=19  Identities=21%  Similarity=0.195  Sum_probs=12.1

Q ss_pred             cEEEecCCCCCchHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~   69 (115)
                      |+++|++.|+|||...-.-
T Consensus         1 HvLleg~PG~GKT~la~~l   19 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKAL   19 (131)
T ss_dssp             -EEEES---HHHHHHHHHH
T ss_pred             CEeeECCCccHHHHHHHHH
Confidence            6899999999999765543

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PF00225 Kinesin: Kinesin motor domain; InterPro: IPR001752 Kinesin [, , ] is a microtubule-associated force-producing protein that may play a role in organelle transport

Probab=90.70  E-value=0.092  Score=42.11  Aligned_cols=39  Identities=13%  Similarity=0.155  Sum_probs=26.7

Q ss_pred             CCHHHHHHHHHHH----HHHhcC--CcEEEecCCCCCchHHHHHH
Q psy14273         31 AYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        31 ~r~~Q~e~m~~I~----~~l~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      +-..|.++.+.+.    ..+-+|  ..++..|+||+|||.+++-+
T Consensus        51 ~~~~q~~vy~~~~~~~v~~~l~G~n~~i~ayG~tgSGKT~Tm~G~   95 (335)
T PF00225_consen   51 EDATQEDVYEEVVSPLVDSVLDGYNATIFAYGQTGSGKTYTMFGS   95 (335)
T ss_dssp             TTSTHHHHHHHHTHHHHHHHHTT-EEEEEEEESTTSSHHHHHTBS
T ss_pred             CCCCHHHHHHHHHHHHHHHhhcCCceEEEeecccccccccccccc
Confidence            5556777766642    222345  35777999999999987776

The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds. The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyse ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerisation; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles. A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain [, ]: Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E []. CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Emericella nidulans (Aspergillus nidulans) bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. C. elegans hypothetical protein T09A5.2. The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section. The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement; PDB: 3NWN_A 2Y5W_A 2Y65_C 3BFN_A 2WBE_C 2ZFL_A 2ZFI_A 1I6I_A 2ZFM_A 1IA0_K ....

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=90.67  E-value=0.31  Score=44.98  Aligned_cols=34  Identities=21%  Similarity=0.176  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls~   66 (115)
                      -+|.+.+..|.+++...           ..-+|-||||+|||-..
T Consensus       494 iGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELA  538 (786)
T COG0542         494 IGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELA  538 (786)
T ss_pred             eChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHH
Confidence            47889999999888652           35778999999999643

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=90.64  E-value=0.25  Score=35.59  Aligned_cols=28  Identities=21%  Similarity=0.309  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      ++-+.+.+.+..+..+++.|+-|+|||.
T Consensus         3 ~la~~l~~~l~~g~vi~L~GdLGaGKTt   30 (123)
T PF02367_consen    3 RLAKKLAQILKPGDVILLSGDLGAGKTT   30 (123)
T ss_dssp             HHHHHHHHHHSS-EEEEEEESTTSSHHH
T ss_pred             HHHHHHHHhCCCCCEEEEECCCCCCHHH
Confidence            4556777888888899999999999994

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>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=90.64  E-value=0.45  Score=36.47  Aligned_cols=30  Identities=17%  Similarity=0.065  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHhc----CCcEEEecCCCCCchHHH
Q psy14273         37 NFMKNLYYTLDN----SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        37 e~m~~I~~~l~~----~~~~iiEaPTGtGKTls~   66 (115)
                      ..+++|.+.|..    ...+.|.|+.|+|||.-+
T Consensus         3 ~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA   36 (287)
T PF00931_consen    3 KEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLA   36 (287)
T ss_dssp             HHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHH
T ss_pred             HHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceee
Confidence            345677777876    256889999999999543

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.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=90.63  E-value=0.68  Score=41.40  Aligned_cols=31  Identities=23%  Similarity=0.332  Sum_probs=23.6

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~   66 (115)
                      -+.|+..+   ..++ .+...||.|+.|||||.+.
T Consensus       154 ~d~Qk~Av---~~a~-~~~~~vItGgpGTGKTt~v  184 (615)
T PRK10875        154 VDWQKVAA---AVAL-TRRISVISGGPGTGKTTTV  184 (615)
T ss_pred             CHHHHHHH---HHHh-cCCeEEEEeCCCCCHHHHH
Confidence            47888844   3444 4678999999999999764

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.62  E-value=0.34  Score=43.58  Aligned_cols=38  Identities=16%  Similarity=0.066  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~a   70 (115)
                      -+|......+.+++.+++   ..||.||.|+|||....+-+
T Consensus        19 iGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilA   59 (624)
T PRK14959         19 AGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFA   59 (624)
T ss_pred             cCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHH
Confidence            378888889999998874   47789999999998765543

>TIGR00602 rad24 checkpoint protein rad24

Probab=90.60  E-value=0.37  Score=43.39  Aligned_cols=38  Identities=16%  Similarity=0.267  Sum_probs=28.1

Q ss_pred             CHHHHHHHHHHHHHHhcC-------CcEEEecCCCCCchHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNS-------KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~-------~~~iiEaPTGtGKTls~L~~   69 (115)
                      .-+|.+.+..|..++...       ..++|.||+|+|||.++-+-
T Consensus        86 l~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~l  130 (637)
T TIGR00602        86 LAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKIL  130 (637)
T ss_pred             hcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHH
Confidence            356777777888887642       34899999999999864443

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

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=90.59  E-value=0.91  Score=43.07  Aligned_cols=46  Identities=26%  Similarity=0.289  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..|+.|.+.+.-+.....++..+||.-..|.|||+..|+- +.++..
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIal-L~~L~~  214 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISL-LGYLHE  214 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHHH-HHHHHH
Confidence            4799999999998888888889999999999999986554 455543

>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=90.52  E-value=0.13  Score=35.37  Aligned_cols=18  Identities=28%  Similarity=0.455  Sum_probs=15.7

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|.+++|.||+|+|||.
T Consensus         9 ~~g~~~~i~G~nGsGKSt   26 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKST   26 (137)
T ss_dssp             ETTSEEEEEESTTSSHHH
T ss_pred             cCCCEEEEEccCCCcccc
Confidence            457889999999999995

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 ....

>PF13173 AAA_14: AAA domain

Probab=90.49  E-value=0.24  Score=34.35  Aligned_cols=20  Identities=40%  Similarity=0.557  Sum_probs=16.3

Q ss_pred             cCCcEEEecCCCCCchHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L   67 (115)
                      +++.+++.||.|+|||..+.
T Consensus         1 n~~~~~l~G~R~vGKTtll~   20 (128)
T PF13173_consen    1 NRKIIILTGPRGVGKTTLLK   20 (128)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            45789999999999996543

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=90.47  E-value=0.18  Score=44.28  Aligned_cols=33  Identities=21%  Similarity=0.370  Sum_probs=25.0

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .++|++|-+.||||||.++-+-|=.+.. .+-.|
T Consensus        18 ~NRHGLIaGATGTGKTvTLqvlAE~fS~-~GVPV   50 (502)
T PF05872_consen   18 ANRHGLIAGATGTGKTVTLQVLAEQFSD-AGVPV   50 (502)
T ss_pred             ccccceeeccCCCCceehHHHHHHHhhh-cCCcE
Confidence            3679999999999999998777655553 34444

This family is restricted to bacterial proteins, none of which have currently been characterised.

>KOG0926|consensus

Probab=90.47  E-value=0.22  Score=46.78  Aligned_cols=27  Identities=19%  Similarity=0.309  Sum_probs=22.4

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .|..++..+..+||+|.||+|||.-  +|
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTTQ--vP  289 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTTQ--VP  289 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCcccc--ch
Confidence            4666778889999999999999964  55

>PRK05541 adenylylsulfate kinase; Provisional

Probab=90.45  E-value=0.12  Score=37.49  Aligned_cols=19  Identities=21%  Similarity=0.197  Sum_probs=16.0

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..+..++++|+.|+|||.-
T Consensus         5 ~~~~~I~i~G~~GsGKst~   23 (176)
T PRK05541          5 PNGYVIWITGLAGSGKTTI   23 (176)
T ss_pred             CCCCEEEEEcCCCCCHHHH
Confidence            4567899999999999854

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=90.37  E-value=0.4  Score=45.04  Aligned_cols=43  Identities=23%  Similarity=0.146  Sum_probs=28.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..+..||++|.--  .+  +|  +.--|.|+.||-||||++.+|+.-.+
T Consensus        81 ~lG~r~ydVQliG--gl--~L--h~G~IAEM~TGEGKTL~atlpaylnA  123 (939)
T PRK12902         81 VLGMRHFDVQLIG--GM--VL--HEGQIAEMKTGEGKTLVATLPSYLNA  123 (939)
T ss_pred             HhCCCcchhHHHh--hh--hh--cCCceeeecCCCChhHHHHHHHHHHh
Confidence            3455677777542  22  12  33467899999999999988865433

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=90.27  E-value=0.67  Score=37.71  Aligned_cols=36  Identities=25%  Similarity=0.439  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHhcC--CcE-EEecCCCCCchHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KFG-IFESPTGTGKSLSLIC   68 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~~-iiEaPTGtGKTls~L~   68 (115)
                      -+|...++.+.+.+.++  .|+ +|.||.|+||+..+..
T Consensus         9 ~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~   47 (329)
T PRK08058          9 ALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALW   47 (329)
T ss_pred             hhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHH
Confidence            35889999999999887  454 8999999999865433

>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=90.25  E-value=0.36  Score=34.77  Aligned_cols=30  Identities=13%  Similarity=-0.020  Sum_probs=19.9

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||+|+|||.....-+..+. ..+.++
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~-~~g~~v   31 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLK-KKGKKV   31 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HCCCcE
Confidence            468899999999987554444443 334444

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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=90.23  E-value=0.44  Score=40.96  Aligned_cols=42  Identities=14%  Similarity=0.087  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      --+.-.++++.|.++...+..++|.|++||||++.  +-++...
T Consensus       192 ~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~--A~~ih~~  233 (509)
T PRK05022        192 QSPAMQQLKKEIEVVAASDLNVLILGETGVGKELV--ARAIHAA  233 (509)
T ss_pred             cCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHH--HHHHHHh
Confidence            34566666777777777788999999999999964  4444433

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=90.17  E-value=0.42  Score=40.94  Aligned_cols=34  Identities=18%  Similarity=0.045  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         36 SNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        36 ~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .++.+.|......+.++++.|+|||||++.+-..
T Consensus        88 ~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~i  121 (403)
T COG1221          88 QELREQIKAYAPSGLPVLIIGETGTGKELFARLI  121 (403)
T ss_pred             HHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHH
Confidence            4455666665567789999999999999764433

>TIGR00665 DnaB replicative DNA helicase

Probab=90.16  E-value=0.24  Score=41.28  Aligned_cols=41  Identities=15%  Similarity=-0.021  Sum_probs=28.2

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+..-+..|..+||.|++|+|||.-.+--+...+...+..|
T Consensus       187 ~~~~G~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~~g~~v  227 (434)
T TIGR00665       187 KLTSGLQPSDLIILAARPSMGKTAFALNIAENAAIKEGKPV  227 (434)
T ss_pred             hhcCCCCCCeEEEEEeCCCCChHHHHHHHHHHHHHhCCCeE
Confidence            33334556678999999999999766655555565555554

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.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=90.13  E-value=0.29  Score=40.71  Aligned_cols=38  Identities=8%  Similarity=-0.097  Sum_probs=28.2

Q ss_pred             HHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        44 ~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .-+..|..+|+-|++|+|||.-.+--+...+...+.+|
T Consensus       189 ~G~~~g~liviag~pg~GKT~~al~ia~~~a~~~g~~v  226 (421)
T TIGR03600       189 NGLVKGDLIVIGARPSMGKTTLALNIAENVALREGKPV  226 (421)
T ss_pred             cCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHhCCCcE
Confidence            34555678999999999999877776666665556554

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=90.10  E-value=0.4  Score=40.96  Aligned_cols=16  Identities=44%  Similarity=0.584  Sum_probs=13.8

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +.+++.||+|||||+.
T Consensus        89 ~giLL~GppGtGKT~l  104 (495)
T TIGR01241        89 KGVLLVGPPGTGKTLL  104 (495)
T ss_pred             CcEEEECCCCCCHHHH
Confidence            3689999999999965

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.

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=90.04  E-value=0.49  Score=42.36  Aligned_cols=39  Identities=18%  Similarity=0.246  Sum_probs=27.9

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .-+.|++.+.      ...++++|-|+.|||||.++..= +.|+..
T Consensus        10 Ln~~Q~~av~------~~~g~~lV~AgaGSGKT~vl~~R-ia~Li~   48 (721)
T PRK11773         10 LNDKQREAVA------APLGNMLVLAGAGSGKTRVLVHR-IAWLMQ   48 (721)
T ss_pred             cCHHHHHHHh------CCCCCEEEEecCCCCHHHHHHHH-HHHHHH
Confidence            5578888544      23568899999999999886655 445443

>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=90.01  E-value=0.34  Score=36.17  Aligned_cols=26  Identities=23%  Similarity=0.448  Sum_probs=19.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ....+|.||+|+|||.  |+-|+.|+..
T Consensus        24 ~~~~~i~G~NGsGKS~--ileAi~~~l~   49 (220)
T PF02463_consen   24 PGLNVIVGPNGSGKSN--ILEAIEFVLG   49 (220)
T ss_dssp             SSEEEEEESTTSSHHH--HHHHHHHHTT
T ss_pred             CCCEEEEcCCCCCHHH--HHHHHHHHHH
Confidence            3478899999999995  4566766654

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 ....

>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=89.99  E-value=0.26  Score=41.07  Aligned_cols=32  Identities=19%  Similarity=0.203  Sum_probs=22.3

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+|+++-|.||||||. +|-.++..+...+.+.
T Consensus        15 ~~~~li~G~~GsGKT~-~i~~ll~~~~~~g~~~   46 (386)
T PF10412_consen   15 NRHILIIGATGSGKTQ-AIRHLLDQIRARGDRA   46 (386)
T ss_dssp             GG-EEEEE-TTSSHHH-HHHHHHHHHHHTT-EE
T ss_pred             hCcEEEECCCCCCHHH-HHHHHHHHHHHcCCEE
Confidence            4689999999999996 6677777776666553

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=89.98  E-value=0.33  Score=36.57  Aligned_cols=30  Identities=13%  Similarity=0.176  Sum_probs=21.6

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..|....+.||+|+|||.-.+--+...+..
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~~~~~   50 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVEAAKN   50 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            345678999999999997666555555543

>TIGR03744 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family

Probab=89.97  E-value=0.3  Score=45.00  Aligned_cols=32  Identities=25%  Similarity=0.337  Sum_probs=24.0

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ..|++|-||||+|||...-.-+.+++...+.+
T Consensus       475 n~n~~I~G~TGSGKS~l~~~li~q~~~~~~~~  506 (893)
T TIGR03744       475 NAHLLILGPTGAGKSATLTNLLMQVMAVHRPR  506 (893)
T ss_pred             cccEEEECCCCCCHHHHHHHHHHHHHHhcCCE
Confidence            57899999999999987766666666544443

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=89.91  E-value=0.32  Score=42.01  Aligned_cols=32  Identities=28%  Similarity=0.352  Sum_probs=21.5

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..++|.||||+|||....--+..+....+.+|
T Consensus       224 ~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V  255 (432)
T PRK12724        224 KVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSV  255 (432)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCCeE
Confidence            45778999999999875555545544444444

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=89.91  E-value=0.35  Score=35.83  Aligned_cols=27  Identities=15%  Similarity=0.142  Sum_probs=19.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+....+.||+|+|||.-.+--+...+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~   37 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAA   37 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            356788999999999976655444443

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

>cd03241 ABC_RecN RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules

Probab=89.91  E-value=0.37  Score=37.99  Aligned_cols=27  Identities=22%  Similarity=0.372  Sum_probs=20.5

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ...-+|.||||+|||.  |+-|+.|+...
T Consensus        21 ~~~~~i~G~nGsGKS~--il~ai~~~~~~   47 (276)
T cd03241          21 EGLTVLTGETGAGKSI--LLDALSLLLGG   47 (276)
T ss_pred             CCeEEEEcCCCCCHHH--HHHHHHHHhcC
Confidence            3567889999999985  46678887543

The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=89.89  E-value=0.27  Score=41.33  Aligned_cols=20  Identities=30%  Similarity=0.456  Sum_probs=16.4

Q ss_pred             hcCCcEEEecCCCCCchHHH
Q psy14273         47 DNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~   66 (115)
                      ...+.+|+-|+||||||.+.
T Consensus       125 ~kRGLviiVGaTGSGKSTtm  144 (375)
T COG5008         125 AKRGLVIIVGATGSGKSTTM  144 (375)
T ss_pred             ccCceEEEECCCCCCchhhH
Confidence            34568999999999999874

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=89.86  E-value=0.19  Score=35.78  Aligned_cols=13  Identities=38%  Similarity=0.708  Sum_probs=11.6

Q ss_pred             EEEecCCCCCchH
Q psy14273         52 GIFESPTGTGKSL   64 (115)
Q Consensus        52 ~iiEaPTGtGKTl   64 (115)
                      ++|.||||+|||.
T Consensus         2 i~i~GpsGsGKst   14 (137)
T cd00071           2 IVLSGPSGVGKST   14 (137)
T ss_pred             EEEECCCCCCHHH
Confidence            6789999999995

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.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=89.86  E-value=0.69  Score=41.02  Aligned_cols=33  Identities=24%  Similarity=0.322  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      +.|+..   +..++ .+...+|.|+.|||||.+.-.-
T Consensus       148 ~~Qk~A---~~~al-~~~~~vitGgpGTGKTt~v~~l  180 (586)
T TIGR01447       148 NWQKVA---VALAL-KSNFSLITGGPGTGKTTTVARL  180 (586)
T ss_pred             HHHHHH---HHHHh-hCCeEEEEcCCCCCHHHHHHHH
Confidence            677764   33344 4678999999999999764433

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.

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=89.84  E-value=0.68  Score=39.79  Aligned_cols=46  Identities=11%  Similarity=0.085  Sum_probs=28.8

Q ss_pred             CHHHHHHHHHHHHHHhcC----CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         32 YDIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ....++..-.|.+-+.++    +.+++-+|+|||||.-    |+..+++.+..+
T Consensus        29 Q~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAl----A~~ia~eLG~~~   78 (398)
T PF06068_consen   29 QEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTAL----AMAIAKELGEDV   78 (398)
T ss_dssp             -HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHH----HHHHHHHCTTTS
T ss_pred             hHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHH----HHHHHHHhCCCC
Confidence            345566666777777765    5788999999999943    334455555443

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=89.83  E-value=0.34  Score=38.69  Aligned_cols=31  Identities=16%  Similarity=0.125  Sum_probs=21.4

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+++.||+|+|||.+..--+..+ ...+.+|
T Consensus        73 ~vi~l~G~~G~GKTTt~akLA~~l-~~~g~~V  103 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAKLANKL-KKQGKSV  103 (272)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH-HhcCCEE
Confidence            356678999999998766665444 4445554

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.

>KOG0744|consensus

Probab=89.82  E-value=0.26  Score=42.20  Aligned_cols=20  Identities=35%  Similarity=0.803  Sum_probs=16.0

Q ss_pred             CcEEEecCCCCCchHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al   71 (115)
                      +.+++.||+|||||.  ||-|+
T Consensus       178 RliLlhGPPGTGKTS--LCKaL  197 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTS--LCKAL  197 (423)
T ss_pred             eEEEEeCCCCCChhH--HHHHH
Confidence            568899999999994  46554

>PRK05973 replicative DNA helicase; Provisional

Probab=89.76  E-value=0.3  Score=38.72  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=25.5

Q ss_pred             HHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         42 LYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        42 I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +..-+..|..++|.|++|+|||.-.+--+...+. ++.++
T Consensus        57 l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~-~Ge~v   95 (237)
T PRK05973         57 LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMK-SGRTG   95 (237)
T ss_pred             hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHh-cCCeE
Confidence            3334455678999999999999765544444443 35443

>KOG0923|consensus

Probab=89.64  E-value=0.28  Score=45.22  Aligned_cols=33  Identities=18%  Similarity=0.308  Sum_probs=25.7

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+..++..++.+||+|-||||||.-  +|  +||.+-
T Consensus       272 ell~av~e~QVLiI~GeTGSGKTTQ--iP--QyL~Ea  304 (902)
T KOG0923|consen  272 ELLKAVKEHQVLIIVGETGSGKTTQ--IP--QYLYEA  304 (902)
T ss_pred             HHHHHHHhCcEEEEEcCCCCCcccc--cc--HHHHhc
Confidence            4556678899999999999999965  55  666553

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=89.62  E-value=0.21  Score=36.50  Aligned_cols=16  Identities=31%  Similarity=0.505  Sum_probs=14.2

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      |..++|||+.|+|||.
T Consensus         3 g~~IvieG~~GsGKsT   18 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTT   18 (195)
T ss_pred             ceEEEEECCCCCCHHH
Confidence            5679999999999994

Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.

>KOG4284|consensus

Probab=89.59  E-value=0.078  Score=48.77  Aligned_cols=47  Identities=19%  Similarity=0.210  Sum_probs=36.1

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .|. |.++|...|..+    ..+..+|+.|-.|||||+.|-+.++.-+..+.
T Consensus        44 ~f~~ptkiQaaAIP~~----~~kmDliVQaKSGTGKTlVfsv~av~sl~~~~   91 (980)
T KOG4284|consen   44 AFALPTKIQAAAIPAI----FSKMDLIVQAKSGTGKTLVFSVLAVESLDSRS   91 (980)
T ss_pred             cccCCCchhhhhhhhh----hcccceEEEecCCCCceEEEEeeeehhcCccc
Confidence            355 667777766654    34568999999999999999988887776544

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

Probab=89.59  E-value=0.26  Score=40.14  Aligned_cols=24  Identities=17%  Similarity=0.187  Sum_probs=18.7

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ..+||+|..|||||+-++.-+-.+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            468899999999998766555544

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

>TIGR01075 uvrD DNA helicase II

Probab=89.44  E-value=0.56  Score=41.87  Aligned_cols=39  Identities=18%  Similarity=0.219  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .-+.|.+.+.      ...+.++|-|+.|||||.++..= +.|+..
T Consensus         5 Ln~~Q~~av~------~~~g~~lV~AgaGSGKT~~L~~R-ia~Li~   43 (715)
T TIGR01075         5 LNDKQREAVA------APPGNLLVLAGAGSGKTRVLTHR-IAWLLS   43 (715)
T ss_pred             cCHHHHHHHc------CCCCCEEEEecCCCCHHHHHHHH-HHHHHH
Confidence            4578888544      23568899999999999986555 445443

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=89.44  E-value=0.72  Score=39.65  Aligned_cols=30  Identities=10%  Similarity=0.111  Sum_probs=20.9

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.|++|+|||.+..--+. ++...+.++
T Consensus        97 vI~lvG~~GsGKTTtaakLA~-~L~~~g~kV  126 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAKLAR-YFKKKGLKV  126 (437)
T ss_pred             EEEEECCCCCcHHHHHHHHHH-HHHHcCCeE
Confidence            577899999999987655554 444445444

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=89.41  E-value=0.48  Score=43.21  Aligned_cols=40  Identities=13%  Similarity=0.248  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .-+.|.++|+.     ..++.+|+.|..|||||...|-= ++|+..
T Consensus       213 IQkEQneIIR~-----ek~~ilVVQGaAGSGKTtiALHR-vAyLlY  252 (747)
T COG3973         213 IQKEQNEIIRF-----EKNKILVVQGAAGSGKTTIALHR-VAYLLY  252 (747)
T ss_pred             hhHhHHHHHhc-----cCCCeEEEecCCCCCchhHHHHH-HHHHHh
Confidence            34667776663     45688999999999999988877 455544

>CHL00176 ftsH cell division protein; Validated

Probab=89.40  E-value=0.45  Score=42.67  Aligned_cols=34  Identities=24%  Similarity=0.298  Sum_probs=23.4

Q ss_pred             CHHHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHH
Q psy14273         32 YDIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLS   65 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls   65 (115)
                      .+.+.+-+..+...+.+.           +.+++.||+|||||+.
T Consensus       188 ~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~L  232 (638)
T CHL00176        188 IEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLL  232 (638)
T ss_pred             hHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHH
Confidence            355555556666555543           3589999999999964

>cd00106 KISc Kinesin motor domain

Probab=89.39  E-value=0.21  Score=39.99  Aligned_cols=38  Identities=13%  Similarity=0.121  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHHH----HHHhcC--CcEEEecCCCCCchHHHHH
Q psy14273         31 AYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        31 ~r~~Q~e~m~~I~----~~l~~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      +-..|.++.+.+.    ..+-.|  ..++..|+||||||.+++-
T Consensus        55 ~~~~q~~v~~~~~~~~v~~~~~G~~~~i~~yG~tgSGKT~tl~G   98 (328)
T cd00106          55 PNSTQEDVYETTAKPLVESVLEGYNGTIFAYGQTGSGKTYTMFG   98 (328)
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCceeEEEecCCCCCCeEEecC
Confidence            3345666655554    222334  3466799999999987544

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

>PLN02165 adenylate isopentenyltransferase

Probab=89.38  E-value=0.32  Score=40.64  Aligned_cols=19  Identities=32%  Similarity=0.398  Sum_probs=15.3

Q ss_pred             CCcEEEecCCCCCchHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L   67 (115)
                      +..++|-||||+|||.-.+
T Consensus        43 g~iivIiGPTGSGKStLA~   61 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSV   61 (334)
T ss_pred             CCEEEEECCCCCcHHHHHH
Confidence            4678999999999996443

>PRK10869 recombination and repair protein; Provisional

Probab=89.36  E-value=0.39  Score=42.12  Aligned_cols=26  Identities=27%  Similarity=0.349  Sum_probs=20.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+.-||.||||+|||  .|+-||.++.-
T Consensus        22 ~glnvitGetGaGKS--~ildAi~~llG   47 (553)
T PRK10869         22 SGMTVITGETGAGKS--IAIDALGLCLG   47 (553)
T ss_pred             CCcEEEECCCCCChH--HHHHHHHHHhC
Confidence            357889999999997  46777888763

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=89.31  E-value=0.31  Score=44.79  Aligned_cols=30  Identities=17%  Similarity=0.139  Sum_probs=21.4

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +..++|-||||+|||.++..-+..+...++
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G  214 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREG  214 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcC
Confidence            356789999999999876665555544443

>cd01394 radB RadB

Probab=89.29  E-value=0.4  Score=35.84  Aligned_cols=28  Identities=21%  Similarity=0.171  Sum_probs=20.2

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ..+...++.|++|+|||.-.+.-+...+
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~~a~~~~   44 (218)
T cd01394          17 ERGTVTQVYGPPGTGKTNIAIQLAVETA   44 (218)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3456788999999999976555544443

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

>smart00129 KISc Kinesin motor, catalytic domain

Probab=89.22  E-value=0.18  Score=40.54  Aligned_cols=38  Identities=16%  Similarity=0.128  Sum_probs=24.7

Q ss_pred             CCCHHHHHHHHHHHHH----HhcC--CcEEEecCCCCCchHHHH
Q psy14273         30 DAYDIQSNFMKNLYYT----LDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~----l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      .+...|.++.+.+..-    +-.|  ..++..|+||||||.++.
T Consensus        55 ~~~~~q~~v~~~~~~p~v~~~~~G~~~~i~~yG~tgSGKT~tl~   98 (335)
T smart00129       55 GATASQEDVFEETAAPLVDSVLEGYNATIFAYGQTGSGKTYTMS   98 (335)
T ss_pred             CCCCChHHHHHHHHHHHHHHHhcCCceeEEEeCCCCCCCceEec
Confidence            3555666666655422    2344  346679999999998775

ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=89.19  E-value=0.49  Score=41.75  Aligned_cols=39  Identities=28%  Similarity=0.252  Sum_probs=31.0

Q ss_pred             CHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~a   70 (115)
                      --+|......+..++.++.  + .+|.||.|+|||.++.+-+
T Consensus        16 iiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LA   57 (535)
T PRK08451         16 LIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFA   57 (535)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHH
Confidence            3578888899999998884  3 3899999999997765543

>KOG0390|consensus

Probab=89.16  E-value=0.34  Score=44.64  Aligned_cols=49  Identities=22%  Similarity=0.142  Sum_probs=39.8

Q ss_pred             CCHHHHHHHHHHHHHHhcC------CcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNS------KFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~------~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .||.|++..+.+++++...      .-||+---.|+|||+-.+.-+..|+...+.
T Consensus       239 LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~  293 (776)
T KOG0390|consen  239 LRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQ  293 (776)
T ss_pred             cCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcC
Confidence            8999999999999999643      236777778999999777777788877665

>PRK00131 aroK shikimate kinase; Reviewed

Probab=89.14  E-value=0.28  Score=34.60  Aligned_cols=18  Identities=22%  Similarity=0.141  Sum_probs=15.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..+++.||+|||||..
T Consensus         3 ~~~~i~l~G~~GsGKstl   20 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTI   20 (175)
T ss_pred             CCCeEEEEcCCCCCHHHH
Confidence            456799999999999954

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=89.13  E-value=0.61  Score=40.37  Aligned_cols=33  Identities=18%  Similarity=0.061  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++++.+.++...+..++|.|.|||||++.
T Consensus       211 ~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~l  243 (520)
T PRK10820        211 PKMRQVVEQARKLAMLDAPLLITGDTGTGKDLL  243 (520)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCccHHHH
Confidence            444566677777777788999999999999964

>TIGR00618 sbcc exonuclease SbcC

Probab=89.11  E-value=0.35  Score=44.94  Aligned_cols=26  Identities=15%  Similarity=0.189  Sum_probs=20.9

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +..+|.||||+|||.  |+-||+|+...
T Consensus        27 gl~~I~G~nGaGKST--ildAI~~aL~G   52 (1042)
T TIGR00618        27 PIFLICGKTGAGKTT--LLDAITYALYG   52 (1042)
T ss_pred             CeEEEECCCCCCHHH--HHHHHHHHhcC
Confidence            678899999999995  46778888643

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

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=89.10  E-value=0.3  Score=35.35  Aligned_cols=17  Identities=29%  Similarity=0.497  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|+|||...
T Consensus         2 ~~~~i~G~sGsGKttl~   18 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLL   18 (179)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            46889999999999654

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.

>KOG1533|consensus

Probab=89.09  E-value=0.29  Score=40.16  Aligned_cols=29  Identities=24%  Similarity=0.365  Sum_probs=24.1

Q ss_pred             EEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         52 GIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        52 ~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -++-||.|+||| +|+....+++.+.++.+
T Consensus         5 qvVIGPPgSGKs-TYc~g~~~fls~~gr~~   33 (290)
T KOG1533|consen    5 QVVIGPPGSGKS-TYCNGMSQFLSAIGRPV   33 (290)
T ss_pred             eEEEcCCCCCcc-chhhhHHHHHHHhCCce
Confidence            467899999999 58888889998888754

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=89.05  E-value=0.85  Score=40.70  Aligned_cols=42  Identities=19%  Similarity=0.345  Sum_probs=35.6

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~   66 (115)
                      ..-||.|++.|...+..+.+.+.++ ...++.|.+|+|||+.+
T Consensus         7 ~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~li   49 (652)
T PRK05298          7 LVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTM   49 (652)
T ss_pred             cccCCCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHH
Confidence            4567999999999999999999766 35678999999999763

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

Probab=89.03  E-value=0.52  Score=40.88  Aligned_cols=36  Identities=28%  Similarity=0.355  Sum_probs=27.6

Q ss_pred             CCCCHHHHHHH---HHHHHHHhcC--CcEEEecCCCCCchH
Q psy14273         29 FDAYDIQSNFM---KNLYYTLDNS--KFGIFESPTGTGKSL   64 (115)
Q Consensus        29 f~~r~~Q~e~m---~~I~~~l~~~--~~~iiEaPTGtGKTl   64 (115)
                      ++-+=+|.+++   .-+.+.+.++  .+.||-||.|+|||.
T Consensus        23 lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTT   63 (436)
T COG2256          23 LDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTT   63 (436)
T ss_pred             HHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHH
Confidence            34556788877   4566777777  579999999999995

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=88.98  E-value=0.45  Score=35.84  Aligned_cols=26  Identities=27%  Similarity=0.310  Sum_probs=20.4

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      -++.+...+.. +..+|.|++|.|||.
T Consensus        25 g~~~l~~~l~~-k~~vl~G~SGvGKSS   50 (161)
T PF03193_consen   25 GIEELKELLKG-KTSVLLGQSGVGKSS   50 (161)
T ss_dssp             THHHHHHHHTT-SEEEEECSTTSSHHH
T ss_pred             CHHHHHHHhcC-CEEEEECCCCCCHHH
Confidence            34566666655 899999999999994

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=88.97  E-value=0.25  Score=35.53  Aligned_cols=16  Identities=25%  Similarity=0.333  Sum_probs=13.8

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..+++.||.|||||.-
T Consensus         4 ~ii~i~G~~GsGKsTl   19 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQ   19 (188)
T ss_pred             cEEEEECCCCCCHHHH
Confidence            5688999999999964

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.

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

Probab=88.90  E-value=0.34  Score=44.23  Aligned_cols=50  Identities=14%  Similarity=-0.028  Sum_probs=38.4

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +++ ..|+|.-   .|.+-|.+|.+.++-++|+|||||.-=++.+.-+...+++
T Consensus       213 G~~eLlPVQ~l---aVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~K  263 (830)
T COG1202         213 GIEELLPVQVL---AVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGKK  263 (830)
T ss_pred             Ccceecchhhh---hhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCCe
Confidence            355 6788887   5667888999999999999999998766666666664444

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=88.90  E-value=0.47  Score=40.73  Aligned_cols=16  Identities=44%  Similarity=0.567  Sum_probs=13.7

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +-+++.||.||||||-
T Consensus       186 KGVLLYGPPGTGKTLL  201 (406)
T COG1222         186 KGVLLYGPPGTGKTLL  201 (406)
T ss_pred             CceEeeCCCCCcHHHH
Confidence            4588999999999964

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=88.88  E-value=0.051  Score=42.91  Aligned_cols=38  Identities=18%  Similarity=0.403  Sum_probs=27.0

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.|.|..+   ...+..+.-.+..|..+++-+|||+|||.-
T Consensus         9 l~~~y~~~---~~~l~~v~~~i~~Ge~~~i~G~nGsGKSTL   46 (235)
T COG1122           9 LSFRYPGR---KAALKDVSLEIEKGERVLLIGPNGSGKSTL   46 (235)
T ss_pred             EEEEcCCC---ceeeeeeEEEECCCCEEEEECCCCCCHHHH
Confidence            35556554   344555555667788999999999999853

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=88.83  E-value=0.86  Score=37.70  Aligned_cols=44  Identities=9%  Similarity=0.077  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .||-|....+.+.+++.+++  | .+|+||.|+||+..+..-+-..+
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~ll   49 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLM   49 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHc
Confidence            36777888888888998873  4 55899999999876555443333

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=88.73  E-value=0.67  Score=40.63  Aligned_cols=34  Identities=15%  Similarity=0.025  Sum_probs=27.3

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .+.-.++.+.+.++...+..++|.|+|||||++.
T Consensus       331 s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~  364 (638)
T PRK11388        331 SPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALL  364 (638)
T ss_pred             CHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHH
Confidence            4556667777777777788899999999999964

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=88.72  E-value=0.61  Score=34.19  Aligned_cols=28  Identities=29%  Similarity=0.500  Sum_probs=19.8

Q ss_pred             HHHHHHhcC---CcEEEecCCCCCchHHHHH
Q psy14273         41 NLYYTLDNS---KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        41 ~I~~~l~~~---~~~iiEaPTGtGKTls~L~   68 (115)
                      .+.+.+.++   ...+|.||.|+|||.....
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~   33 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALA   33 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHH
Confidence            445566666   3488999999999865433

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=88.72  E-value=0.51  Score=34.07  Aligned_cols=31  Identities=16%  Similarity=0.146  Sum_probs=22.5

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhhH
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAGL   82 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v~   82 (115)
                      .+.+.||.|+|||. ++.-++.++...+.++.
T Consensus         2 vv~VvG~~~sGKTT-l~~~Li~~l~~~g~~v~   32 (140)
T PF03205_consen    2 VVQVVGPKNSGKTT-LIRKLINELKRRGYRVA   32 (140)
T ss_dssp             EEEEEESTTSSHHH-HHHHHHHHHHHTT--EE
T ss_pred             EEEEECCCCCCHHH-HHHHHHHHHhHcCCceE
Confidence            46789999999994 56667788877776653

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=88.69  E-value=0.44  Score=36.64  Aligned_cols=35  Identities=17%  Similarity=0.149  Sum_probs=21.7

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +..+..+++.||+|+|||.-.+--+...+ ..+.++
T Consensus        18 ~~~gs~~lI~G~pGsGKT~la~~~l~~~~-~~ge~~   52 (237)
T TIGR03877        18 IPERNVVLLSGGPGTGKSIFSQQFLWNGL-QMGEPG   52 (237)
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHHH-HcCCcE
Confidence            33457899999999999964333233334 334443

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.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=88.67  E-value=0.49  Score=40.56  Aligned_cols=26  Identities=19%  Similarity=0.120  Sum_probs=18.8

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +..+.|-||||+|||.++..-+-.++
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~  216 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAV  216 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            46788999999999987654433343

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=88.63  E-value=0.51  Score=36.55  Aligned_cols=28  Identities=18%  Similarity=0.163  Sum_probs=19.8

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      +..+..+++.||+|+|||.-.+--+...
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~   48 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGF   48 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4456789999999999997643333333

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=88.60  E-value=0.28  Score=41.05  Aligned_cols=21  Identities=29%  Similarity=0.627  Sum_probs=17.9

Q ss_pred             HHhcCCcEEEecCCCCCchHH
Q psy14273         45 TLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .+..|.++++-||+|+|||..
T Consensus        25 ~i~~Gef~vllGPSGcGKSTl   45 (338)
T COG3839          25 DIEDGEFVVLLGPSGCGKSTL   45 (338)
T ss_pred             EEcCCCEEEEECCCCCCHHHH
Confidence            356788999999999999964

>PRK13973 thymidylate kinase; Provisional

Probab=88.57  E-value=0.48  Score=35.95  Aligned_cols=29  Identities=28%  Similarity=0.330  Sum_probs=19.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      |..++|||+-|+|||.- +-.+..++...+
T Consensus         3 g~~IviEG~dGsGKtTq-~~~l~~~l~~~g   31 (213)
T PRK13973          3 GRFITFEGGEGAGKSTQ-IRLLAERLRAAG   31 (213)
T ss_pred             ceEEEEEcCCCCCHHHH-HHHHHHHHHHCC
Confidence            67889999999999853 223345554443

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=88.53  E-value=0.74  Score=43.94  Aligned_cols=38  Identities=21%  Similarity=0.196  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .+.|.+.+.      ..+.++++.|+-|||||.++..=++..+.
T Consensus         3 t~~Q~~ai~------~~~~~~lv~A~AGsGKT~~lv~r~~~~~~   40 (1232)
T TIGR02785         3 TDEQWQAIY------TRGQNILVSASAGSGKTAVLVERIIKKIL   40 (1232)
T ss_pred             CHHHHHHHh------CCCCCEEEEecCCCcHHHHHHHHHHHHHh
Confidence            467888655      35788999999999999998777777664

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=88.52  E-value=0.46  Score=40.90  Aligned_cols=32  Identities=16%  Similarity=0.094  Sum_probs=21.9

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +..++|-||||+|||.+..--+.. +...+.+|
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~-l~~~g~~V  237 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQ-LLKQNRTV  237 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH-HHHcCCeE
Confidence            457889999999999876555543 33444444

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.51  E-value=0.64  Score=41.41  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=31.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLIC   68 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~   68 (115)
                      |+.--+|....+.+.+++.++  .+ .||+||.|+|||....+
T Consensus        16 f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~   58 (614)
T PRK14971         16 FESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARI   58 (614)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHH
Confidence            333347899999999999887  34 78999999999975444

>PRK08233 hypothetical protein; Provisional

Probab=88.37  E-value=0.31  Score=34.84  Aligned_cols=15  Identities=27%  Similarity=0.366  Sum_probs=12.6

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..+.|.|++|+|||.
T Consensus         4 ~iI~I~G~~GsGKtT   18 (182)
T PRK08233          4 KIITIAAVSGGGKTT   18 (182)
T ss_pred             eEEEEECCCCCCHHH
Confidence            457789999999994

>PRK10867 signal recognition particle protein; Provisional

Probab=88.35  E-value=0.48  Score=40.68  Aligned_cols=31  Identities=13%  Similarity=-0.078  Sum_probs=21.0

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||+|+|||.+..--|..+....+.+|
T Consensus       102 vI~~vG~~GsGKTTtaakLA~~l~~~~G~kV  132 (433)
T PRK10867        102 VIMMVGLQGAGKTTTAGKLAKYLKKKKKKKV  132 (433)
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHhcCCcE
Confidence            4778999999999875555444443325555

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=88.35  E-value=0.36  Score=35.58  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.2

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|-||+|+|||.-
T Consensus         2 g~~i~l~G~sGsGKsTl   18 (186)
T PRK10078          2 GKLIWLMGPSGSGKDSL   18 (186)
T ss_pred             CcEEEEECCCCCCHHHH
Confidence            45789999999999953

>KOG2373|consensus

Probab=88.31  E-value=0.28  Score=42.50  Aligned_cols=19  Identities=26%  Similarity=0.580  Sum_probs=15.5

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      ...|..-|+.||||+|||.
T Consensus       270 hR~GElTvlTGpTGsGKTT  288 (514)
T KOG2373|consen  270 HRPGELTVLTGPTGSGKTT  288 (514)
T ss_pred             CCCCceEEEecCCCCCcee
Confidence            3445678999999999995

>PHA00729 NTP-binding motif containing protein

Probab=88.29  E-value=0.78  Score=36.36  Aligned_cols=25  Identities=16%  Similarity=0.272  Sum_probs=17.6

Q ss_pred             HHHHHHhcC--CcEEEecCCCCCchHH
Q psy14273         41 NLYYTLDNS--KFGIFESPTGTGKSLS   65 (115)
Q Consensus        41 ~I~~~l~~~--~~~iiEaPTGtGKTls   65 (115)
                      .+.+.+..+  .+++|.|++|+|||.-
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~L   33 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTY   33 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHH
Confidence            344444444  4689999999999943

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=88.23  E-value=1.1  Score=38.80  Aligned_cols=50  Identities=22%  Similarity=0.254  Sum_probs=33.9

Q ss_pred             cCCCCCCH-HHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFDAYD-IQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~~r~-~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .|+..||. .|.-.++.+   ++.. ..+.+-|+-|||||+-+||+++.-....+
T Consensus       223 vwGi~prn~eQ~~ALdlL---ld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~  274 (436)
T COG1875         223 VWGIRPRNAEQRVALDLL---LDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERK  274 (436)
T ss_pred             hhccCcccHHHHHHHHHh---cCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHh
Confidence            45566774 444444432   3333 56778999999999999999887665543

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

Probab=88.22  E-value=0.46  Score=43.60  Aligned_cols=32  Identities=22%  Similarity=0.200  Sum_probs=23.1

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ...+.-+|.||||+|||.-  +=|+.|+......
T Consensus        23 f~~gi~lI~G~nGsGKSSI--ldAI~~ALyG~~~   54 (908)
T COG0419          23 FDSGIFLIVGPNGAGKSSI--LDAITFALYGKTP   54 (908)
T ss_pred             CCCCeEEEECCCCCcHHHH--HHHHHHHHcCCCC
Confidence            3457788999999999953  5567777654444

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=88.21  E-value=0.81  Score=40.89  Aligned_cols=39  Identities=18%  Similarity=0.118  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .-+.|.+.+.      ...+.++|-|+.|||||.+++.=+...+.
T Consensus         5 Ln~~Q~~av~------~~~g~~lV~AgaGSGKT~~l~~ria~Li~   43 (726)
T TIGR01073         5 LNPEQREAVK------TTEGPLLIMAGAGSGKTRVLTHRIAHLIA   43 (726)
T ss_pred             cCHHHHHHHh------CCCCCEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            4578888554      23567899999999999987776555554

Designed to identify pcrA members of the uvrD/rep subfamily.

>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=88.14  E-value=0.62  Score=39.51  Aligned_cols=14  Identities=50%  Similarity=0.883  Sum_probs=12.3

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      ++++.||||+|||-
T Consensus        89 I~~VYGPTG~GKSq  102 (369)
T PF02456_consen   89 IGVVYGPTGSGKSQ  102 (369)
T ss_pred             EEEEECCCCCCHHH
Confidence            58899999999993

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

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=88.11  E-value=0.92  Score=36.22  Aligned_cols=37  Identities=19%  Similarity=0.091  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHhcC--Cc-EEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KF-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~-~iiEaPTGtGKTls~L~~   69 (115)
                      -+|...++.+.+++.++  .| .+|.||-|+|||..+..-
T Consensus         7 ~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~   46 (313)
T PRK05564          7 IGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEI   46 (313)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHH
Confidence            36888888999999887  34 489999999999765444

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=88.05  E-value=0.82  Score=40.28  Aligned_cols=33  Identities=21%  Similarity=0.267  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++.+.+.+....+..++|.|++||||++.
T Consensus       226 ~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~  258 (538)
T PRK15424        226 PQMEQVRQTILLYARSSAAVLIQGETGTGKELA  258 (538)
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHH
Confidence            444445555555556678999999999999964

>PRK13975 thymidylate kinase; Provisional

Probab=88.03  E-value=0.32  Score=35.49  Aligned_cols=16  Identities=44%  Similarity=0.754  Sum_probs=13.7

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..++|+|+-|+|||.
T Consensus         2 ~~~I~ieG~~GsGKtT   17 (196)
T PRK13975          2 NKFIVFEGIDGSGKTT   17 (196)
T ss_pred             CeEEEEECCCCCCHHH
Confidence            3578999999999985

>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown

Probab=88.00  E-value=0.39  Score=36.16  Aligned_cols=20  Identities=25%  Similarity=0.278  Sum_probs=16.0

Q ss_pred             CCcEEEecCCCCCchHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~   68 (115)
                      .+|+.+-|-||||||.+.-.
T Consensus        23 ~~H~~I~G~TGsGKS~~~~~   42 (229)
T PF01935_consen   23 NRHIAIFGTTGSGKSNTVKV   42 (229)
T ss_pred             cceEEEECCCCCCHHHHHHH
Confidence            46888999999999976433

It contains several conserved aspartates and histidines that could be metal ligands.

>PRK05595 replicative DNA helicase; Provisional

Probab=87.99  E-value=0.52  Score=39.82  Aligned_cols=41  Identities=5%  Similarity=-0.144  Sum_probs=28.8

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+..-+..|..+|+-|.||.|||.-.+--+..++..++.+|
T Consensus       193 ~~~~G~~~g~liviaarpg~GKT~~al~ia~~~a~~~g~~v  233 (444)
T PRK05595        193 AKTSGFQKGDMILIAARPSMGKTTFALNIAEYAALREGKSV  233 (444)
T ss_pred             HhcCCCCCCcEEEEEecCCCChHHHHHHHHHHHHHHcCCcE
Confidence            33344556778999999999999876666555555556554

>PRK06547 hypothetical protein; Provisional

Probab=87.98  E-value=0.58  Score=34.91  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=16.1

Q ss_pred             HHHHHhcC--CcEEEecCCCCCchHH
Q psy14273         42 LYYTLDNS--KFGIFESPTGTGKSLS   65 (115)
Q Consensus        42 I~~~l~~~--~~~iiEaPTGtGKTls   65 (115)
                      +...+..+  ..++|.||+|||||.-
T Consensus         6 ~~~~~~~~~~~~i~i~G~~GsGKTt~   31 (172)
T PRK06547          6 IAARLCGGGMITVLIDGRSGSGKTTL   31 (172)
T ss_pred             HHHHhhcCCCEEEEEECCCCCCHHHH
Confidence            33444444  3567789999999953

>KOG0731|consensus

Probab=87.96  E-value=0.7  Score=42.69  Aligned_cols=18  Identities=39%  Similarity=0.458  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      +-+++.||.||||||-+-
T Consensus       345 kGvLL~GPPGTGKTLLAK  362 (774)
T KOG0731|consen  345 KGVLLVGPPGTGKTLLAK  362 (774)
T ss_pred             CceEEECCCCCcHHHHHH
Confidence            358899999999997533

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

Probab=87.93  E-value=0.43  Score=39.05  Aligned_cols=16  Identities=31%  Similarity=0.449  Sum_probs=13.8

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||||+|||.-
T Consensus         5 ~~i~i~GptgsGKt~l   20 (307)
T PRK00091          5 KVIVIVGPTASGKTAL   20 (307)
T ss_pred             eEEEEECCCCcCHHHH
Confidence            5688999999999954

>PRK13768 GTPase; Provisional

Probab=87.90  E-value=0.52  Score=36.98  Aligned_cols=30  Identities=17%  Similarity=0.340  Sum_probs=20.1

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||.|+|||... ..+..++...+.++
T Consensus         4 ~i~v~G~~G~GKTt~~-~~~~~~l~~~g~~v   33 (253)
T PRK13768          4 IVFFLGTAGSGKTTLT-KALSDWLEEQGYDV   33 (253)
T ss_pred             EEEEECCCCccHHHHH-HHHHHHHHhcCCce
Confidence            5788999999999643 33344555555554

>KOG0060|consensus

Probab=87.87  E-value=0.29  Score=44.23  Aligned_cols=20  Identities=20%  Similarity=0.381  Sum_probs=17.2

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.+|++++|+||+|+|||.-
T Consensus       458 V~~g~~LLItG~sG~GKtSL  477 (659)
T KOG0060|consen  458 VPSGQNLLITGPSGCGKTSL  477 (659)
T ss_pred             ecCCCeEEEECCCCCchhHH
Confidence            35689999999999999953

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=87.82  E-value=0.31  Score=45.67  Aligned_cols=30  Identities=17%  Similarity=0.107  Sum_probs=24.7

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ++=|+|-||||||.+||=.+...=+.++..
T Consensus        76 NiDI~METGTGKTy~YlrtmfeLhk~YG~~  105 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFELHKKYGLF  105 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHHHHHHhCce
Confidence            466899999999999998888777777644

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=87.81  E-value=0.31  Score=36.14  Aligned_cols=20  Identities=30%  Similarity=0.639  Sum_probs=16.7

Q ss_pred             HHhcCCcEEEecCCCCCchH
Q psy14273         45 TLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+..|..+.|.||+|+|||.
T Consensus        23 ~i~~G~~~~i~G~nGsGKST   42 (214)
T cd03292          23 SISAGEFVFLVGPSGAGKST   42 (214)
T ss_pred             EEcCCCEEEEECCCCCCHHH
Confidence            34568889999999999984

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=87.79  E-value=1.4  Score=36.43  Aligned_cols=34  Identities=15%  Similarity=0.017  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHhcC----CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~   66 (115)
                      +........+.....+.    ..++|.||+|+|||.-+
T Consensus       116 ~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~  153 (405)
T TIGR00362       116 KSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLL  153 (405)
T ss_pred             CcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHH
Confidence            44444444444444431    35789999999999654

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).

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=87.78  E-value=1.4  Score=37.52  Aligned_cols=35  Identities=17%  Similarity=-0.022  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L   67 (115)
                      +........+.+...+.   ..+++.||+|+|||.-+.
T Consensus       111 ~~n~~a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~  148 (440)
T PRK14088        111 PGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQ  148 (440)
T ss_pred             CchHHHHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHH
Confidence            44444444554444432   358999999999996443

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=87.72  E-value=0.3  Score=38.79  Aligned_cols=32  Identities=22%  Similarity=0.431  Sum_probs=22.1

Q ss_pred             HHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         42 LYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        42 I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      |.=.+..|..+.|-||+|||||.  |+-++..+.
T Consensus        24 v~l~i~~Ge~vaI~GpSGSGKST--LLniig~ld   55 (226)
T COG1136          24 VNLEIEAGEFVAIVGPSGSGKST--LLNLLGGLD   55 (226)
T ss_pred             ceEEEcCCCEEEEECCCCCCHHH--HHHHHhccc
Confidence            33345678899999999999984  344444443

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=87.71  E-value=0.44  Score=34.70  Aligned_cols=17  Identities=24%  Similarity=0.313  Sum_probs=14.6

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ++.+++.||.|+|||..
T Consensus         2 ~~~i~l~G~~gsGKst~   18 (175)
T cd00227           2 GRIIILNGGSSAGKSSI   18 (175)
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            56799999999999953

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK11054 helD DNA helicase IV; Provisional

Probab=87.70  E-value=1.1  Score=40.43  Aligned_cols=40  Identities=13%  Similarity=0.027  Sum_probs=27.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +...+.|++.+.      ....+++|-|+.|||||.+++.-+...+
T Consensus       195 ~~L~~~Q~~av~------~~~~~~lV~agaGSGKT~vl~~r~ayLl  234 (684)
T PRK11054        195 SPLNPSQARAVV------NGEDSLLVLAGAGSGKTSVLVARAGWLL  234 (684)
T ss_pred             CCCCHHHHHHHh------CCCCCeEEEEeCCCCHHHHHHHHHHHHH
Confidence            335688887443      2345788999999999988766543333

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=87.64  E-value=0.88  Score=43.48  Aligned_cols=52  Identities=23%  Similarity=0.207  Sum_probs=37.1

Q ss_pred             hhcCCCCCCccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHH
Q psy14273         14 EQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        14 ~~~~~~~~~~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      |+-.-+..|..+.....+|++|.--  -+  +|  +.--|.||.||=||||+.-+|+.
T Consensus       153 ~~~~w~~~g~~~~W~m~~yDVQliG--gi--vL--h~G~IAEM~TGEGKTLvAtlp~y  204 (1112)
T PRK12901        153 WKNHWDAGGNEITWDMVHYDVQLIG--GV--VL--HQGKIAEMATGEGKTLVATLPVY  204 (1112)
T ss_pred             hhcccccccccccCCCcccchHHhh--hh--hh--cCCceeeecCCCCchhHHHHHHH
Confidence            4445566777777788888988642  22  23  33467899999999999888854

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=87.61  E-value=0.32  Score=36.71  Aligned_cols=20  Identities=20%  Similarity=0.227  Sum_probs=17.0

Q ss_pred             HHhcCCcEEEecCCCCCchH
Q psy14273         45 TLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+..|..+.|.||+|+|||.
T Consensus        27 ~i~~Ge~~~l~G~nGsGKST   46 (233)
T cd03258          27 SVPKGEIFGIIGRSGAGKST   46 (233)
T ss_pred             EEcCCCEEEEECCCCCCHHH
Confidence            34578899999999999994

Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=87.56  E-value=0.28  Score=34.94  Aligned_cols=13  Identities=31%  Similarity=0.409  Sum_probs=10.9

Q ss_pred             EEEecCCCCCchH
Q psy14273         52 GIFESPTGTGKSL   64 (115)
Q Consensus        52 ~iiEaPTGtGKTl   64 (115)
                      +++.||+|+|||.
T Consensus         1 i~l~G~~GsGKST   13 (163)
T TIGR01313         1 FVLMGVAGSGKST   13 (163)
T ss_pred             CEEECCCCCCHHH
Confidence            4678999999984

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.

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

Probab=87.53  E-value=0.58  Score=34.90  Aligned_cols=31  Identities=10%  Similarity=0.024  Sum_probs=21.9

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..+....|.||+|+|||.-.+.-+...+..
T Consensus        16 ~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~   46 (226)
T cd01393          16 IPTGRITEIFGEFGSGKTQLCLQLAVEAQLP   46 (226)
T ss_pred             CcCCcEEEEeCCCCCChhHHHHHHHHHhhcc
Confidence            3445788999999999998666554444433

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=87.47  E-value=0.69  Score=41.45  Aligned_cols=16  Identities=44%  Similarity=0.567  Sum_probs=13.9

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||+|||||+.
T Consensus       213 ~giLL~GppGtGKT~l  228 (733)
T TIGR01243       213 KGVLLYGPPGTGKTLL  228 (733)
T ss_pred             ceEEEECCCCCChHHH
Confidence            5689999999999954

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=87.47  E-value=1.2  Score=37.47  Aligned_cols=35  Identities=14%  Similarity=-0.004  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHHHHHhcC----CcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~L   67 (115)
                      +........+.+...+.    ..++|.||+|+|||.-+-
T Consensus       128 ~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~  166 (450)
T PRK00149        128 KSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLH  166 (450)
T ss_pred             CCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHH
Confidence            44444555555444331    458999999999996543

>TIGR00634 recN DNA repair protein RecN

Probab=87.45  E-value=0.61  Score=40.65  Aligned_cols=27  Identities=26%  Similarity=0.449  Sum_probs=20.8

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+.-+|.||||+|||.  |+-++.|+.-.
T Consensus        22 ~g~~vitG~nGaGKS~--ll~al~~~~g~   48 (563)
T TIGR00634        22 RGLTVLTGETGAGKSM--IIDALSLLGGQ   48 (563)
T ss_pred             CCeEEEECCCCCCHHH--HHHHHHHHhCc
Confidence            3578899999999985  46678887543

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=87.43  E-value=1.2  Score=42.52  Aligned_cols=50  Identities=10%  Similarity=0.088  Sum_probs=36.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++...+.|.+.+..|   ...+..+++.|+-|||||..+- ++...+...+.+|
T Consensus       379 ~~~Ls~eQ~~Av~~i---~~~~r~~~v~G~AGTGKTt~l~-~~~~~~e~~G~~V  428 (1102)
T PRK13826        379 HARLSDEQKTAIEHV---AGPARIAAVVGRAGAGKTTMMK-AAREAWEAAGYRV  428 (1102)
T ss_pred             CCCCCHHHHHHHHHH---hccCCeEEEEeCCCCCHHHHHH-HHHHHHHHcCCeE
Confidence            466789999987765   3557889999999999997644 4455555556554

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=87.42  E-value=0.65  Score=35.29  Aligned_cols=34  Identities=18%  Similarity=0.032  Sum_probs=21.0

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+..+++.||+|+|||.-.+.-+...+. ++.++
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~~~~-~g~~~   56 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYGALK-QGKKV   56 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHHHh-CCCEE
Confidence            34567899999999999543333333333 34443

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=87.35  E-value=0.35  Score=35.49  Aligned_cols=20  Identities=20%  Similarity=0.288  Sum_probs=17.0

Q ss_pred             HHhcCCcEEEecCCCCCchH
Q psy14273         45 TLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+..|.++.|-||+|+|||.
T Consensus        14 ~i~~Ge~~~i~G~nGsGKST   33 (190)
T TIGR01166        14 AAERGEVLALLGANGAGKST   33 (190)
T ss_pred             EEcCCCEEEEECCCCCCHHH
Confidence            35678899999999999994

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=87.31  E-value=0.48  Score=40.00  Aligned_cols=17  Identities=29%  Similarity=0.477  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      +.+++.||+|||||+..
T Consensus       180 kgvLL~GppGTGKT~LA  196 (398)
T PTZ00454        180 RGVLLYGPPGTGKTMLA  196 (398)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            56899999999999754

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=87.28  E-value=0.34  Score=36.12  Aligned_cols=20  Identities=30%  Similarity=0.662  Sum_probs=16.9

Q ss_pred             HHhcCCcEEEecCCCCCchH
Q psy14273         45 TLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+..|..+.|.||+|+|||.
T Consensus        26 ~i~~G~~~~l~G~nGsGKST   45 (218)
T cd03255          26 SIEKGEFVAIVGPSGSGKST   45 (218)
T ss_pred             EEcCCCEEEEEcCCCCCHHH
Confidence            34568899999999999994

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=87.17  E-value=0.34  Score=35.71  Aligned_cols=19  Identities=26%  Similarity=0.443  Sum_probs=16.3

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+.|.||+|+|||.
T Consensus        21 i~~Ge~~~i~G~nGsGKST   39 (206)
T TIGR03608        21 IEKGKMYAIIGESGSGKST   39 (206)
T ss_pred             EeCCcEEEEECCCCCCHHH
Confidence            4567889999999999994

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>cd03242 ABC_RecF RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage

Probab=87.11  E-value=0.71  Score=36.24  Aligned_cols=25  Identities=8%  Similarity=0.179  Sum_probs=18.9

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..+|.||+|+|||.  |+-|+.++..
T Consensus        22 ~~~~i~G~NGsGKS~--ll~Ai~~~~~   46 (270)
T cd03242          22 GVTVLVGENAQGKTN--LLEAISLLAT   46 (270)
T ss_pred             CeEEEECCCCCCHHH--HHHHHHHhcc
Confidence            467899999999985  3566666653

When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=87.06  E-value=1.3  Score=36.48  Aligned_cols=39  Identities=18%  Similarity=0.097  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~~   69 (115)
                      .||-|...-+.+.+.+.+++   ..+|.||.|+||+..+..-
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~   45 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELF   45 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHH
Confidence            57888888888888888874   4789999999998654433

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=87.05  E-value=0.66  Score=40.27  Aligned_cols=31  Identities=23%  Similarity=0.209  Sum_probs=21.4

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..++|-||||+|||.++..-+..+. ..+.++
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~~L~-~~GkkV  272 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAWQFH-GKKKTV  272 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH-HcCCcE
Confidence            4678999999999987665554443 444444

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=87.02  E-value=0.42  Score=34.20  Aligned_cols=14  Identities=43%  Similarity=0.743  Sum_probs=12.5

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+||.|+|||.
T Consensus         2 ~I~ieG~~GsGKtT   15 (200)
T cd01672           2 FIVFEGIDGAGKTT   15 (200)
T ss_pred             EEEEECCCCCCHHH
Confidence            57899999999985

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=87.01  E-value=0.63  Score=36.58  Aligned_cols=33  Identities=18%  Similarity=-0.073  Sum_probs=20.8

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+...++.||+|+|||.-.+--+...+. .+.++
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~-~Ge~v   67 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQAS-RGNPV   67 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHh-CCCcE
Confidence            4567899999999999644333333333 34443

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

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=86.99  E-value=0.69  Score=42.43  Aligned_cols=38  Identities=13%  Similarity=0.121  Sum_probs=28.0

Q ss_pred             CCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         30 DAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      +|-=+|.+-++.+...|.++  .+.|+.||+|+|||..+-
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHHH
Confidence            34445666677888877654  689999999999996543

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.

>KOG0745|consensus

Probab=86.99  E-value=0.38  Score=42.53  Aligned_cols=25  Identities=28%  Similarity=0.339  Sum_probs=17.7

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +.++++-+|||+||||-  +-.|+-..
T Consensus       226 KSNvLllGPtGsGKTll--aqTLAr~l  250 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLL--AQTLARVL  250 (564)
T ss_pred             cccEEEECCCCCchhHH--HHHHHHHh
Confidence            35799999999999963  44444433

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=86.98  E-value=0.71  Score=41.35  Aligned_cols=30  Identities=13%  Similarity=-0.013  Sum_probs=20.4

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .+|.++-|+||+|||..+ ...+..+..++.
T Consensus       176 ~~H~lv~G~TGsGKT~l~-~~l~~q~i~~g~  205 (634)
T TIGR03743       176 VGHTLVLGTTGVGKTRLA-ELLITQDIRRGD  205 (634)
T ss_pred             CCcEEEECCCCCCHHHHH-HHHHHHHHHcCC
Confidence            368999999999999765 333433334333

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>PRK14738 gmk guanylate kinase; Provisional

Probab=86.96  E-value=0.38  Score=36.36  Aligned_cols=17  Identities=24%  Similarity=0.536  Sum_probs=14.5

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .+..+||.||.|+|||.
T Consensus        12 ~~~~ivi~GpsG~GK~t   28 (206)
T PRK14738         12 KPLLVVISGPSGVGKDA   28 (206)
T ss_pred             CCeEEEEECcCCCCHHH
Confidence            34678999999999995

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=86.95  E-value=1.2  Score=34.89  Aligned_cols=33  Identities=24%  Similarity=0.344  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      |-=..+...+..++..+..+.+.||+|||||-+
T Consensus        16 plt~r~~~~l~~al~~~~~~~~~GpagtGKtet   48 (231)
T PF12774_consen   16 PLTDRCFLTLTQALSLNLGGALSGPAGTGKTET   48 (231)
T ss_dssp             HHHHHHHHHHHHHHCTTTEEEEESSTTSSHHHH
T ss_pred             hHHHHHHHHHHHHhccCCCCCCcCCCCCCchhH
Confidence            444556666777787778899999999999976

>PRK05748 replicative DNA helicase; Provisional

Probab=86.88  E-value=0.65  Score=39.19  Aligned_cols=37  Identities=11%  Similarity=-0.004  Sum_probs=26.1

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -+..|..+||-|+||+|||.-.+--+...+..++..+
T Consensus       199 G~~~G~livIaarpg~GKT~~al~ia~~~a~~~g~~v  235 (448)
T PRK05748        199 GLQPNDLIIVAARPSVGKTAFALNIAQNVATKTDKNV  235 (448)
T ss_pred             CCCCCceEEEEeCCCCCchHHHHHHHHHHHHhCCCeE
Confidence            3445678999999999999766655555555555554

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=86.83  E-value=0.46  Score=37.26  Aligned_cols=26  Identities=23%  Similarity=0.588  Sum_probs=18.4

Q ss_pred             EecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         54 FESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        54 iEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +-||-||||| +|+...-.|+...++.
T Consensus         1 ViGpaGSGKT-T~~~~~~~~~~~~~~~   26 (238)
T PF03029_consen    1 VIGPAGSGKT-TFCKGLSEWLESNGRD   26 (238)
T ss_dssp             -EESTTSSHH-HHHHHHHHHHTTT-S-
T ss_pred             CCCCCCCCHH-HHHHHHHHHHHhccCC
Confidence            3589999998 4667777888777544

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>cd01363 Motor_domain Myosin and Kinesin motor domain

Probab=86.80  E-value=0.69  Score=34.41  Aligned_cols=18  Identities=22%  Similarity=0.237  Sum_probs=15.0

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      ..++..|+||+|||.+..
T Consensus        25 ~~i~~yG~tGsGKT~Tm~   42 (186)
T cd01363          25 VCIFAYGQTGSGKTYTME   42 (186)
T ss_pred             eeEEEECCCCCcceEecC
Confidence            557789999999998764

These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=86.76  E-value=1.1  Score=39.38  Aligned_cols=33  Identities=15%  Similarity=0.089  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++.+.+.+....+..++|.|.+||||++.
T Consensus       219 ~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~l  251 (526)
T TIGR02329       219 APMEQVRALVRLYARSDATVLILGESGTGKELV  251 (526)
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHH
Confidence            444455555555566678999999999999964

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK14737 gmk guanylate kinase; Provisional

Probab=86.67  E-value=0.41  Score=36.02  Aligned_cols=16  Identities=44%  Similarity=0.476  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..+||.||+|+|||.
T Consensus         4 ~~~ivl~GpsG~GK~t   19 (186)
T PRK14737          4 PKLFIISSVAGGGKST   19 (186)
T ss_pred             CeEEEEECCCCCCHHH
Confidence            4678999999999994

>PRK10246 exonuclease subunit SbcC; Provisional

Probab=86.67  E-value=0.61  Score=43.72  Aligned_cols=29  Identities=17%  Similarity=0.173  Sum_probs=21.7

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..++..+|.||||+|||..  +=+|+|+..
T Consensus        27 l~~~~l~~I~G~tGaGKSti--ldai~~aLy   55 (1047)
T PRK10246         27 FASNGLFAITGPTGAGKTTL--LDAICLALY   55 (1047)
T ss_pred             CCCCCEEEEECCCCCCHHHH--HHHHHHHhc
Confidence            34567889999999999964  456677654

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=86.66  E-value=1.7  Score=33.69  Aligned_cols=34  Identities=21%  Similarity=0.184  Sum_probs=26.6

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .....+++..++|.|||.+.+.-++..+- ++.+|
T Consensus        20 ~~~g~v~v~~g~GkGKtt~a~g~a~ra~g-~G~~V   53 (191)
T PRK05986         20 EEKGLLIVHTGNGKGKSTAAFGMALRAVG-HGKKV   53 (191)
T ss_pred             ccCCeEEEECCCCCChHHHHHHHHHHHHH-CCCeE
Confidence            35678999999999999999988887664 34444

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=86.65  E-value=0.4  Score=35.64  Aligned_cols=24  Identities=21%  Similarity=0.541  Sum_probs=18.6

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchH
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+.=.+..|..+.|.||+|+|||.
T Consensus        20 ~is~~i~~G~~~~l~G~nGsGKST   43 (214)
T TIGR02673        20 DVSLHIRKGEFLFLTGPSGAGKTT   43 (214)
T ss_pred             ceeEEEcCCCEEEEECCCCCCHHH
Confidence            333345678899999999999985

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>PHA02562 46 endonuclease subunit; Provisional

Probab=86.65  E-value=0.6  Score=39.68  Aligned_cols=26  Identities=23%  Similarity=0.183  Sum_probs=20.1

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+..+|.||||+|||..  +-|++|+..
T Consensus        27 ~g~~~i~G~NG~GKStl--l~aI~~~l~   52 (562)
T PHA02562         27 VKKTLITGKNGAGKSTM--LEALTFALF   52 (562)
T ss_pred             CCEEEEECCCCCCHHHH--HHHHHHHHc
Confidence            46788899999999853  566777764

>PRK08760 replicative DNA helicase; Provisional

Probab=86.64  E-value=0.67  Score=39.93  Aligned_cols=38  Identities=13%  Similarity=-0.048  Sum_probs=28.0

Q ss_pred             HHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        44 ~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .-+..|..+||-|.+|+|||.-.|--+...+..++..|
T Consensus       224 ~G~~~G~LivIaarPg~GKTafal~iA~~~a~~~g~~V  261 (476)
T PRK08760        224 AGLQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGV  261 (476)
T ss_pred             cCCCCCceEEEEeCCCCChhHHHHHHHHHHHHhcCCce
Confidence            34556778999999999999877766666655555554

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=86.62  E-value=0.3  Score=38.65  Aligned_cols=20  Identities=30%  Similarity=0.468  Sum_probs=17.0

Q ss_pred             HHhcCCcEEEecCCCCCchH
Q psy14273         45 TLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTl   64 (115)
                      ++..|..++|++|+|+|||.
T Consensus        24 ~l~~Ge~~~i~G~NG~GKTt   43 (209)
T COG4133          24 TLNAGEALQITGPNGAGKTT   43 (209)
T ss_pred             EEcCCCEEEEECCCCCcHHH
Confidence            35668899999999999994

>CHL00195 ycf46 Ycf46; Provisional

Probab=86.57  E-value=0.68  Score=40.30  Aligned_cols=17  Identities=35%  Similarity=0.378  Sum_probs=14.4

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      +.+++.||.|||||+..
T Consensus       260 kGILL~GPpGTGKTllA  276 (489)
T CHL00195        260 RGLLLVGIQGTGKSLTA  276 (489)
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            45899999999999654

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=86.48  E-value=0.41  Score=35.56  Aligned_cols=19  Identities=21%  Similarity=0.406  Sum_probs=16.3

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+.|-||+|+|||.
T Consensus        23 i~~G~~~~i~G~nGsGKST   41 (210)
T cd03269          23 VEKGEIFGLLGPNGAGKTT   41 (210)
T ss_pred             EcCCcEEEEECCCCCCHHH
Confidence            4567889999999999994

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

---

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	115
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	2e-11
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	6e-10
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	7e-07

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620

 Score = 58.2 bits (141), Expect = 2e-11
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 9/74 (12%)

Query: 29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW---------YSDHKI 79
          ++    Q   +  L  +L  S     ESPTG+GK++  +   L++         Y     
Sbjct: 2  YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTN 61

Query: 80 AGLEKIEAEIKDLE 93
          +  E++  E++ L 
Sbjct: 62 SQEEQVIKELRSLS 75

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540

 Score = 53.8 bits (129), Expect = 6e-10
 Identities = 10/82 (12%), Positives = 25/82 (30%), Gaps = 5/82 (6%)

Query: 27  FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW-----YSDHKIAG 81
                   Q+  +      L + K  +  +  G GK++ +    ++            + 
Sbjct: 4   LKLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHSQ 63

Query: 82  LEKIEAEIKDLEISKNETVSED 103
           L+ I    K L +     + + 
Sbjct: 64  LDSIYKNAKLLGLKTGFLIGKS 85

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551

 Score = 45.4 bits (107), Expect = 7e-07
 Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 5/66 (7%)

Query: 32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW-----YSDHKIAGLEKIE 86
           D Q      +   L N+      +PTG+GK+L  +   L+      +          I 
Sbjct: 5  RDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVKPKVLFVVRTHNEFYPIY 64

Query: 87 AEIKDL 92
           ++  +
Sbjct: 65 RDLTKI 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	115
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.39
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.22
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.17
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	98.91
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	98.9
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	98.89
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.86
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	98.84
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	98.83
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	98.82
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	98.81
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	98.8
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	98.79
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	98.79
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	98.78
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	98.77
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	98.77
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	98.73
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	98.72
3bor_A	237	Human initiation factor 4A-II; translation initiat	98.72
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.71
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	98.7
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	98.69
3b6e_A	216	Interferon-induced helicase C domain-containing P;	98.69
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	98.69
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	98.68
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	98.67
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	98.65
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	98.65
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	98.64
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	98.63
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	98.61
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	98.6
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	98.59
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	98.58
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	98.56
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.55
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.49
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.46
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	98.45
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	98.45
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.38
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.34
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.34
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	98.34
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.33
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	98.32
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.31
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.28
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.27
3h1t_A	590	Type I site-specific restriction-modification syst	98.27
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	98.27
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	98.23
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	98.21
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	98.19
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.17
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	98.13
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	98.11
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	98.11
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.02
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.01
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	97.91
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	97.89
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	97.85
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	97.82
1yks_A	440	Genome polyprotein [contains: flavivirin protease	97.82
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	97.71
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	97.69
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	97.66
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	97.62
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	97.56
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.55
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	97.55
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	97.53
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	97.28
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	97.15
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	97.14
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	97.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.93
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.79
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.79
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.79
3co5_A	143	Putative two-component system transcriptional RES	96.65
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.58
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	96.47
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.47
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.47
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	96.36
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	96.35
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	96.31
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.24
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	96.24
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	96.24
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	96.21
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	96.2
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.19
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	96.19
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	96.13
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	96.11
2qgz_A	308	Helicase loader, putative primosome component; str	96.02
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.0
3bos_A	242	Putative DNA replication factor; P-loop containing	95.99
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.98
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.93
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	95.82
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	95.8
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	95.71
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	95.7
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.64
3jux_A	822	Protein translocase subunit SECA; protein transloc	95.59
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.57
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	95.56
2chq_A	319	Replication factor C small subunit; DNA-binding pr	95.56
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	95.53
1p9r_A	418	General secretion pathway protein E; bacterial typ	95.45
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	95.43
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	95.31
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	95.28
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.23
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.23
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.22
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	95.19
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.11
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.07
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	95.05
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	94.99
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.98
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.94
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	94.92
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	94.91
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	94.83
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	94.82
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	94.79
3pvs_A	447	Replication-associated recombination protein A; ma	94.77
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	94.69
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	94.69
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	94.61
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.6
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	94.52
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	94.48
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	94.47
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.47
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	94.46
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.46
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	94.44
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	94.36
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	94.35
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	94.28
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	94.2
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	94.15
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	94.12
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.12
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	94.08
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	94.08
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.95
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	93.93
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	93.92
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	93.89
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	93.88
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	93.88
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	93.8
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	93.7
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	93.64
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	93.57
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	93.51
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	93.5
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.49
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	93.49
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	93.48
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	93.45
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	93.37
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.35
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	93.29
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	93.29
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	93.27
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	93.26
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	93.09
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	92.99
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	92.93
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	92.91
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.9
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	92.88
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	92.88
4h1g_A	715	Maltose binding protein-cakar3 motor domain fusio;	92.84
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	92.81
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	92.8
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	92.79
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	92.79
3u06_A	412	Protein claret segregational; motor domain, stalk	92.76
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	92.7
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	92.63
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.55
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	92.5
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	92.48
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.33
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	92.32
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	92.27
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	92.26
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	92.25
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	92.2
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	92.09
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	92.03
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	92.02
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	91.99
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	91.96
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	91.95
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	91.93
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	91.92
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	91.87
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	91.87
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	91.85
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	91.84
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	91.82
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	91.76
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	91.71
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	91.62
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	91.57
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	91.53
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	91.29
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	91.28
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	91.22
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	91.22
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	91.2
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	91.05
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	91.04
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	91.02
2cvh_A	220	DNA repair and recombination protein RADB; filamen	90.97
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	90.94
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	90.87
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	90.87
2r6a_A	454	DNAB helicase, replicative helicase; replication,	90.82
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	90.79
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	90.67
2ewv_A	372	Twitching motility protein PILT; pilus retraction	90.65
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	90.56
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	90.51
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	90.36
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	90.35
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	90.34
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	90.33
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	90.28
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	90.25
4a74_A	231	DNA repair and recombination protein RADA; hydrola	90.21
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	90.16
2fna_A	357	Conserved hypothetical protein; structural genomic	90.15
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	90.15
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	90.1
3kta_A	182	Chromosome segregation protein SMC; structural mai	90.09
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	90.07
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	90.06
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	90.04
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	90.01
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	90.01
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	89.88
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	89.85
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	89.78
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	89.74
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	89.7
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	89.65
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	89.63
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	89.58
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	89.58
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	89.55
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	89.51
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	89.46
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	89.46
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	89.43
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	89.38
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	89.37
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	89.34
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	89.28
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	89.2
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	89.1
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	89.09
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	89.05
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	88.98
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	88.88
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	88.83
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	88.81
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	88.79
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	88.76
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	88.74
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	88.73
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	88.69
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	88.65
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	88.53
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	88.52
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	88.52
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	88.45
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	88.43
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	88.39
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	88.38
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	88.37
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	88.3
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	88.21
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	88.08
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	88.04
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	88.01
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	87.96
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	87.91
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	87.81
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	87.76
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	87.74
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	87.6
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	87.35
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	87.34
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	87.33
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	87.33
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	87.33
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	87.18
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	87.16
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	87.12
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	87.11
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	87.07
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	87.06
2vli_A	183	Antibiotic resistance protein; transferase, tunica	86.95
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	86.79
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	86.77
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	86.7
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	86.69
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	86.69
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	86.6
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	86.58
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	86.54
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	86.51
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	86.45
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	86.39
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	86.21
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	86.18
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	86.01
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	85.99
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	85.98
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	85.94
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	85.91
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	85.91
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	85.83
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	85.82
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	85.71
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	85.66
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	85.66
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	85.63
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	85.62
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	85.44
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	85.29
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	85.28
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	85.27
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	85.27
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	85.27
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	85.26
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	85.12
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	85.03
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	85.01
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	84.96
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	84.9
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	84.81
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	84.62
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	84.61
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	84.56
1sgw_A	214	Putative ABC transporter; structural genomics, P p	84.43
1g6h_A	257	High-affinity branched-chain amino acid transport	84.33
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	84.33
2ghi_A	260	Transport protein; multidrug resistance protein, M	84.19
1ji0_A	240	ABC transporter; ATP binding protein, structural g	83.97
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	83.97
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	83.96
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	83.9
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	83.86
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	83.7
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	83.63
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	83.56
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	83.56
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	83.54
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	83.52
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	83.49
1e69_A	322	Chromosome segregation SMC protein; structural mai	83.47
2z43_A	324	DNA repair and recombination protein RADA; archaea	83.44
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	83.26
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	83.23
1b0u_A	262	Histidine permease; ABC transporter, transport pro	83.06
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	83.05
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	83.05
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	83.03
1via_A	175	Shikimate kinase; structural genomics, transferase	82.98
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	82.89
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	82.88
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	82.77
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	82.77
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	82.68
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	82.68
1u94_A	356	RECA protein, recombinase A; homologous recombinat	82.4
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	82.33
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	82.26
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	82.25
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	82.24
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	82.16
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	82.01
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	81.92
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	81.82
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	81.74
2og2_A	359	Putative signal recognition particle receptor; nuc	81.41
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	81.32
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	81.31
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	81.02
3qkt_A	339	DNA double-strand break repair RAD50 ATPase; RECA-	80.8
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	80.65
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	80.6
2xxa_A	433	Signal recognition particle protein; protein trans	80.45
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	80.45
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	80.44
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	80.43
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	80.16
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	80.06
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	80.05

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.39  E-value=2.4e-13  Score=116.50  Aligned_cols=53  Identities=26%  Similarity=0.360  Sum_probs=46.8

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |+||++|.+||..|++++.++++++++||||||||++||+|++.++...+.++
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~kv   54 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKV   54 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHTCEE
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcCCeE
Confidence            78999999999999999999999999999999999999999999987765554

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.22  E-value=1.1e-11  Score=103.72  Aligned_cols=45  Identities=24%  Similarity=0.283  Sum_probs=43.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      .|++||+|.+||+.|++++.++++++++||||||||++||+|++.
T Consensus         1 ~~~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~   45 (551)
T 3crv_A            1 MVKLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLE   45 (551)
T ss_dssp             CCSCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHh
Confidence            378999999999999999999999999999999999999999987

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.17  E-value=2e-11  Score=102.23  Aligned_cols=47  Identities=13%  Similarity=0.145  Sum_probs=40.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      .+|++||+|.++++.|.+++.++++++++||||||||++||+|++.+
T Consensus         4 ~~~~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~   50 (540)
T 2vl7_A            4 LKLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL   50 (540)
T ss_dssp             -----CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC
Confidence            46889999999999999999999999999999999999999998764

>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=98.91  E-value=1.6e-09  Score=80.49  Aligned_cols=47  Identities=19%  Similarity=0.080  Sum_probs=40.8

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. |++.|.+.+..+    .+++.+++.||||+|||++|++|++..+..
T Consensus        46 ~~g~~~~~~~Q~~~i~~~----~~g~~~l~~apTGsGKT~~~~l~~l~~l~~   93 (242)
T 3fe2_A           46 RQNFTEPTAIQAQGWPVA----LSGLDMVGVAQTGSGKTLSYLLPAIVHINH   93 (242)
T ss_dssp             TTTCCSCCHHHHHHHHHH----HHTCCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCcCHHHHHHHHHHHHHHHh
Confidence            35777 999999988765    367899999999999999999999988864

>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=98.90  E-value=1.7e-09  Score=79.16  Aligned_cols=47  Identities=23%  Similarity=0.089  Sum_probs=39.5

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. |++.|.+.++.+    .+++.+++.||||+|||++|++|++..+..
T Consensus        37 ~~g~~~~~~~Q~~~i~~~----~~~~~~l~~apTGsGKT~~~~l~~~~~l~~   84 (228)
T 3iuy_A           37 RVGILKPTPIQSQAWPII----LQGIDLIVVAQTGTGKTLSYLMPGFIHLDS   84 (228)
T ss_dssp             HHTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHC-
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            35665 999999988765    478899999999999999999999987754

>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=98.89  E-value=2.5e-09  Score=76.65  Aligned_cols=47  Identities=17%  Similarity=0.145  Sum_probs=40.0

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. +|+.|.+.++.+    .+++.+++.+|||+|||++|++|++..+..
T Consensus        20 ~~g~~~~~~~Q~~~i~~~----~~~~~~lv~apTGsGKT~~~~~~~~~~~~~   67 (206)
T 1vec_A           20 EMGWEKPSPIQEESIPIA----LSGRDILARAKNGTGKSGAYLIPLLERLDL   67 (206)
T ss_dssp             TTTCCSCCHHHHHHHHHH----HTTCCEEEECCSSSTTHHHHHHHHHHHCCT
T ss_pred             HCCCCCCCHHHHHHHHHH----ccCCCEEEECCCCCchHHHHHHHHHHHhcc
Confidence            35676 999999988765    467899999999999999999999987754

>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=98.86  E-value=3.6e-09  Score=78.24  Aligned_cols=47  Identities=23%  Similarity=0.271  Sum_probs=40.3

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. |++.|.+.+..+    .+++.+++.||||+|||++|++|++..+..
T Consensus        46 ~~g~~~~~~~Q~~~i~~~----~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~   93 (245)
T 3dkp_A           46 DAGFQMPTPIQMQAIPVM----LHGRELLASAPTGSGKTLAFSIPILMQLKQ   93 (245)
T ss_dssp             HTTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHCS
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCCCcHHHHHHHHHHHHHhh
Confidence            34677 999999988765    467889999999999999999999988864

>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=98.84  E-value=5.1e-09  Score=77.92  Aligned_cols=48  Identities=17%  Similarity=0.199  Sum_probs=41.0

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .++|. |++.|.+.++.+    .+++.+++.||||+|||++|++|++..+...
T Consensus        40 ~~g~~~~~~~Q~~~i~~i----~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~   88 (253)
T 1wrb_A           40 LASYQRPTPIQKNAIPAI----LEHRDIMACAQTGSGKTAAFLIPIINHLVCQ   88 (253)
T ss_dssp             TTTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCCChHHHHHHHHHHHHHHhh
Confidence            45676 999999988865    4678899999999999999999999888653

>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=98.83  E-value=3.8e-09  Score=76.76  Aligned_cols=48  Identities=17%  Similarity=0.226  Sum_probs=40.5

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .++|. +|+.|.+.+..+    .+++.+++.+|||+|||++|++|++.++...
T Consensus        31 ~~g~~~~~~~Q~~~i~~~----~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~   79 (224)
T 1qde_A           31 GYGFEEPSAIQQRAIMPI----IEGHDVLAQAQSGTGKTGTFSIAALQRIDTS   79 (224)
T ss_dssp             HHTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHCCTT
T ss_pred             HCCCCCCcHHHHHHHHHH----hcCCCEEEECCCCCcHHHHHHHHHHHHHhcc
Confidence            35676 999999988765    4678899999999999999999999887544

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=98.82  E-value=6.9e-09  Score=76.32  Aligned_cols=46  Identities=20%  Similarity=0.212  Sum_probs=39.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +.|. +++.|.+.+..+    .+++.+++.+|||+|||++|++|++..+..
T Consensus        43 ~~~~~~~~~Q~~~i~~~----~~~~~~li~a~TGsGKT~~~~~~~l~~l~~   89 (236)
T 2pl3_A           43 AQYRLVTEIQKQTIGLA----LQGKDVLGAAKTGSGKTLAFLVPVLEALYR   89 (236)
T ss_dssp             TTCCBCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH----hCCCCEEEEeCCCCcHHHHHHHHHHHHHHh
Confidence            4666 999999988764    467899999999999999999999988754

>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=98.81  E-value=6.2e-09  Score=74.46  Aligned_cols=46  Identities=24%  Similarity=0.142  Sum_probs=39.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. |++.|.+.++.+    .+++.+++.+|||+|||++|+.|++..+..
T Consensus        19 ~~~~~~~~~Q~~~i~~~----~~~~~~li~~~TGsGKT~~~~~~~~~~l~~   65 (207)
T 2gxq_A           19 RGLTTPTPIQAAALPLA----LEGKDLIGQARTGTGKTLAFALPIAERLAP   65 (207)
T ss_dssp             TTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHCCC
T ss_pred             cCCCCCCHHHHHHHHHH----cCCCCEEEECCCCChHHHHHHHHHHHHHhh
Confidence            5665 999999988765    467889999999999999999999988753

>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=98.80  E-value=8.3e-09  Score=77.77  Aligned_cols=49  Identities=18%  Similarity=0.090  Sum_probs=41.7

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++|. +++.|.+.+..+    .+++.+++.||||+|||++|++|++..+...+
T Consensus        60 ~~g~~~~~~~Q~~~i~~i----~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~  109 (249)
T 3ber_A           60 QLGWTKPTKIQIEAIPLA----LQGRDIIGLAETGSGKTGAFALPILNALLETP  109 (249)
T ss_dssp             HTTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC
T ss_pred             HcCCCCCCHHHHHHHHHH----hCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC
Confidence            46776 999999988765    46789999999999999999999998876653

>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=98.79  E-value=7.5e-09  Score=76.36  Aligned_cols=47  Identities=17%  Similarity=0.031  Sum_probs=40.4

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. +++.|.+.++.+    .+++.+++.+|||+|||++|++|++..+..
T Consensus        41 ~~g~~~~~~~Q~~~i~~~----~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~   88 (230)
T 2oxc_A           41 AAGFERPSPVQLKAIPLG----RCGLDLIVQAKSGTGKTCVFSTIALDSLVL   88 (230)
T ss_dssp             HTTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHCCT
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            36777 999999988864    467899999999999999999999888754

>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=98.79  E-value=8.1e-09  Score=78.35  Aligned_cols=46  Identities=20%  Similarity=0.330  Sum_probs=39.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. +++.|.+++..+.    +++.+++.||||+|||++|++|++..+..
T Consensus        72 ~g~~~~~~~Q~~~i~~~~----~~~~~lv~a~TGsGKT~~~~l~~l~~l~~  118 (262)
T 3ly5_A           72 MGFTNMTEIQHKSIRPLL----EGRDLLAAAKTGSGKTLAFLIPAVELIVK  118 (262)
T ss_dssp             TTCCBCCHHHHHHHHHHH----HTCCCEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCcEEEEccCCCCchHHHHHHHHHHHHh
Confidence            4566 9999999888754    46789999999999999999999988865

>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=98.78  E-value=8.1e-09  Score=75.03  Aligned_cols=48  Identities=13%  Similarity=0.189  Sum_probs=40.6

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .++|. |++.|.+.+..+.    ++..+++.+|||+|||++|++|++..+...
T Consensus        31 ~~g~~~~~~~Q~~~i~~~~----~~~~~li~~~TGsGKT~~~~~~~~~~~~~~   79 (220)
T 1t6n_A           31 DCGFEHPSEVQHECIPQAI----LGMDVLCQAKSGMGKTAVFVLATLQQLEPV   79 (220)
T ss_dssp             HTTCCCCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHCCCC
T ss_pred             HCCCCCCCHHHHHHHHHHh----CCCCEEEECCCCCchhhhhhHHHHHhhhcc
Confidence            36777 9999999887653    567899999999999999999999887553

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=98.77  E-value=8.8e-09  Score=80.28  Aligned_cols=48  Identities=15%  Similarity=0.182  Sum_probs=40.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ++|. |++.|.+.+..+    .+++.+++.||||+|||++|++|++..+...+
T Consensus        33 ~~~~~~~~~Q~~~i~~i----~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~   81 (417)
T 2i4i_A           33 TRYTRPTPVQKHAIPII----KEKRDLMACAQTGSGKTAAFLLPILSQIYSDG   81 (417)
T ss_dssp             HTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHH----ccCCCEEEEcCCCCHHHHHHHHHHHHHHHhcc
Confidence            4665 999999988754    57889999999999999999999998876543

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=98.77  E-value=4.3e-09  Score=76.80  Aligned_cols=47  Identities=21%  Similarity=0.273  Sum_probs=39.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++|. +++.|.+.++.+.    +++.+++.+|||+|||++|++|++..+...
T Consensus        22 ~g~~~~~~~Q~~~i~~~~----~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~   69 (219)
T 1q0u_A           22 LRFYKPTEIQERIIPGAL----RGESMVGQSQTGTGKTHAYLLPIMEKIKPE   69 (219)
T ss_dssp             TTCCSCCHHHHHHHHHHH----HTCCEEEECCSSHHHHHHHHHHHHHHCCTT
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHHHhC
Confidence            5555 9999999887653    568899999999999999999999887643

>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=98.73  E-value=1.6e-08  Score=81.64  Aligned_cols=47  Identities=17%  Similarity=0.189  Sum_probs=41.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++|. |+|.|.+.+..+    .+++.+++.||||+|||++|++|++..+...
T Consensus        74 ~g~~~pt~iQ~~ai~~i----~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~  121 (434)
T 2db3_A           74 SGYKIPTPIQKCSIPVI----SSGRDLMACAQTGSGKTAAFLLPILSKLLED  121 (434)
T ss_dssp             TTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             cCCCCCCHHHHHHHHHH----hcCCCEEEECCCCCCchHHHHHHHHHHHHhc
Confidence            5677 999999988865    5788999999999999999999999888664

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=98.72  E-value=7.3e-09  Score=81.80  Aligned_cols=47  Identities=23%  Similarity=0.157  Sum_probs=40.1

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .|+|.|+|.|.+.++.+    .+++.+++.||||+|||++|+.+++..+..
T Consensus        17 ~~~~~~~~~Q~~~i~~i----~~~~~~lv~apTGsGKT~~~l~~~~~~~~~   63 (414)
T 3oiy_A           17 KFGKDLTGYQRLWAKRI----VQGKSFTMVAPTGVGKTTFGMMTALWLARK   63 (414)
T ss_dssp             HHSSCCCHHHHHHHHHH----TTTCCEECCSCSSSSHHHHHHHHHHHHHTT
T ss_pred             hcCCCCCHHHHHHHHHH----hcCCCEEEEeCCCCCHHHHHHHHHHHHhcC
Confidence            46889999999988865    467899999999999999999998877633

>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=98.72  E-value=6.7e-09  Score=77.12  Aligned_cols=47  Identities=21%  Similarity=0.230  Sum_probs=40.4

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. +++.|.+.+..+    .++..+++.||||+|||++|++|++..+..
T Consensus        47 ~~g~~~~~~~Q~~ai~~i----~~~~~~li~apTGsGKT~~~~l~~l~~l~~   94 (237)
T 3bor_A           47 AYGFEKPSAIQQRAIIPC----IKGYDVIAQAQSGTGKTATFAISILQQLEI   94 (237)
T ss_dssp             HHTCCSCCHHHHHHHHHH----HTTCCEEECCCSSHHHHHHHHHHHHHHCCT
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            35777 999999988765    467889999999999999999999988754

>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=98.71  E-value=1.4e-08  Score=79.08  Aligned_cols=49  Identities=22%  Similarity=0.273  Sum_probs=40.2

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      +.|. |++.|.+.+..+    .++  +++|+.||||||||++|++|++..+...+.
T Consensus       110 ~g~~~pt~iQ~~ai~~i----l~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~~  161 (300)
T 3fmo_B          110 MGFNRPSKIQENALPLM----LAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANK  161 (300)
T ss_dssp             TTCCSCCHHHHHHHHHH----TSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTSC
T ss_pred             cCCCCCCHHHHHHHHHH----HcCCCCeEEEECCCCCCccHHHHHHHHHhhhccCC
Confidence            4566 899999988765    344  899999999999999999999988765433

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=98.70  E-value=2e-08  Score=80.42  Aligned_cols=46  Identities=20%  Similarity=0.234  Sum_probs=40.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ||.||+.|.+.++.+    .+++.+|+.+|||+|||++|++|++..+...
T Consensus         2 ~~~~~~~Q~~~i~~~----~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~   47 (555)
T 3tbk_A            2 PLKPRNYQLELALPA----KKGKNTIICAPTGCGKTFVSLLICEHHLKKF   47 (555)
T ss_dssp             CCCCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCcHHHHHHHHHH----hCCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            688999999988865    3678999999999999999999999888764

>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=98.69  E-value=1.3e-08  Score=83.52  Aligned_cols=50  Identities=22%  Similarity=0.337  Sum_probs=42.5

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHh-cCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~-~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++|. ++|.|.+++..+.   . +++.+|+.||||+|||++|++|++..+...+
T Consensus        89 ~~g~~~~~~~Q~~~i~~~l---~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~  140 (563)
T 3i5x_A           89 RMEFPGLTPVQQKTIKPIL---SSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK  140 (563)
T ss_dssp             TTCCSSCCHHHHHHHHHHH---SSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCCCHHHHHHHHHHh---cCCCCeEEEECCCCCCccHHHHHHHHHHHHhcc
Confidence            36788 9999999887653   3 4678999999999999999999999987754

>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=98.69  E-value=1.9e-08  Score=71.82  Aligned_cols=48  Identities=17%  Similarity=0.093  Sum_probs=40.4

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+.+.+|+.|.++++.+.    +++.+++.+|||+|||++++.+++..+...
T Consensus        29 ~~~~~l~~~Q~~~i~~~~----~~~~~li~~~tGsGKT~~~~~~~~~~~~~~   76 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPAL----EGKNIIICLPTGSGKTRVAVYIAKDHLDKK   76 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHH----TTCCEEEECSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCchHHHHHHHHHHh----cCCCEEEEcCCCCCHHHHHHHHHHHHHhhc
Confidence            445779999999888653    568899999999999999999998877654

>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=98.69  E-value=1.2e-08  Score=78.92  Aligned_cols=51  Identities=22%  Similarity=0.287  Sum_probs=40.9

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++|. |++.|.+.+..+...  .++.+++.||||+|||++|++|++..+....
T Consensus        42 ~~g~~~~~~~Q~~~i~~~~~~--~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~   93 (412)
T 3fht_A           42 AMGFNRPSKIQENALPLMLAE--PPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN   93 (412)
T ss_dssp             HTTCCSCCHHHHHHHHHHHSS--SCCCEEEECCTTSCHHHHHHHHHHHHCCTTS
T ss_pred             HcCCCCCCHHHHHHHHHHhcC--CCCeEEEECCCCchHHHHHHHHHHHHhhhcC
Confidence            35676 999999988776421  2489999999999999999999998876543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=98.68  E-value=1.4e-08  Score=84.54  Aligned_cols=50  Identities=22%  Similarity=0.337  Sum_probs=42.6

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHh-cCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~-~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++|. ++|.|.+.+..+.   . .++.+|+.||||+|||++|++|++..+....
T Consensus        38 ~~g~~~~~~~Q~~~i~~il---~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~   89 (579)
T 3sqw_A           38 RMEFPGLTPVQQKTIKPIL---SSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK   89 (579)
T ss_dssp             TTTCSSCCHHHHHHHHHHH---CSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCCCHHHHHHHHHHH---ccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcc
Confidence            57888 9999999887653   3 4678999999999999999999999887653

>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=98.67  E-value=3.1e-08  Score=74.54  Aligned_cols=43  Identities=23%  Similarity=0.306  Sum_probs=36.9

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      .++|. +||.|.+.+..+    .+++.+++.+|||+|||++|+.|++.
T Consensus        11 ~~g~~~l~~~Q~~~i~~i----~~~~~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           11 EMGFKNFTEVQSKTIPLM----LQGKNVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             HTTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             HcCCCCCCHHHHHHHHHH----hcCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            36776 999999988765    46789999999999999999999775

>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=98.65  E-value=2e-08  Score=76.89  Aligned_cols=48  Identities=23%  Similarity=0.270  Sum_probs=38.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. |++.|.+.++.+...  .++.+++.||||+|||++|+.|++..+..
T Consensus        23 ~~~~~~~~~Q~~~i~~~~~~--~~~~~lv~a~TGsGKT~~~~~~~~~~~~~   71 (395)
T 3pey_A           23 MKFQKPSKIQERALPLLLHN--PPRNMIAQSQSGTGKTAAFSLTMLTRVNP   71 (395)
T ss_dssp             TTCCSCCHHHHHHHHHHHCS--SCCCEEEECCTTSCHHHHHHHHHHHHCCT
T ss_pred             CCCCCCCHHHHHHHHHHHcC--CCCeEEEECCCCCcHHHHHHHHHHHHhcc
Confidence            4565 999999988765321  13889999999999999999999887754

>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=98.65  E-value=2.2e-08  Score=78.20  Aligned_cols=45  Identities=24%  Similarity=0.393  Sum_probs=39.5

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ++|. |++.|.+.+..+    .+++.+++.+|||+|||++|++|++..+.
T Consensus        55 ~g~~~~~~~Q~~ai~~i----~~~~~~lv~a~TGsGKT~~~~~~~~~~l~  100 (410)
T 2j0s_A           55 YGFEKPSAIQQRAIKQI----IKGRDVIAQSQSGTGKTATFSISVLQCLD  100 (410)
T ss_dssp             HTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHTCC
T ss_pred             cCCCCCCHHHHHHHHHH----hCCCCEEEECCCCCCchHHHHHHHHHHHh
Confidence            6777 999999988865    46788999999999999999999998775

>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=98.64  E-value=2.8e-08  Score=76.61  Aligned_cols=46  Identities=13%  Similarity=0.194  Sum_probs=39.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. +||.|.+.++.+    .+++.+++.+|||+|||++|++|++..+..
T Consensus        26 ~g~~~~~~~Q~~~i~~~----~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~   72 (391)
T 1xti_A           26 CGFEHPSEVQHECIPQA----ILGMDVLCQAKSGMGKTAVFVLATLQQLEP   72 (391)
T ss_dssp             HSCCSCCHHHHHHHHHH----TTTCCEEEECSSCSSHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCHHHHHHHHHH----hcCCcEEEECCCCCcHHHHHHHHHHHhhcc
Confidence            5677 999999988765    457889999999999999999999987654

>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=98.63  E-value=3.6e-08  Score=76.60  Aligned_cols=46  Identities=17%  Similarity=0.186  Sum_probs=39.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. +|+.|.+.++.+.    +++.+++.+|||+|||++|++|++..+..
T Consensus        39 ~g~~~~~~~Q~~~i~~i~----~~~~~li~a~TGsGKT~~~~~~~~~~~~~   85 (400)
T 1s2m_A           39 AGFEKPSPIQEEAIPVAI----TGRDILARAKNGTGKTAAFVIPTLEKVKP   85 (400)
T ss_dssp             TTCCSCCHHHHHHHHHHH----HTCCEEEECCTTSCHHHHHHHHHHHHCCT
T ss_pred             CCCCCCCHHHHHHHHHHh----cCCCEEEECCCCcHHHHHHHHHHHHHHhh
Confidence            4677 9999999888754    56789999999999999999999987754

>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=98.61  E-value=3.9e-08  Score=76.33  Aligned_cols=47  Identities=21%  Similarity=0.224  Sum_probs=40.1

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|. +++.|.+.+..+    .+++.+++.||||+|||++|++|++..+..
T Consensus        57 ~~~~~~~~~~Q~~~i~~~----~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~  104 (414)
T 3eiq_A           57 AYGFEKPSAIQQRAILPC----IKGYDVIAQAQSGTGKTATFAISILQQIEL  104 (414)
T ss_dssp             HTTCCSCCHHHHHHHHHH----HTTCCEEECCCSCSSSHHHHHHHHHHHCCT
T ss_pred             HcCCCCCCHHHHHHhHHH----hCCCCEEEECCCCCcccHHHHHHHHHHHhh
Confidence            36776 999999988765    457889999999999999999999988754

>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=98.60  E-value=5e-08  Score=78.50  Aligned_cols=47  Identities=21%  Similarity=0.198  Sum_probs=38.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+|.|||.|.+.++.+    .++..+|+.+|||+|||++|+.|++..+...
T Consensus         4 ~~~~~~~~Q~~~i~~~----~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~   50 (556)
T 4a2p_A            4 ETKKARSYQIELAQPA----INGKNALICAPTGSGKTFVSILICEHHFQNM   50 (556)
T ss_dssp             ----CCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHH----HcCCCEEEEcCCCChHHHHHHHHHHHHHHhC
Confidence            4688999999988765    3578899999999999999999999888764

>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=98.59  E-value=2.5e-08  Score=76.75  Aligned_cols=47  Identities=17%  Similarity=0.264  Sum_probs=39.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++|. +|+.|.+.+..+.    +++.+++.+|||+|||++|++|++..+...
T Consensus        39 ~g~~~~~~~Q~~~i~~i~----~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~   86 (394)
T 1fuu_A           39 YGFEEPSAIQQRAIMPII----EGHDVLAQAQSGTGKTGTFSIAALQRIDTS   86 (394)
T ss_dssp             HTCCSCCHHHHHHHHHHH----HTCCEEECCCSSHHHHHHHHHHHHHHCCTT
T ss_pred             cCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHhhcc
Confidence            5665 9999999887753    567899999999999999999999887653

>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=98.58  E-value=5.7e-08  Score=73.67  Aligned_cols=47  Identities=21%  Similarity=0.332  Sum_probs=39.2

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. +|+.|.+.+..+   +..+..+++.+|||+|||++++.|++.++..
T Consensus        24 ~g~~~~~~~Q~~~i~~~---~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~   71 (367)
T 1hv8_A           24 KGFEKPTDIQMKVIPLF---LNDEYNIVAQARTGSGKTASFAIPLIELVNE   71 (367)
T ss_dssp             HTCCSCCHHHHHHHHHH---HHTCSEEEEECCSSSSHHHHHHHHHHHHSCS
T ss_pred             cCCCCCCHHHHHHHHHH---hCCCCCEEEECCCCChHHHHHHHHHHHHhcc
Confidence            4565 999999987765   4445799999999999999999999988765

>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=98.56  E-value=4.3e-08  Score=83.47  Aligned_cols=44  Identities=25%  Similarity=0.178  Sum_probs=38.4

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      -.|+|. +||.|.+.++.+    .+++.+++.+|||+|||++|++|++.
T Consensus        38 ~~fg~~~~rp~Q~~~i~~i----l~g~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           38 NVFKLEKFRPLQLETINVT----MAGKEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             HTSCCCSCCTTHHHHHHHH----HTTCCEEEECCTTSCTTHHHHHHHHT
T ss_pred             HHhCCCCCCHHHHHHHHHH----HcCCCEEEEECCCChHHHHHHHHHHH
Confidence            358998 999999988875    45788999999999999999999874

>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=98.55  E-value=2.7e-08  Score=80.28  Aligned_cols=50  Identities=22%  Similarity=0.309  Sum_probs=39.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ++|. |++.|.+.+..+..  ..+..+|+.||||+|||++|++|++..+...+
T Consensus       110 ~g~~~p~~~Q~~ai~~il~--~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~  160 (479)
T 3fmp_B          110 MGFNRPSKIQENALPLMLA--EPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN  160 (479)
T ss_dssp             TTCCSCCHHHHHHHHHHTS--BSCCEEEEECCSSSSHHHHHHHHHHTTCCTTS
T ss_pred             cCCCCCCHHHHHHHHHHHc--CCCCcEEEEcCCCCchhHHHHHHHHHHHhhcC
Confidence            4566 88999998877632  12488999999999999999999998776544

>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=98.49  E-value=1.1e-07  Score=79.64  Aligned_cols=47  Identities=19%  Similarity=0.121  Sum_probs=39.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +|.+|+.|.+.++.+.    +++.+|+.+|||+|||++|+.|++..+....
T Consensus         5 ~~~l~~~Q~~~i~~il----~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~   51 (699)
T 4gl2_A            5 MLQLRPYQMEVAQPAL----EGKNIIICLPTGCGKTRVAVYIAKDHLDKKK   51 (699)
T ss_dssp             --CCCHHHHHHHHHHH----SSCCEEECCCTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHH----hCCCEEEEcCCCCcHHHHHHHHHHHHHHhcc
Confidence            5789999999888753    4788999999999999999999998887653

>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=98.46  E-value=1.9e-07  Score=82.44  Aligned_cols=52  Identities=17%  Similarity=0.293  Sum_probs=46.4

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+||.+++.|.+.++.|.+.+.++  .++++.||||+|||++|+.|++..+...
T Consensus       364 ~lpf~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g  417 (780)
T 1gm5_A          364 SLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG  417 (780)
T ss_dssp             HSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT
T ss_pred             hCCCCCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcC
Confidence            689999999999999999888776  4899999999999999999999887543

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=98.45  E-value=2e-07  Score=78.12  Aligned_cols=49  Identities=16%  Similarity=0.072  Sum_probs=40.4

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      -.|+|. +|+.|.+.++.+    .+++.+|+.+|||+|||++|+.|++..+...
T Consensus         7 ~~~g~~~lr~~Q~~~i~~~----l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~   56 (696)
T 2ykg_A            7 NLYSPFKPRNYQLELALPA----MKGKNTIICAPTGCGKTFVSLLICEHHLKKF   56 (696)
T ss_dssp             CTTC--CCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             cccCCCCccHHHHHHHHHH----HcCCCEEEEcCCCchHHHHHHHHHHHHHHhC
Confidence            356766 999999988765    4578999999999999999999999888664

>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=98.45  E-value=7e-08  Score=80.51  Aligned_cols=44  Identities=23%  Similarity=0.227  Sum_probs=38.0

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      -.|+|. +|+.|.+.++.+    .+++.+++.||||+|||++|++|++.
T Consensus        19 ~~~g~~~~r~~Q~~~i~~i----l~g~d~lv~apTGsGKTl~~~lp~l~   63 (523)
T 1oyw_A           19 ETFGYQQFRPGQEEIIDTV----LSGRDCLVVMPTGGGKSLCYQIPALL   63 (523)
T ss_dssp             HTTCCSSCCTTHHHHHHHH----HTTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HHhCCCCCCHHHHHHHHHH----HcCCCEEEECCCCcHHHHHHHHHHHH
Confidence            358887 999999988865    46789999999999999999999874

>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=98.38  E-value=4.7e-07  Score=82.47  Aligned_cols=53  Identities=15%  Similarity=0.170  Sum_probs=46.6

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ..|||+++|.|.+.++.+.+.+.+++  .+++++|||+|||++++.+++..+...
T Consensus       598 ~~f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g  652 (1151)
T 2eyq_A          598 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH  652 (1151)
T ss_dssp             HTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT
T ss_pred             HhCCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhC
Confidence            36899999999999999998888776  899999999999999999988766543

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=98.34  E-value=3.8e-07  Score=73.89  Aligned_cols=47  Identities=15%  Similarity=0.091  Sum_probs=39.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +|.+|+.|.+.++.+.+    +..+++.+|||+|||++++.++...+...+
T Consensus       111 ~~~l~~~Q~~ai~~~~~----~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~  157 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLV----NRRRILNLPTSAGRSLIQALLARYYLENYE  157 (510)
T ss_dssp             EECCCHHHHHHHHHHHH----HSEEEEECCSTTTHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCHHHHHHHHHHHh----cCCcEEEeCCCCCHHHHHHHHHHHHHhCCC
Confidence            66899999998887653    478999999999999999999888776443

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=98.34  E-value=6e-07  Score=80.79  Aligned_cols=50  Identities=16%  Similarity=0.203  Sum_probs=42.0

Q ss_pred             ccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        23 ~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ....|||++++.|.+.+..+    .+++.+++.||||+|||++|+.++...+..
T Consensus        32 ~~~~~~f~l~~~Q~~aI~~i----l~g~~vlv~apTGsGKTlv~~~~i~~~~~~   81 (997)
T 4a4z_A           32 PARSWPFELDTFQKEAVYHL----EQGDSVFVAAHTSAGKTVVAEYAIAMAHRN   81 (997)
T ss_dssp             CSCCCSSCCCHHHHHHHHHH----HTTCEEEEECCTTSCSHHHHHHHHHHHHHT
T ss_pred             HHHhCCCCCCHHHHHHHHHH----HcCCCEEEEECCCCcHHHHHHHHHHHHHhc
Confidence            44578999999999987754    578899999999999999999997776644

>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=98.34  E-value=5.3e-07  Score=82.03  Aligned_cols=52  Identities=15%  Similarity=0.250  Sum_probs=44.3

Q ss_pred             ccccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        23 ~~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ....|||.+++.|.+.+..|    .++..+|+.||||+|||++|++|++..+...+
T Consensus       177 ~~~~~~f~ltp~Q~~AI~~i----~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g~  228 (1108)
T 3l9o_A          177 EARTYPFTLDPFQDTAISCI----DRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQ  228 (1108)
T ss_dssp             CSSCCSSCCCHHHHHHHHHH----TTTCCEEEECCSSSHHHHHHHHHHHHHHHTTC
T ss_pred             HHHhCCCCCCHHHHHHHHHH----HcCCCEEEECCCCCChHHHHHHHHHHHHhcCC
Confidence            45678999999999988764    67899999999999999999999988875443

>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=98.33  E-value=7.1e-07  Score=71.66  Aligned_cols=46  Identities=24%  Similarity=0.259  Sum_probs=37.4

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ...+++.+|+.|.+.++.+    .++..+++.+|||+|||++++.++...
T Consensus        87 ~~~~~~~l~~~Q~~ai~~i----~~~~~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A           87 YFDAEISLRDYQEKALERW----LVDKRGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             CCCCCCCBCHHHHHHHHHH----TTTTEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cccCCCCcCHHHHHHHHHH----HhcCCEEEEeCCCCCHHHHHHHHHHHc
Confidence            3457788999999988764    345679999999999999999986643

>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=98.32  E-value=6.4e-07  Score=77.56  Aligned_cols=45  Identities=22%  Similarity=0.235  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +.+|+.|.+.+..+    .++..+|+.+|||+|||++|++|++..+...
T Consensus       247 ~~l~~~Q~~~i~~~----l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~  291 (797)
T 4a2q_A          247 KKARSYQIELAQPA----INGKNALICAPTGSGKTFVSILICEHHFQNM  291 (797)
T ss_dssp             -CCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHH----HhCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            45999999988765    4678999999999999999999999888764

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=98.31  E-value=5.3e-07  Score=81.36  Aligned_cols=50  Identities=16%  Similarity=0.249  Sum_probs=43.0

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ...|||++++.|.+.+..+    .++..+++.||||+|||++|+++++..+...
T Consensus        80 ~~~~~f~L~~~Q~eai~~l----~~g~~vLV~apTGSGKTlva~lai~~~l~~g  129 (1010)
T 2xgj_A           80 ARTYPFTLDPFQDTAISCI----DRGESVLVSAHTSAGKTVVAEYAIAQSLKNK  129 (1010)
T ss_dssp             SCCCSSCCCHHHHHHHHHH----HHTCEEEEECCTTSCHHHHHHHHHHHHHHTT
T ss_pred             HHhCCCCCCHHHHHHHHHH----HcCCCEEEECCCCCChHHHHHHHHHHHhccC
Confidence            5678999999999988864    5688999999999999999999988777543

>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=98.28  E-value=3.8e-07  Score=70.46  Aligned_cols=45  Identities=16%  Similarity=0.058  Sum_probs=37.4

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      |.+||.|.+.+..+.    ++ .+|+.+|||+|||++++.+++..+...+
T Consensus         8 ~~l~~~Q~~~i~~~~----~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~~   52 (494)
T 1wp9_A            8 IQPRIYQEVIYAKCK----ET-NCLIVLPTGLGKTLIAMMIAEYRLTKYG   52 (494)
T ss_dssp             HCCCHHHHHHHHHGG----GS-CEEEECCTTSCHHHHHHHHHHHHHHHSC
T ss_pred             CCccHHHHHHHHHHh----hC-CEEEEcCCCCCHHHHHHHHHHHHHhcCC
Confidence            779999999887653    34 8999999999999999999888876333

>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=98.27  E-value=1.6e-06  Score=65.25  Aligned_cols=45  Identities=24%  Similarity=0.270  Sum_probs=35.7

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      .+.+++.+++.|.+.+..+    .++..+++.+|||+|||+.++.++..
T Consensus        87 ~~~~~~~l~~~Q~~ai~~~----~~~~~~ll~~~tG~GKT~~a~~~~~~  131 (237)
T 2fz4_A           87 YFDAEISLRDYQEKALERW----LVDKRGCIVLPTGSGKTHVAMAAINE  131 (237)
T ss_dssp             CCCCCCCCCHHHHHHHHHH----TTTSEEEEEESSSTTHHHHHHHHHHH
T ss_pred             cccCCCCcCHHHHHHHHHH----HhCCCEEEEeCCCCCHHHHHHHHHHH
Confidence            4456678999999987754    34566999999999999998887654

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=98.27  E-value=1.4e-06  Score=72.41  Aligned_cols=47  Identities=19%  Similarity=0.174  Sum_probs=38.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +.+|+.|.+.++.+...+.++ ..+++.+|||+|||++++..+...+.
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~~~~~l~~  224 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQISWKLWS  224 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHHHHHHHHh
Confidence            369999999999999888876 56899999999999997766555444

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=98.27  E-value=6.2e-07  Score=76.25  Aligned_cols=51  Identities=24%  Similarity=0.223  Sum_probs=41.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ++|. +++.|.+.+..+   +.+++++|+.||||+|||+++..+++..+...+.+
T Consensus        26 ~g~~~l~~~Q~~~i~~~---~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~   77 (715)
T 2va8_A           26 RGIKKLNPPQTEAVKKG---LLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGK   77 (715)
T ss_dssp             TSCCBCCHHHHHHHHTT---TTTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCSE
T ss_pred             CCCCCCCHHHHHHHHHH---hcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHCCCe
Confidence            6785 999999987752   45689999999999999999999998877644433

>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=98.23  E-value=1.5e-06  Score=65.95  Aligned_cols=45  Identities=16%  Similarity=0.093  Sum_probs=36.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +.+|+.|.+.+..+.+    +..+++.+|||+|||++++.++...+...
T Consensus       112 ~~l~~~Q~~ai~~~l~----~~~~ll~~~tGsGKT~~~~~~~~~~~~~~  156 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLV----NRRRILNLPTSAGRSLIQALLARYYLENY  156 (282)
T ss_dssp             CCCCHHHHHHHHHHHH----HSEEEECCCTTSCHHHHHHHHHHHHHHHC
T ss_pred             cCccHHHHHHHHHHHh----cCCeEEEcCCCCCcHHHHHHHHHHHHHcC
Confidence            6799999998876543    35678899999999999998887776543

>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=98.21  E-value=6.7e-07  Score=76.35  Aligned_cols=51  Identities=18%  Similarity=0.170  Sum_probs=41.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ++|. +++.|.+.+..+   +.+++++|+.||||+|||+++..+++..+...+.+
T Consensus        19 ~g~~~l~~~Q~~~i~~~---~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~~~   70 (720)
T 2zj8_A           19 RGIESFYPPQAEALKSG---ILEGKNALISIPTASGKTLIAEIAMVHRILTQGGK   70 (720)
T ss_dssp             TTCCBCCHHHHHHHTTT---GGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHCSE
T ss_pred             CCCCCCCHHHHHHHHHH---hcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCCCE
Confidence            6785 999999987752   45689999999999999999999999877644433

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=98.17  E-value=1.5e-06  Score=79.04  Aligned_cols=47  Identities=23%  Similarity=0.157  Sum_probs=39.9

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++|.|++.|.+.+..+    .+++.+|+.||||+|||++++.+++..+..
T Consensus        74 ~~gf~pt~iQ~~ai~~i----l~g~dvlv~ApTGSGKTl~~l~~il~~~~~  120 (1104)
T 4ddu_A           74 KFGKDLTGYQRLWAKRI----VQGKSFTMVAPTGVGKTTFGMMTALWLARK  120 (1104)
T ss_dssp             HSSSCCCHHHHHHHHHH----TTTCCEEECCSTTCCHHHHHHHHHHHHHTT
T ss_pred             hcCCCCCHHHHHHHHHH----HcCCCEEEEeCCCCcHHHHHHHHHHHHHhc
Confidence            47889999999988765    457899999999999999998888777643

>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=98.13  E-value=1.6e-06  Score=77.10  Aligned_cols=46  Identities=22%  Similarity=0.231  Sum_probs=38.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ++.||+.|.+.++.+    .++..+|+.+|||+|||++|+.|++..+...
T Consensus       246 ~~~~r~~Q~~ai~~i----l~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~  291 (936)
T 4a2w_A          246 TKKARSYQIELAQPA----INGKNALICAPTGSGKTFVSILICEHHFQNM  291 (936)
T ss_dssp             --CCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHTTTTTC
T ss_pred             CCCCCHHHHHHHHHH----HcCCCEEEEeCCCchHHHHHHHHHHHHHHhc
Confidence            345999999988765    4678999999999999999999998887664

>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=98.11  E-value=5.6e-07  Score=76.65  Aligned_cols=46  Identities=15%  Similarity=0.160  Sum_probs=37.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ++|. +++.|.+.++.+    .+++++|+.||||+|||+++..+++..+..
T Consensus        21 ~g~~~l~~~Q~~~i~~i----~~~~~~lv~apTGsGKT~~~~l~il~~~~~   67 (702)
T 2p6r_A           21 EGIEELFPPQAEAVEKV----FSGKNLLLAMPTAAGKTLLAEMAMVREAIK   67 (702)
T ss_dssp             C---CCCCCCHHHHHHH----TTCSCEEEECSSHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHH----hCCCcEEEEcCCccHHHHHHHHHHHHHHHh
Confidence            6774 899999988873    468899999999999999999999877654

>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=98.11  E-value=2.5e-06  Score=63.32  Aligned_cols=48  Identities=17%  Similarity=0.221  Sum_probs=38.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .++..++.|.+.+..+    .++..+++.||||+|||..+.++++..+...+
T Consensus        58 ~~~p~~~~q~~~i~~i----~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~  105 (235)
T 3llm_A           58 ELLPVKKFESEILEAI----SQNSVVIIRGATGCGKTTQVPQFILDDFIQND  105 (235)
T ss_dssp             HTSGGGGGHHHHHHHH----HHCSEEEEECCTTSSHHHHHHHHHHHHHHHTT
T ss_pred             hcCChHHHHHHHHHHH----hcCCEEEEEeCCCCCcHHhHHHHHhcchhhcC
Confidence            3455778898877765    57889999999999999998888877665443

>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=98.02  E-value=4.4e-06  Score=75.36  Aligned_cols=49  Identities=16%  Similarity=0.066  Sum_probs=40.1

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .++|.| +.|.+.+..+    .+++++|+.||||||||+ |++|++..+...+..
T Consensus        53 ~~g~~p-~iQ~~ai~~i----l~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~~~  101 (1054)
T 1gku_B           53 CVGEPR-AIQKMWAKRI----LRKESFAATAPTGVGKTS-FGLAMSLFLALKGKR  101 (1054)
T ss_dssp             TTCSCC-HHHHHHHHHH----HTTCCEECCCCBTSCSHH-HHHHHHHHHHTTSCC
T ss_pred             hcCCCH-HHHHHHHHHH----HhCCCEEEEcCCCCCHHH-HHHHHHHHHhhcCCe
Confidence            467778 9999988875    367899999999999999 888988877655443

>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=98.01  E-value=6.5e-06  Score=77.99  Aligned_cols=49  Identities=27%  Similarity=0.428  Sum_probs=41.6

Q ss_pred             cCC-CC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFP-FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fp-f~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .|+ |+ +.+.|.+.+..   ++.++.++|++||||+|||+++.++++..+..+
T Consensus        73 ~f~g~~~ln~iQs~~~~~---al~~~~N~lv~APTGsGKTlva~l~il~~l~~~  123 (1724)
T 4f92_B           73 GFEGFKTLNRIQSKLYRA---ALETDENLLLCAPTGAGKTNVALMCMLREIGKH  123 (1724)
T ss_dssp             TCTTCSBCCHHHHHTHHH---HHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGG
T ss_pred             hcCCCCCCCHHHHHHHHH---HHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhh
Confidence            355 77 88999997765   467889999999999999999999999888653

>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=97.91  E-value=1.5e-05  Score=75.60  Aligned_cols=48  Identities=21%  Similarity=0.353  Sum_probs=40.1

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .|. ..|.|.+.+..+   +..+.++++.||||+|||+++.+|++..+...+
T Consensus       923 ~f~~fnpiQ~q~~~~l---~~~~~nvlv~APTGSGKTliaelail~~l~~~~  971 (1724)
T 4f92_B          923 KFPFFNPIQTQVFNTV---YNSDDNVFVGAPTGSGKTICAEFAILRMLLQSS  971 (1724)
T ss_dssp             TCSBCCHHHHHHHHHH---HSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCT
T ss_pred             cCCCCCHHHHHHHHHH---hcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCC
Confidence            355 789999987765   467789999999999999999999998876643

>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=97.89  E-value=3.1e-06  Score=69.29  Aligned_cols=38  Identities=16%  Similarity=0.287  Sum_probs=31.5

Q ss_pred             HHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         43 YYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        43 ~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ..++.+++++|+.||||+|||++|+.|++..+...+.+
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~~~   52 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLR   52 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTTCC
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCc
Confidence            44567789999999999999999999999877655443

>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=97.85  E-value=3.4e-05  Score=62.23  Aligned_cols=48  Identities=13%  Similarity=-0.050  Sum_probs=38.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +...+||.|.+.+..+......+..+|+.++||+|||+.++..+..+.
T Consensus        34 ~~~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~~   81 (500)
T 1z63_A           34 IKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAK   81 (500)
T ss_dssp             CSSCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             hhccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHHH
Confidence            445599999999988877777788899999999999999776544443

>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=97.82  E-value=1.5e-05  Score=71.54  Aligned_cols=41  Identities=22%  Similarity=0.152  Sum_probs=34.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ++|.|+++|...+..+    .+|+  |.+|+||+|||++|++|++..
T Consensus        80 lG~~pt~VQ~~~ip~l----l~G~--Iaea~TGeGKTlaf~LP~~l~  120 (844)
T 1tf5_A           80 TGMFPFKVQLMGGVAL----HDGN--IAEMKTGEGKTLTSTLPVYLN  120 (844)
T ss_dssp             HSCCCCHHHHHHHHHH----HTTS--EEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCcHHHHHhhHHH----hCCC--EEEccCCcHHHHHHHHHHHHH
Confidence            5678999999988765    3565  899999999999999998743

>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=97.82  E-value=6e-06  Score=67.33  Aligned_cols=35  Identities=17%  Similarity=0.296  Sum_probs=29.7

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      ++.+++++|+.||||||||++|+.|++..+...+.
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~~   38 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRRL   38 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTC
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcCC
Confidence            35678999999999999999999999987766553

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=97.71  E-value=1.6e-06  Score=75.28  Aligned_cols=50  Identities=16%  Similarity=0.268  Sum_probs=35.9

Q ss_pred             CCHHHH-----HHHHHHH--HHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         31 AYDIQS-----NFMKNLY--YTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        31 ~r~~Q~-----e~m~~I~--~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      |.+.|.     ..+..+.  .++.+++.+|+.||||||||++|+.|++..+...+.+
T Consensus       216 pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~~~  272 (673)
T 2wv9_A          216 VSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKRLR  272 (673)
T ss_dssp             EEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTTCC
T ss_pred             cCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCCCc
Confidence            667777     5555433  3344789999999999999999999999876655433

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=97.69  E-value=1.8e-05  Score=64.25  Aligned_cols=32  Identities=9%  Similarity=0.304  Sum_probs=26.7

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ++++++.||||+|||++|+.|++..+...+.+
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~g~~   33 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKKRLR   33 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHTTCC
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhCCCC
Confidence            67899999999999999999999666555544

>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=97.66  E-value=1.5e-05  Score=64.92  Aligned_cols=35  Identities=14%  Similarity=0.305  Sum_probs=27.7

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      +..+..+|+.||||||||++|+.|++..+...+.+
T Consensus        16 l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~   50 (451)
T 2jlq_A           16 FRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLR   50 (451)
T ss_dssp             GSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTTCC
T ss_pred             HhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcCCc
Confidence            44456669999999999999999998776665533

>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=97.62  E-value=4.1e-05  Score=69.68  Aligned_cols=46  Identities=15%  Similarity=0.195  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHHHHhc----------CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         30 DAYDIQSNFMKNLYYTLDN----------SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~----------~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+|+.|.+.++.+...+.+          ++.+++.+|||||||+++ ++++.++..
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~  326 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATE  326 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTT
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHh
Confidence            4999999999999887754          257999999999999997 555566543

>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=97.56  E-value=6.3e-05  Score=67.68  Aligned_cols=42  Identities=26%  Similarity=0.188  Sum_probs=34.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ++..||++|...+..+    .+|.  |.+|+||+|||++|++|++..+
T Consensus        71 lg~~p~~VQ~~~i~~l----l~G~--Iaem~TGsGKTlaf~LP~l~~~  112 (853)
T 2fsf_A           71 FGMRHFDVQLLGGMVL----NERC--IAEMRTGEGKTLTATLPAYLNA  112 (853)
T ss_dssp             HSCCCCHHHHHHHHHH----HSSE--EEECCTTSCHHHHHHHHHHHHH
T ss_pred             cCCCCChHHHhhcccc----cCCe--eeeecCCchHHHHHHHHHHHHH
Confidence            4567999999987754    3555  9999999999999999988543

>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=97.55  E-value=0.00017  Score=58.83  Aligned_cols=55  Identities=20%  Similarity=0.194  Sum_probs=42.4

Q ss_pred             cccCCCC-CCHHHHHHHHHHHHHHhcCC-cEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         24 EFPFPFD-AYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        24 ~~~fpf~-~r~~Q~e~m~~I~~~l~~~~-~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      -.+.+|+ .-+.|.+.+..+..++.++. +++|.||.|||||. ++...+.++...+.
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~-ll~~~~~~l~~~~~   74 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATT-LTKFIIEALISTGE   74 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHH-HHHHHHHHHHHTTC
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHH-HHHHHHHHHHhcCC
Confidence            3456677 78999999999988888775 89999999999995 45666777766554

>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=97.55  E-value=5.7e-05  Score=68.44  Aligned_cols=43  Identities=21%  Similarity=0.183  Sum_probs=35.0

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+++.||++|...+..+    .+|+  |.+|+||+|||+++++|++..+
T Consensus       107 ~lG~rP~~VQ~~~ip~L----l~G~--Iaem~TGeGKTLa~~LP~~l~a  149 (922)
T 1nkt_A          107 VLDQRPFDVQVMGAAAL----HLGN--VAEMKTGEGKTLTCVLPAYLNA  149 (922)
T ss_dssp             HHSCCCCHHHHHHHHHH----HTTE--EEECCTTSCHHHHTHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHhH----hcCC--EEEecCCCccHHHHHHHHHHHH
Confidence            36778999999987765    3554  9999999999999999986433

>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=97.53  E-value=3.1e-05  Score=66.33  Aligned_cols=38  Identities=13%  Similarity=0.267  Sum_probs=31.6

Q ss_pred             HHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         43 YYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        43 ~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ...+.+++.+|+.||||||||++|++|++..+...+.+
T Consensus       180 i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~~~  217 (618)
T 2whx_A          180 EDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRRLR  217 (618)
T ss_dssp             GGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCC
T ss_pred             HHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCCCe
Confidence            44567889999999999999999999999887665433

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=97.28  E-value=0.00021  Score=65.21  Aligned_cols=42  Identities=26%  Similarity=0.209  Sum_probs=34.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ..+|.|+++|...+..+    .+|.  |.+|.||+|||+++++|++..
T Consensus        75 ~lG~~Pt~VQ~~~ip~L----lqG~--IaeakTGeGKTLvf~Lp~~L~  116 (997)
T 2ipc_A           75 YLGMRHFDVQLIGGAVL----HEGK--IAEMKTGEGKTLVATLAVALN  116 (997)
T ss_dssp             HTCCCCCHHHHHHHHHH----HTTS--EEECCSTHHHHHHHHHHHHHH
T ss_pred             HhCCCCcHHHHhhcccc----cCCc--eeeccCCCchHHHHHHHHHHH
Confidence            36778999999988754    4565  899999999999999998543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=97.15  E-value=0.0007  Score=58.98  Aligned_cols=46  Identities=17%  Similarity=0.171  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      ...||.|.+.+..+.....++..+|+..+||.|||+..++.+...+
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~  280 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLI  280 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHH
Confidence            3589999999999888888899999999999999998877654443

>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=97.14  E-value=0.00055  Score=61.22  Aligned_cols=50  Identities=10%  Similarity=-0.019  Sum_probs=38.2

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ..++.+||.|.+.+..+..  ..+..+|+.++||+|||+.++..+..++...
T Consensus       149 ~~~~~LrpyQ~eav~~~l~--~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g  198 (968)
T 3dmq_A          149 GQRTSLIPHQLNIAHDVGR--RHAPRVLLADEVGLGKTIEAGMILHQQLLSG  198 (968)
T ss_dssp             CCSSCCCHHHHHHHHHHHH--SSSCEEEECCCTTSCHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCcHHHHHHHHHHHH--hcCCCEEEECCCCCcHHHHHHHHHHHHHHhC
Confidence            4568899999998776543  2246789999999999999988876665443

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.00  E-value=0.0012  Score=56.12  Aligned_cols=47  Identities=17%  Similarity=0.286  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .-+.|.+   +|..++.+....||.||.|||||.++... +.++...+.+|
T Consensus       190 LN~~Q~~---AV~~al~~~~~~lI~GPPGTGKT~ti~~~-I~~l~~~~~~I  236 (646)
T 4b3f_X          190 LDTSQKE---AVLFALSQKELAIIHGPPGTGKTTTVVEI-ILQAVKQGLKV  236 (646)
T ss_dssp             CCHHHHH---HHHHHHHCSSEEEEECCTTSCHHHHHHHH-HHHHHHTTCCE
T ss_pred             CCHHHHH---HHHHHhcCCCceEEECCCCCCHHHHHHHH-HHHHHhCCCeE
Confidence            5689998   55566777789999999999999886554 44555556555

>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=97.00  E-value=0.00096  Score=56.82  Aligned_cols=48  Identities=25%  Similarity=0.129  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHHHHHHHHh-----cCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         29 FDAYDIQSNFMKNLYYTLD-----NSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~-----~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ...||.|.+.++.++.++.     ++..+|+..+||+|||+..++.+..++..
T Consensus        54 ~~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~  106 (644)
T 1z3i_X           54 KVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQ  106 (644)
T ss_dssp             TTCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHC
T ss_pred             hcccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHh
Confidence            4589999999999988773     45679999999999999988887666544

>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=96.93  E-value=0.00052  Score=60.19  Aligned_cols=37  Identities=19%  Similarity=0.273  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      |.+.|.+   .|..++..+..+++.||||+|||+  ++|.+.
T Consensus        94 P~~~q~~---~i~~~l~~~~~vii~gpTGSGKTt--llp~ll  130 (773)
T 2xau_A           94 PVHAQRD---EFLKLYQNNQIMVFVGETGSGKTT--QIPQFV  130 (773)
T ss_dssp             GGGGGHH---HHHHHHHHCSEEEEECCTTSSHHH--HHHHHH
T ss_pred             ChHHHHH---HHHHHHhCCCeEEEECCCCCCHHH--HHHHHH
Confidence            3345555   455567788899999999999998  566653

>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=96.79  E-value=0.0031  Score=44.21  Aligned_cols=35  Identities=17%  Similarity=0.094  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHHHHHHh-----cCCcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYTLD-----NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~-----~~~~~iiEaPTGtGKTls~   66 (115)
                      .+.|.+.+..+.+.+.     .+..+++.||+|+|||.-+
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHH
Confidence            4789998888887774     3678999999999999643

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.79  E-value=0.0015  Score=44.91  Aligned_cols=33  Identities=12%  Similarity=0.150  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++.+.+..+...+.+++|.||+|||||+.
T Consensus         8 ~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~l   40 (145)
T 3n70_A            8 EWINQYRRRLQQLSETDIAVWLYGAPGTGRMTG   40 (145)
T ss_dssp             HHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHH
Confidence            344455556666666778999999999999964

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.79  E-value=0.002  Score=45.73  Aligned_cols=34  Identities=18%  Similarity=0.069  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHHHhcC------CcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~------~~~iiEaPTGtGKTls~   66 (115)
                      +.|.+++..+.+++.+.      ..++|.||+|||||..+
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la   71 (202)
T 2w58_A           32 DGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLL   71 (202)
T ss_dssp             HHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHH
Confidence            47777888888888765      68999999999999743

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=96.65  E-value=0.0019  Score=44.38  Aligned_cols=33  Identities=3%  Similarity=-0.026  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++.+.+..+...+..+++.||+|||||..
T Consensus        11 ~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           11 AAIQEMNREVEAAAKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEECCCCccHHHH
Confidence            334455555556666678899999999999964

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.58  E-value=0.0019  Score=43.75  Aligned_cols=33  Identities=12%  Similarity=0.169  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      ++.+.++.+.+.+..+  .+++|.||+|+|||..+
T Consensus        26 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           26 GRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHH
T ss_pred             cchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHH
Confidence            3444556677777654  67999999999999754

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=96.47  E-value=0.0016  Score=45.39  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~   66 (115)
                      ++.+.++.+..++..+.   .++|.||+|+|||..+
T Consensus        27 g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           27 GQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             SCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHH
Confidence            34556667777777765   6899999999999643

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.47  E-value=0.0012  Score=50.55  Aligned_cols=33  Identities=21%  Similarity=0.204  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      -+|.+.++.+..++..+.+++|.||+|||||..
T Consensus        30 ~g~~~~~~~l~~~l~~~~~vll~G~pGtGKT~l   62 (331)
T 2r44_A           30 VGQKYMINRLLIGICTGGHILLEGVPGLAKTLS   62 (331)
T ss_dssp             CSCHHHHHHHHHHHHHTCCEEEESCCCHHHHHH
T ss_pred             eCcHHHHHHHHHHHHcCCeEEEECCCCCcHHHH
Confidence            456778888888888899999999999999964

>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=96.47  E-value=0.002  Score=44.64  Aligned_cols=33  Identities=24%  Similarity=0.379  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      ++.+.++.+..++.++  .+++|.||+|+|||...
T Consensus        21 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           21 GQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATA   55 (226)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHH
T ss_pred             CcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHH
Confidence            4455666777788766  46999999999999643

>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=96.36  E-value=0.0028  Score=53.96  Aligned_cols=38  Identities=18%  Similarity=0.234  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCch--HHHHHHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKS--LSLICGILKW   73 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKT--ls~L~~al~~   73 (115)
                      -+.|...+..+   + .++.+++.||+|||||  ++++++.+.-
T Consensus       151 ~~~Q~~Ai~~~---l-~~~~~vi~G~pGTGKTt~l~~ll~~l~~  190 (608)
T 1w36_D          151 INWQKVAAAVA---L-TRRISVISGGPGTGKTTTVAKLLAALIQ  190 (608)
T ss_dssp             CCHHHHHHHHH---H-TBSEEEEECCTTSTHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHH---h-cCCCEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            47788876654   3 6789999999999999  5566665543

>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=96.35  E-value=0.0013  Score=57.58  Aligned_cols=28  Identities=21%  Similarity=0.323  Sum_probs=23.5

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      ++.+++.+++.||||+|||++++.+++.
T Consensus       228 ~L~~~~~vlv~ApTGSGKT~a~~l~ll~  255 (666)
T 3o8b_A          228 VPQSFQVAHLHAPTGSGKSTKVPAAYAA  255 (666)
T ss_dssp             CCSSCEEEEEECCTTSCTTTHHHHHHHH
T ss_pred             HHHcCCeEEEEeCCchhHHHHHHHHHHH
Confidence            4556788999999999999999887664

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=96.31  E-value=0.0023  Score=43.59  Aligned_cols=33  Identities=15%  Similarity=0.165  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      ++.+.+..+.+.+.+  ..+++|.||+|+|||...
T Consensus        26 g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           26 GRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHH
T ss_pred             cchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHH
Confidence            344455667777765  367999999999999654

>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=96.24  E-value=0.0034  Score=46.68  Aligned_cols=18  Identities=33%  Similarity=0.377  Sum_probs=15.2

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      ..+++|.||+|||||...
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999653

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=96.24  E-value=0.0017  Score=56.48  Aligned_cols=26  Identities=23%  Similarity=0.364  Sum_probs=19.4

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +++.+++.||||+|||+    +++..+...
T Consensus       154 ~rk~vlv~apTGSGKT~----~al~~l~~~  179 (677)
T 3rc3_A          154 QRKIIFHSGPTNSGKTY----HAIQKYFSA  179 (677)
T ss_dssp             CCEEEEEECCTTSSHHH----HHHHHHHHS
T ss_pred             CCCEEEEEcCCCCCHHH----HHHHHHHhc
Confidence            56789999999999998    444444443

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.24  E-value=0.0037  Score=48.37  Aligned_cols=36  Identities=25%  Similarity=0.413  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHhcCCc--EEEecCCCCCchHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNSKF--GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~~--~iiEaPTGtGKTls~L~~   69 (115)
                      +|.+.++.+..++.++..  ++|.||.|+|||..+.+-
T Consensus        29 g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~l   66 (340)
T 1sxj_C           29 GQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVAL   66 (340)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHH
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHH
Confidence            577888899999998854  999999999999765543

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=96.21  E-value=0.0037  Score=46.70  Aligned_cols=39  Identities=23%  Similarity=0.363  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      |+..-+|.+.++.+..++.++.  +++|.||+|+|||...-
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~   64 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAAL   64 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHH
Confidence            3333457777888888888774  79999999999997643

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=96.20  E-value=0.0023  Score=53.84  Aligned_cols=32  Identities=19%  Similarity=0.156  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         34 IQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +|.+.++.+..++..+.++++.||+|||||..
T Consensus        26 Gq~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           26 ERSHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             SCHHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            56678888888999999999999999999964

>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=96.19  E-value=0.0052  Score=45.57  Aligned_cols=33  Identities=18%  Similarity=0.119  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-..+.+.+..+...+..++|.||+|||||..
T Consensus        13 ~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           13 NSFLEVLEQVSHLAPLDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             HHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHH
Confidence            444455555556566678999999999999964

>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=96.19  E-value=0.0041  Score=48.64  Aligned_cols=33  Identities=27%  Similarity=0.228  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHHHHh-----------------cCCcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLD-----------------NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~-----------------~~~~~iiEaPTGtGKTls~   66 (115)
                      +|.+.++.|..++.                 ...+++|.||+|||||+..
T Consensus        19 G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           19 GQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHH
Confidence            35556666666662                 3467999999999999753

>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=96.13  E-value=0.0041  Score=46.87  Aligned_cols=17  Identities=24%  Similarity=0.348  Sum_probs=14.7

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||..+
T Consensus        39 ~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCEEECCTTCCCHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            67999999999999653

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=96.11  E-value=0.0021  Score=48.86  Aligned_cols=35  Identities=29%  Similarity=0.439  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      -+|.+.++.+..++..+  .+++|.||+|+|||..+-
T Consensus        40 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~   76 (353)
T 1sxj_D           40 TAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTIL   76 (353)
T ss_dssp             CSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHH
T ss_pred             hCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHH
Confidence            45666778888888887  679999999999996543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.02  E-value=0.012  Score=45.83  Aligned_cols=35  Identities=17%  Similarity=0.113  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHhc-----CCcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~-----~~~~iiEaPTGtGKTls~L   67 (115)
                      +.+..++..+.+++.+     +..++|.||+|+|||.-+.
T Consensus       131 ~~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~  170 (308)
T 2qgz_A          131 ASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLA  170 (308)
T ss_dssp             HHHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHH
Confidence            3666677777777775     5789999999999996543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.00  E-value=0.003  Score=47.42  Aligned_cols=34  Identities=21%  Similarity=0.214  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls~L   67 (115)
                      +|...++.+..++...           .+++|.||+|||||..+-
T Consensus        21 G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~   65 (311)
T 4fcw_A           21 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAK   65 (311)
T ss_dssp             SCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHH
Confidence            4555666666666553           468999999999996543

>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=95.99  E-value=0.0071  Score=42.87  Aligned_cols=33  Identities=9%  Similarity=0.100  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      .+.+.+..+.+++..  +..++|.||+|+|||..+
T Consensus        35 ~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           35 GNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHH
Confidence            345667777777764  578999999999999653

>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=95.98  E-value=0.0074  Score=47.01  Aligned_cols=39  Identities=10%  Similarity=0.108  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      .||.|.+.++.+.+++.+++  + .+|.||.|+|||.....-
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~l   44 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYAL   44 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHH
Confidence            47889999999999998874  3 889999999999765544

>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=95.93  E-value=0.0077  Score=51.13  Aligned_cols=47  Identities=17%  Similarity=0.216  Sum_probs=31.6

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+.|.+.+..+   + .+...+|.||+|||||.++..-+..++...+.++
T Consensus       181 ln~~Q~~av~~~---l-~~~~~li~GppGTGKT~~~~~~i~~l~~~~~~~i  227 (624)
T 2gk6_A          181 LNHSQVYAVKTV---L-QRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPV  227 (624)
T ss_dssp             CCHHHHHHHHHH---H-TCSEEEEECCTTSCHHHHHHHHHHHHHTSSSCCE
T ss_pred             CCHHHHHHHHHH---h-cCCCeEEECCCCCCHHHHHHHHHHHHHHcCCCeE
Confidence            568999976654   3 4678899999999999875544333333234443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=95.82  E-value=0.0062  Score=48.58  Aligned_cols=38  Identities=13%  Similarity=-0.038  Sum_probs=25.6

Q ss_pred             CHHHHH-HHHHHHHHHhcC--CcEEEecCCCCCchHHHHHH
Q psy14273         32 YDIQSN-FMKNLYYTLDNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        32 r~~Q~e-~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      |+.|.+ +...|..++..+  .+++|.||+|||||++.-.-
T Consensus        25 Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v   65 (318)
T 3te6_A           25 QVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDV   65 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHH
Confidence            334444 344666666544  67899999999999875444

>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=95.80  E-value=0.012  Score=50.03  Aligned_cols=49  Identities=14%  Similarity=0.178  Sum_probs=35.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        28 pf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++...+.|.+.+..+    .+++.++|.||.|||||.. +..++..+...+.++
T Consensus       187 ~~~L~~~Q~~Av~~~----~~~~~~~I~G~pGTGKTt~-i~~l~~~l~~~g~~V  235 (574)
T 3e1s_A          187 RKGLSEEQASVLDQL----AGHRLVVLTGGPGTGKSTT-TKAVADLAESLGLEV  235 (574)
T ss_dssp             TTTCCHHHHHHHHHH----TTCSEEEEECCTTSCHHHH-HHHHHHHHHHTTCCE
T ss_pred             cCCCCHHHHHHHHHH----HhCCEEEEEcCCCCCHHHH-HHHHHHHHHhcCCeE
Confidence            666779999977654    3568999999999999965 344455555555544

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=95.71  E-value=0.0046  Score=47.25  Aligned_cols=33  Identities=27%  Similarity=0.353  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHhc----C---CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDN----S---KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~----~---~~~iiEaPTGtGKTls~   66 (115)
                      +|...++.+..++..    +   .+++|.||+|||||..+
T Consensus        33 G~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           33 GQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             SCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHH
Confidence            444445555555543    2   58999999999999653

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=95.70  E-value=0.0062  Score=45.70  Aligned_cols=32  Identities=22%  Similarity=0.193  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      -|+.+.+   .+.+++.++..++|.||.|+|||.-
T Consensus        16 gR~~el~---~L~~~l~~~~~v~i~G~~G~GKT~L   47 (350)
T 2qen_A           16 DREEESR---KLEESLENYPLTLLLGIRRVGKSSL   47 (350)
T ss_dssp             SCHHHHH---HHHHHHHHCSEEEEECCTTSSHHHH
T ss_pred             ChHHHHH---HHHHHHhcCCeEEEECCCcCCHHHH
Confidence            4555544   5556666678999999999999964

>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=95.64  E-value=0.0037  Score=47.55  Aligned_cols=39  Identities=31%  Similarity=0.259  Sum_probs=23.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHh--cCCcEEEecCCCCCchHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~--~~~~~iiEaPTGtGKTls   65 (115)
                      +.|+..-+|..+.+.+..++.  ...+++|.||+|||||..
T Consensus        21 ~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~l   61 (350)
T 1g8p_A           21 FPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTA   61 (350)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHH
T ss_pred             CCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHH
Confidence            344422334444444443333  346799999999999965

>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=95.59  E-value=0.015  Score=52.25  Aligned_cols=43  Identities=26%  Similarity=0.256  Sum_probs=31.8

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+++.||++|.--.-    +|.+|+  |.|+.||.||||++.+|++..+
T Consensus        71 ~lg~r~~dvQligg~----~L~~G~--iaEM~TGEGKTLva~lp~~lnA  113 (822)
T 3jux_A           71 TLGMRPFDVQVMGGI----ALHEGK--VAEMKTGEGKTLAATMPIYLNA  113 (822)
T ss_dssp             HTSCCCCHHHHHHHH----HHHTTC--EEECCTTSCHHHHTHHHHHHHH
T ss_pred             HhCCCCcHHHHHHHH----HHhCCC--hhhccCCCCccHHHHHHHHHHH
Confidence            456678888866433    344554  8899999999999999976444

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.57  E-value=0.011  Score=45.76  Aligned_cols=33  Identities=15%  Similarity=0.273  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++++.+..+...+..++|.||+|||||+.
T Consensus         9 ~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A            9 PAMQHLLNEIAMVAPSDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             HHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCcEEEECCCCchHHHH
Confidence            444555566666556678899999999999964

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=95.56  E-value=0.0066  Score=45.15  Aligned_cols=18  Identities=39%  Similarity=0.468  Sum_probs=15.1

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      ...++|.||+|||||..+
T Consensus        51 ~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           51 PKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CSEEEEESSSSSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            467999999999999653

>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=95.56  E-value=0.006  Score=45.40  Aligned_cols=35  Identities=26%  Similarity=0.381  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      -+|.+.++.+.+++.++.  +++|.||+|+|||....
T Consensus        20 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~   56 (319)
T 2chq_A           20 VGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAI   56 (319)
T ss_dssp             CSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHH
T ss_pred             hCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHH
Confidence            356777788888887763  69999999999996543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=95.53  E-value=0.021  Score=43.76  Aligned_cols=37  Identities=11%  Similarity=0.091  Sum_probs=26.6

Q ss_pred             CCHHHHHHHHHHHHHHhcC----CcEEEecCCCCCchHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~L   67 (115)
                      -++.+.+.+..+.+.+..+    ..++|.||+|+|||..+-
T Consensus        48 G~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~   88 (368)
T 3uk6_A           48 GQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAM   88 (368)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHH
Confidence            3455555566677777665    369999999999997543

>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=95.45  E-value=0.012  Score=48.48  Aligned_cols=42  Identities=19%  Similarity=0.249  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      +.+...+..+.  ...+..++|.||||+|||.. |-.++.++...
T Consensus       153 ~~~~~~L~~l~--~~~ggii~I~GpnGSGKTTl-L~allg~l~~~  194 (418)
T 1p9r_A          153 AHNHDNFRRLI--KRPHGIILVTGPTGSGKSTT-LYAGLQELNSS  194 (418)
T ss_dssp             HHHHHHHHHHH--TSSSEEEEEECSTTSCHHHH-HHHHHHHHCCT
T ss_pred             HHHHHHHHHHH--HhcCCeEEEECCCCCCHHHH-HHHHHhhcCCC
Confidence            45666666652  24566789999999999965 34445555443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=95.43  E-value=0.0093  Score=44.68  Aligned_cols=18  Identities=33%  Similarity=0.423  Sum_probs=15.3

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      ...++|.||+|||||+.+
T Consensus        54 ~~~vll~Gp~GtGKT~la   71 (297)
T 3b9p_A           54 AKGLLLFGPPGNGKTLLA   71 (297)
T ss_dssp             CSEEEEESSSSSCHHHHH
T ss_pred             CCeEEEECcCCCCHHHHH
Confidence            467999999999999654

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=95.31  E-value=0.013  Score=44.79  Aligned_cols=34  Identities=21%  Similarity=0.199  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~   66 (115)
                      -+|.+.++.+.+++.++.   .++|.||.|+|||..+
T Consensus        19 vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           19 VGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIA   55 (373)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHH
T ss_pred             cCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHH
Confidence            456677778888887764   3789999999999654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=95.28  E-value=0.014  Score=51.57  Aligned_cols=36  Identities=25%  Similarity=0.427  Sum_probs=27.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~a   70 (115)
                      .-+.|.+.+..+   + ++...+|.||.|||||.++..-+
T Consensus       361 Ln~~Q~~Av~~~---l-~~~~~lI~GppGTGKT~~i~~~i  396 (802)
T 2xzl_A          361 LNSSQSNAVSHV---L-QRPLSLIQGPPGTGKTVTSATIV  396 (802)
T ss_dssp             CCHHHHHHHHHH---T-TCSEEEEECSTTSSHHHHHHHHH
T ss_pred             CCHHHHHHHHHH---h-cCCCEEEECCCCCCHHHHHHHHH
Confidence            559999976654   3 46688999999999998755443

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.23  E-value=0.015  Score=43.56  Aligned_cols=18  Identities=28%  Similarity=0.348  Sum_probs=15.1

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      .+++|.||+|||||..+-
T Consensus        68 ~~vll~G~~GtGKT~la~   85 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVAL   85 (309)
T ss_dssp             CEEEEEECTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            469999999999997543

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.23  E-value=0.009  Score=45.42  Aligned_cols=33  Identities=21%  Similarity=0.227  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHHHh------cCCcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLD------NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~------~~~~~iiEaPTGtGKTls~   66 (115)
                      ++.+.++.+..++.      ....++|.||+|+|||..+
T Consensus        23 gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           23 HREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             TCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHH
Confidence            34444455555552      3467999999999999654

>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=95.22  E-value=0.014  Score=43.39  Aligned_cols=34  Identities=18%  Similarity=0.170  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      +|.+.++.+.+++.++  .+++|.||.|+|||...-
T Consensus        25 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~   60 (323)
T 1sxj_B           25 GNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVH   60 (323)
T ss_dssp             SCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHH
Confidence            4666777888888876  359999999999996543

>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=95.19  E-value=0.018  Score=44.72  Aligned_cols=33  Identities=27%  Similarity=0.376  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHhcC-------CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNS-------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~-------~~~iiEaPTGtGKTls~   66 (115)
                      +|...++.+..++..+       .+++|.||+|+|||..+
T Consensus        29 g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa   68 (334)
T 1in4_A           29 GQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLA   68 (334)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHH
Confidence            3445556666666543       68999999999999643

>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=95.11  E-value=0.019  Score=50.78  Aligned_cols=46  Identities=17%  Similarity=0.208  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh-hhhhh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD-HKIAG   81 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~-~~~~v   81 (115)
                      .-+.|.+.+..+   + .+...+|.||.|||||.++..- +..+.. .+.++
T Consensus       357 Ln~~Q~~Av~~~---l-~~~~~lI~GppGTGKT~ti~~~-i~~l~~~~~~~i  403 (800)
T 2wjy_A          357 LNHSQVYAVKTV---L-QRPLSLIQGPPGTGKTVTSATI-VYHLARQGNGPV  403 (800)
T ss_dssp             CCHHHHHHHHHH---H-TSSEEEEECCTTSCHHHHHHHH-HHHHHTTCSSCE
T ss_pred             CCHHHHHHHHHh---c-cCCeEEEEcCCCCCHHHHHHHH-HHHHHHcCCCcE
Confidence            568999966654   3 4578899999999999875444 444433 34443

>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=95.07  E-value=0.016  Score=44.35  Aligned_cols=17  Identities=35%  Similarity=0.417  Sum_probs=14.7

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|+|||..+
T Consensus        46 ~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           46 FSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            56999999999999754

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=95.05  E-value=0.019  Score=48.20  Aligned_cols=36  Identities=19%  Similarity=0.373  Sum_probs=26.3

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +++.+.-++..+..++|.||||+|||..+ -.++.++
T Consensus       249 ~l~~l~~~v~~g~~i~I~GptGSGKTTlL-~aL~~~i  284 (511)
T 2oap_1          249 VLAYLWLAIEHKFSAIVVGETASGKTTTL-NAIMMFI  284 (511)
T ss_dssp             HHHHHHHHHHTTCCEEEEESTTSSHHHHH-HHHGGGS
T ss_pred             HHHHHHHHHhCCCEEEEECCCCCCHHHHH-HHHHhhC
Confidence            45566667788999999999999999643 3334444

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=94.99  E-value=0.015  Score=47.28  Aligned_cols=40  Identities=20%  Similarity=0.248  Sum_probs=28.3

Q ss_pred             CCCCHHHHHHHHH-----HHHHHhcCCc--EEEecCCCCCchHHHHH
Q psy14273         29 FDAYDIQSNFMKN-----LYYTLDNSKF--GIFESPTGTGKSLSLIC   68 (115)
Q Consensus        29 f~~r~~Q~e~m~~-----I~~~l~~~~~--~iiEaPTGtGKTls~L~   68 (115)
                      |.+...|.++.+.     |..++..|.+  ++..|+||||||.+.+-
T Consensus        58 f~~~~~Q~~Vy~~~~~plv~~~~~~G~n~tifAYGqTGSGKTyTM~G  104 (360)
T 1ry6_A           58 FDDTVDNFTVYENTIKPLIIDLYENGCVCSCFAYGQTGSGKTYTMLG  104 (360)
T ss_dssp             ECTTCCHHHHHHHHTHHHHHHHHHHCCEEEEEEECCTTSSHHHHHHB
T ss_pred             ecCCCCHHHHHHHHhhhhhhhhccCCceeEEEeeCCCCCCCCEEEec
Confidence            4466678877765     3345555654  57799999999998753

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.98  E-value=0.019  Score=48.47  Aligned_cols=34  Identities=18%  Similarity=0.140  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~   66 (115)
                      -+|...++.+..++..+.+++|.||+|||||..+
T Consensus        44 ~G~~~~l~~l~~~i~~g~~vll~Gp~GtGKTtla   77 (604)
T 3k1j_A           44 IGQEHAVEVIKTAANQKRHVLLIGEPGTGKSMLG   77 (604)
T ss_dssp             CSCHHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             ECchhhHhhccccccCCCEEEEEeCCCCCHHHHH
Confidence            4678889999999999999999999999999654

>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=94.94  E-value=0.051  Score=39.48  Aligned_cols=17  Identities=35%  Similarity=0.524  Sum_probs=14.2

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||..+
T Consensus        40 ~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           40 KGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            45899999999999653

>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=94.92  E-value=0.04  Score=44.73  Aligned_cols=36  Identities=14%  Similarity=0.234  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHhcC----CcEEEecCCCCCchHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~L~   68 (115)
                      ....+.+..+.+.+..+    ..++|.||+|||||+...+
T Consensus        43 ~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~a   82 (456)
T 2c9o_A           43 ENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALA   82 (456)
T ss_dssp             HHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHH
Confidence            34444444455555554    4799999999999975443

>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=94.91  E-value=0.023  Score=44.44  Aligned_cols=18  Identities=33%  Similarity=0.482  Sum_probs=15.1

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      ..+++|.||+|||||..+
T Consensus        72 ~~~ill~Gp~GtGKT~la   89 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMA   89 (376)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCCCHHHHH
Confidence            457999999999999653

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=94.83  E-value=0.043  Score=40.35  Aligned_cols=16  Identities=44%  Similarity=0.576  Sum_probs=13.9

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||+|||||..
T Consensus        46 ~~vll~G~~GtGKT~l   61 (257)
T 1lv7_A           46 KGVLMVGPPGTGKTLL   61 (257)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEEECcCCCCHHHH
Confidence            4689999999999964

>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=94.82  E-value=0.02  Score=43.45  Aligned_cols=37  Identities=14%  Similarity=0.081  Sum_probs=27.1

Q ss_pred             CHHHHHHHHHHHHHHhcCC---cEEEecCCCCCchHHHHH
Q psy14273         32 YDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~---~~iiEaPTGtGKTls~L~   68 (115)
                      .-+|.+.++.+.+++.++.   .+++.+|+|+|||...-+
T Consensus        28 ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~   67 (324)
T 3u61_B           28 CILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKA   67 (324)
T ss_dssp             SCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHH
T ss_pred             HhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHH
Confidence            3466677788888888763   356788899999976443

>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=94.79  E-value=0.022  Score=47.04  Aligned_cols=34  Identities=21%  Similarity=0.209  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHhc-------------------CCcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDN-------------------SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~-------------------~~~~iiEaPTGtGKTls~L   67 (115)
                      +|...++.+..++..                   ...++|.||+|+|||..+-
T Consensus        43 G~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~   95 (516)
T 1sxj_A           43 GNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAH   95 (516)
T ss_dssp             SCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHH
Confidence            455556666666654                   2579999999999997543

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=94.77  E-value=0.012  Score=48.40  Aligned_cols=38  Identities=26%  Similarity=0.329  Sum_probs=29.6

Q ss_pred             CCCCHHHHHHH---HHHHHHHhcCC--cEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFM---KNLYYTLDNSK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m---~~I~~~l~~~~--~~iiEaPTGtGKTls~   66 (115)
                      |+-.-+|.+.+   ..+.+.+.++.  .++|.||+|||||..+
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHH
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHH
Confidence            44455777777   77888888775  5999999999999653

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=94.69  E-value=0.022  Score=46.66  Aligned_cols=39  Identities=15%  Similarity=0.133  Sum_probs=28.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~L   67 (115)
                      +++--+|.+.|+.+...+..  ..+++|.||+|+|||...-
T Consensus       179 ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la~  219 (468)
T 3pxg_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAE  219 (468)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHHH
T ss_pred             CCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHHH
Confidence            34444566677778888854  4689999999999997543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=94.69  E-value=0.016  Score=45.75  Aligned_cols=38  Identities=21%  Similarity=0.184  Sum_probs=25.9

Q ss_pred             CCCCHHHHHHHHHHHHHHh--------------cCCcEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLD--------------NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~--------------~~~~~iiEaPTGtGKTls~   66 (115)
                      |+-.-+|...++.|...+.              ....++|.||+|||||+.+
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHH
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHH
Confidence            4434456666666666552              2367999999999999653

>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=94.61  E-value=0.017  Score=46.64  Aligned_cols=44  Identities=25%  Similarity=0.442  Sum_probs=30.5

Q ss_pred             cccCC--CCCCHHHHHHHHHHHHHHh---cC--CcEEEecCCCCCchHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLYYTLD---NS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~~~l~---~~--~~~iiEaPTGtGKTls~L   67 (115)
                      .|.|.  |.+...|.++.+.|...+.   +|  ..++..|+||||||.+.+
T Consensus        53 ~f~FD~Vf~~~~~Q~~Vy~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTM~  103 (347)
T 1f9v_A           53 EFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML  103 (347)
T ss_dssp             EEEESEEECTTCCHHHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             EEeeCEEECCCCCHHHHHHHHHHHHHHhcCCceeEEEEECCCCCCCcEecc
Confidence            34444  4466778888887765443   34  346679999999999874

>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=94.60  E-value=0.019  Score=43.92  Aligned_cols=16  Identities=31%  Similarity=0.484  Sum_probs=14.2

Q ss_pred             cEEEecCCCCCchHHH
Q psy14273         51 FGIFESPTGTGKSLSL   66 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~   66 (115)
                      +++|.||+|+|||..+
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=94.52  E-value=0.039  Score=43.90  Aligned_cols=26  Identities=19%  Similarity=0.230  Sum_probs=22.7

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.+.-++..|..++|.||||+|||..
T Consensus       166 ~~l~~~i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          166 SFLRRAVQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHHHHHHHTTCCEEEEESSSSCHHHH
T ss_pred             HHHHHHHhcCCEEEEECCCCCCHHHH
Confidence            67777888999999999999999953

>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=94.48  E-value=0.045  Score=41.69  Aligned_cols=33  Identities=21%  Similarity=0.088  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHhcC----CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~   66 (115)
                      .+......+.+.+...    ..++|.||+|+|||..+
T Consensus        18 ~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la   54 (324)
T 1l8q_A           18 GNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLL   54 (324)
T ss_dssp             TTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHH
T ss_pred             cHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHH
Confidence            3344445555555543    57999999999999653

>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=94.47  E-value=0.014  Score=44.56  Aligned_cols=34  Identities=18%  Similarity=0.189  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHH-hcC--CcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTL-DNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l-~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      +|.+.++.+.+++ ..+  .+++|.||+|+|||..+-
T Consensus        18 g~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~   54 (354)
T 1sxj_E           18 HNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCM   54 (354)
T ss_dssp             SCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHH
T ss_pred             CCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHH
Confidence            5677778888887 554  469999999999997643

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.47  E-value=0.037  Score=42.45  Aligned_cols=31  Identities=29%  Similarity=0.369  Sum_probs=22.5

Q ss_pred             HHHHHHHHHhcC---CcEEEecCCCCCchHHHHH
Q psy14273         38 FMKNLYYTLDNS---KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        38 ~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~   68 (115)
                      ++..+...+..-   .++++.||.|||||...++
T Consensus        44 f~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~a   77 (212)
T 1tue_A           44 FLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMS   77 (212)
T ss_dssp             HHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHH
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHH
Confidence            366666666653   3689999999999976543

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=94.46  E-value=0.017  Score=47.48  Aligned_cols=43  Identities=23%  Similarity=0.375  Sum_probs=28.8

Q ss_pred             ccCC--CCCCHHHHHHHHHHHHHH---hcC--CcEEEecCCCCCchHHHH
Q psy14273         25 FPFP--FDAYDIQSNFMKNLYYTL---DNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        25 ~~fp--f~~r~~Q~e~m~~I~~~l---~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      |.|.  |.+...|.++.+.|...+   .+|  ..++..|+||||||.+.+
T Consensus       110 F~FD~VF~~~~~Q~~Vf~~v~~lv~~~l~G~N~tifAYGqTGSGKTyTM~  159 (403)
T 4etp_A          110 FKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVAIFAYGQTGSGKTFTML  159 (403)
T ss_dssp             EEESEEECTTCCHHHHHHHHHHHHHHHHTTCCEEEEEESCTTSSHHHHHH
T ss_pred             EEcCEEECCCCchHHHHHHHHHHHHHHhCCcceEEEEECCCCCCCceEeC
Confidence            4444  446667777776654433   245  346679999999999974

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.46  E-value=0.02  Score=49.34  Aligned_cols=34  Identities=24%  Similarity=0.205  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHHHHhcCC-----------cEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK-----------FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~-----------~~iiEaPTGtGKTls~L   67 (115)
                      +|.+.++.|.+++....           +++|.||||||||...-
T Consensus       495 Gq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~  539 (758)
T 3pxi_A          495 GQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELAR  539 (758)
T ss_dssp             SCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHH
Confidence            46677777777765421           59999999999996543

>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=94.44  E-value=0.025  Score=44.40  Aligned_cols=18  Identities=39%  Similarity=0.392  Sum_probs=15.1

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      ...++|.||+|||||+.+
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            357999999999999654

>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=94.36  E-value=0.035  Score=45.97  Aligned_cols=40  Identities=20%  Similarity=0.106  Sum_probs=29.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .-+.|.+.+.      ..++.++|.||.|||||.+++.=+...+..
T Consensus        10 Ln~~Q~~av~------~~~~~~lV~a~aGsGKT~~l~~ri~~l~~~   49 (647)
T 3lfu_A           10 LNDKQREAVA------APRSNLLVLAGAGSGKTRVLVHRIAWLMSV   49 (647)
T ss_dssp             CCHHHHHHHT------CCSSCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHh------CCCCCEEEEECCCCCHHHHHHHHHHHHHHh
Confidence            4578888665      235778999999999998877665555543

>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=94.35  E-value=0.02  Score=46.84  Aligned_cols=43  Identities=19%  Similarity=0.306  Sum_probs=30.0

Q ss_pred             ccCC--CCCCHHHHHHHHHHHHHHh---cC--CcEEEecCCCCCchHHHH
Q psy14273         25 FPFP--FDAYDIQSNFMKNLYYTLD---NS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        25 ~~fp--f~~r~~Q~e~m~~I~~~l~---~~--~~~iiEaPTGtGKTls~L   67 (115)
                      |.|.  |.+...|.++.+.|...+.   +|  ..++..|.||||||.+.+
T Consensus        85 F~FD~Vf~~~~~Q~~Vy~~v~~lv~~~l~G~N~tifAYGqTGSGKTyTM~  134 (376)
T 2rep_A           85 FSFDRVFPPGSGQDEVFEEIAMLVQSALDGYPVCIFAYGQTGSGKTFTME  134 (376)
T ss_dssp             EECSEEECTTCCHHHHHHHHHHHHHGGGGTCCEEEEEECSTTSSHHHHHT
T ss_pred             eeecEEcCCcccchhhhhhHHHHHHHhcCCCceEEEEeCCCCCCCceEee
Confidence            4444  4466788888887765443   34  346679999999999874

>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=94.28  E-value=0.031  Score=43.70  Aligned_cols=36  Identities=6%  Similarity=-0.110  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L~~   69 (115)
                      +|.+.+..+.+.+.++.  +.+|.||.|+|||....+-
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~l   38 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLEL   38 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHH
Confidence            57888999999998875  6889999999998765443

>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=94.20  E-value=0.022  Score=46.03  Aligned_cols=44  Identities=16%  Similarity=0.230  Sum_probs=29.4

Q ss_pred             ccccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~   66 (115)
                      ..|.|.  |.+...|.++.+.+.    ..+.+|.  .++..|+||||||.+.
T Consensus        44 ~~F~FD~Vf~~~~tQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           44 KSFNFDRVFHGNETTKNVYEEIAAPIIDSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             CEEECSCEECTTSCHHHHHHHTTHHHHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             eEEECCEEECCCCCHHHHHHHHHHHHHHHHHcCCccceeeecCCCCCCCeEE
Confidence            345555  346667888776543    3333553  4667999999999997

>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=94.15  E-value=0.026  Score=43.47  Aligned_cols=17  Identities=35%  Similarity=0.362  Sum_probs=14.5

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||+.+
T Consensus        52 ~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           52 SGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CEEEEECSSSSCHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46899999999999654

>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=94.12  E-value=0.13  Score=38.08  Aligned_cols=17  Identities=24%  Similarity=0.307  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||..+
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            46999999999999754

>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=94.12  E-value=0.073  Score=40.63  Aligned_cols=18  Identities=44%  Similarity=0.560  Sum_probs=15.1

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      +..++|.||+|||||+.+
T Consensus        49 ~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           49 SKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CSEEEEECSSSSSHHHHH
T ss_pred             CceEEEECCCCcCHHHHH
Confidence            457899999999999653

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=94.08  E-value=0.039  Score=47.48  Aligned_cols=38  Identities=16%  Similarity=0.160  Sum_probs=29.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      +++--+|.+.|+.+...+..  ..+++|.||+|||||...
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~la  218 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIA  218 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHHH
Confidence            44445667777788888855  468999999999999753

>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=94.08  E-value=0.019  Score=42.38  Aligned_cols=17  Identities=41%  Similarity=0.526  Sum_probs=14.2

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||..+
T Consensus        45 ~~vll~G~~GtGKT~la   61 (268)
T 2r62_A           45 KGVLLVGPPGTGKTLLA   61 (268)
T ss_dssp             SCCCCBCSSCSSHHHHH
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            45889999999999653

>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=93.95  E-value=0.038  Score=41.80  Aligned_cols=34  Identities=15%  Similarity=0.118  Sum_probs=24.7

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+...++.||+|+|||.++|-.+..+... +.++
T Consensus        10 ~~G~i~litG~mGsGKTT~ll~~~~r~~~~-g~kV   43 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELIRRLHRLEYA-DVKY   43 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHHHHHHHHHHT-TCCE
T ss_pred             CCcEEEEEECCCCCcHHHHHHHHHHHHHhc-CCEE
Confidence            456788899999999998877776666543 4443

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=93.93  E-value=0.071  Score=45.78  Aligned_cols=41  Identities=22%  Similarity=0.227  Sum_probs=34.7

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCC-cEEEecCCCCCchHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSL   66 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~-~~iiEaPTGtGKTls~   66 (115)
                      +-||.|.+.|.+.+..+...+.++. ..++.+.||+|||+++
T Consensus         4 ~~~~~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~   45 (664)
T 1c4o_A            4 YRGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTM   45 (664)
T ss_dssp             CCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH
T ss_pred             CCCCCCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHH
Confidence            4568899999999999999988874 5678899999999864

>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=93.92  E-value=0.03  Score=42.32  Aligned_cols=33  Identities=21%  Similarity=0.130  Sum_probs=22.2

Q ss_pred             CCHHHHHHHHHHHHHHhc------CCcEEEecCCCCCchHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDN------SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~------~~~~iiEaPTGtGKTls~   66 (115)
                      -|..+.+   .+.+++..      +..++|.||+|+|||..+
T Consensus        24 gr~~e~~---~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           24 HREDQIR---KIASILAPLYREEKPNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             TCHHHHH---HHHHSSGGGGGTCCCCCEEEEECTTSSHHHHH
T ss_pred             ChHHHHH---HHHHHHHHHHcCCCCCeEEEECCCCCCHHHHH
Confidence            3444444   55555542      467999999999999654

>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=93.89  E-value=0.03  Score=45.18  Aligned_cols=45  Identities=33%  Similarity=0.360  Sum_probs=29.8

Q ss_pred             CccccCC--CCCCHHHHHHHHHHH----HHHhcC--CcEEEecCCCCCchHHH
Q psy14273         22 PSEFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        22 ~~~~~fp--f~~r~~Q~e~m~~I~----~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      ...|.|.  |.+...|.++.+.+.    ..+.+|  ..++..|+||||||.+.
T Consensus        60 ~~~F~FD~Vf~~~~sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           60 QNEFHFDHAFPATISQDEMYQALILPLVDKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             TEEEECSEEECTTCCHHHHHHHHTHHHHHHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             CcEEEcceEECCCCCHHHHHHhhccchhhHhhCCCceEEEEecCCCCCCCeEE
Confidence            3455555  446677888776632    333345  34667999999999986

>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=93.88  E-value=0.024  Score=48.59  Aligned_cols=33  Identities=24%  Similarity=0.265  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHhc---C--------CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDN---S--------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~---~--------~~~iiEaPTGtGKTls~   66 (115)
                      +|.+.++.|.+++..   |        .+++|.||||||||..+
T Consensus       462 g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la  505 (758)
T 1r6b_X          462 GQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVT  505 (758)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHH
Confidence            455666666666543   1        26899999999999653

>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=93.88  E-value=0.022  Score=46.45  Aligned_cols=38  Identities=18%  Similarity=0.294  Sum_probs=26.0

Q ss_pred             CCCCHHHHHHHHHH---HHHHhcCC--cEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNL---YYTLDNSK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I---~~~l~~~~--~~iiEaPTGtGKTls~   66 (115)
                      |.+...|.++.+.+   ...+.+|.  .++..|+||||||.+.
T Consensus        55 f~~~~~Q~~Vy~~~~~lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           55 FDGNATQDDVFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             ECTTCCHHHHHHTTTHHHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             ECCCCCcceehhhhhhhhHhhhcCCceEEEEECCCCCCCeEee
Confidence            44667788777653   22333553  4667999999999997

>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=93.80  E-value=0.034  Score=43.80  Aligned_cols=17  Identities=35%  Similarity=0.362  Sum_probs=14.4

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||+.+
T Consensus        85 ~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCEEEECSTTSCHHHHH
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            46899999999999754

>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=93.70  E-value=0.043  Score=44.64  Aligned_cols=17  Identities=35%  Similarity=0.389  Sum_probs=14.5

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||+.+
T Consensus       168 ~~vLL~GppGtGKT~lA  184 (444)
T 2zan_A          168 RGILLFGPPGTGKSYLA  184 (444)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            56899999999999654

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=93.64  E-value=0.016  Score=46.42  Aligned_cols=39  Identities=15%  Similarity=0.174  Sum_probs=26.2

Q ss_pred             CCCCHHHHHHHHHHHH---HHhcCC--cEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYY---TLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~---~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      |.+...|.++.+.|..   .+.+|.  .++..|+||||||.+.+
T Consensus        56 f~~~~~Q~~Vy~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTm~   99 (330)
T 2h58_A           56 FSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTME   99 (330)
T ss_dssp             ECTTCCHHHHHTTTHHHHHHHHTTCCEEEEEESSTTSSHHHHHT
T ss_pred             eCCCCCcHhHHHHHHHHHHHHhCCCEEEEEeECCCCCCCcEEEe
Confidence            3466678777765432   223453  46679999999999873

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=93.57  E-value=0.034  Score=44.78  Aligned_cols=39  Identities=13%  Similarity=0.307  Sum_probs=28.2

Q ss_pred             CCCCHHHHHHHHHHHHHHh---cC--CcEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLD---NS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~---~~--~~~iiEaPTGtGKTls~L   67 (115)
                      |.+...|.++.+.|...+.   +|  ..++..|+||||||.+.+
T Consensus        61 f~~~~~Q~~vf~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTm~  104 (349)
T 3t0q_A           61 FEPSHTNKEIFEEIRQLVQSSLDGYNVCIFAYGQTGSGKTYTML  104 (349)
T ss_dssp             ECTTCCHHHHHHHHHHHHHGGGTTCEEEEEEECSTTSSHHHHHH
T ss_pred             ECCCccHHHHHHHHHHHHHHHHCCcceeEEEeCCCCCCCceEeC
Confidence            4466778888877665443   34  346679999999999874

>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=93.51  E-value=0.021  Score=45.68  Aligned_cols=46  Identities=13%  Similarity=0.144  Sum_probs=30.6

Q ss_pred             CccccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         22 PSEFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        22 ~~~~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      +..|.|.  |.+...|.++.+.+.    ..+.+|.  .++..|+||||||.+..
T Consensus        43 ~~~f~FD~Vf~~~~sQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~   96 (325)
T 1bg2_A           43 SKPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTME   96 (325)
T ss_dssp             TEEEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             CEEEECCeEeCCCCCHHHHHHHHhhhhHHHHhCCCeEEEEEECCCCCCCceEec
Confidence            3445555  446677888776643    3333553  46679999999999975

>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=93.50  E-value=0.022  Score=46.15  Aligned_cols=39  Identities=21%  Similarity=0.192  Sum_probs=27.1

Q ss_pred             CCCCHHHHHHHHHHHH----HHhcCC--cEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYY----TLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~----~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      |.+...|.++.+.+..    .+.+|.  .++..|+||||||.+.+
T Consensus        63 f~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM~  107 (359)
T 1x88_A           63 FGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTME  107 (359)
T ss_dssp             ECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHHT
T ss_pred             EeccCchhHHHHHHHHHhHHHHhCCCceEEEEeCCCCCCCceEEe
Confidence            3466678887776543    333453  46679999999999875

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.49  E-value=0.055  Score=42.04  Aligned_cols=17  Identities=35%  Similarity=0.389  Sum_probs=14.4

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      +.++|.||+|||||+.+
T Consensus        46 ~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             SEEEEESSSSSCHHHHH
T ss_pred             ceEEEECCCCccHHHHH
Confidence            46899999999999653

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=93.49  E-value=0.024  Score=46.11  Aligned_cols=46  Identities=13%  Similarity=0.080  Sum_probs=30.7

Q ss_pred             CccccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         22 PSEFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        22 ~~~~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      +..|.|.  |.+...|.++.+.+.    ..+.+|.  .++..|+||||||.+..
T Consensus        50 ~~~f~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~  103 (365)
T 2y65_A           50 GKVYLFDKVFKPNASQEKVYNEAAKSIVTDVLAGYNGTIFAYGQTSSGKTHTME  103 (365)
T ss_dssp             TEEEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             CEEEeCceEecCCCCHHHHHHHhhhhHHHHHhCCCceEEEeecCCCCCCceEEe
Confidence            3445555  447778888776643    2333553  46679999999999873

>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=93.48  E-value=0.064  Score=42.25  Aligned_cols=28  Identities=21%  Similarity=0.179  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+.+.+.-.+..+..+++.||||+|||.
T Consensus       159 ~~l~~l~~~i~~g~~v~i~G~~GsGKTT  186 (330)
T 2pt7_A          159 QAISAIKDGIAIGKNVIVCGGTGSGKTT  186 (330)
T ss_dssp             HHHHHHHHHHHHTCCEEEEESTTSCHHH
T ss_pred             HHHhhhhhhccCCCEEEEECCCCCCHHH
Confidence            3566777778889999999999999996

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=93.45  E-value=0.033  Score=38.91  Aligned_cols=18  Identities=28%  Similarity=0.292  Sum_probs=15.8

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|.||+|+|||.-
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            678899999999999854

>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=93.37  E-value=0.046  Score=43.93  Aligned_cols=44  Identities=16%  Similarity=0.107  Sum_probs=28.9

Q ss_pred             cccCC--CCCCHHHHHHHHHH----HHHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I----~~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      .|.|.  |.+...|.++.+.+    ...+.+|.  .++..|+||||||.+..
T Consensus        51 ~f~FD~Vf~~~~~Q~~vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~  102 (344)
T 4a14_A           51 HFGFHVVLAEDAGQEAVYQACVQPLLEAFFEGFNATVFAYGQTGSGKTYTMG  102 (344)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEESSTTSSHHHHHC
T ss_pred             eEEEEEEEecCcchhHHHHHHHHHHHHHHHhhcCeeEEEecccCCCceEeec
Confidence            34444  44667788777663    33333553  46679999999999863

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.35  E-value=0.049  Score=38.96  Aligned_cols=35  Identities=23%  Similarity=0.123  Sum_probs=23.2

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..|..+++.|++|+|||.-.+--+...+...+..+
T Consensus        28 ~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v   62 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPG   62 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCE
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCc
Confidence            34578999999999999654444444444444443

>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=93.29  E-value=0.026  Score=49.48  Aligned_cols=33  Identities=21%  Similarity=0.241  Sum_probs=23.3

Q ss_pred             HHHHHHHHHHHHHhcC-----------CcEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~-----------~~~iiEaPTGtGKTls~   66 (115)
                      +|...|+.+..++...           ..++|.||||||||..+
T Consensus       562 G~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA  605 (854)
T 1qvr_A          562 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELA  605 (854)
T ss_dssp             SCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHH
T ss_pred             CcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHH
Confidence            3556666666666432           36899999999999653

>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=93.29  E-value=0.089  Score=44.45  Aligned_cols=40  Identities=13%  Similarity=0.029  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..+.|.+.+..      .++.++|.|+.|||||.+++.=+...+..
T Consensus         3 L~~~Q~~av~~------~~~~~lV~AgaGSGKT~~l~~ri~~ll~~   42 (673)
T 1uaa_A            3 LNPGQQQAVEF------VTGPCLVLAGAGSGKTRVITNKIAHLIRG   42 (673)
T ss_dssp             CCHHHHHHHHC------CSSEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC------CCCCEEEEeCCCCChHHHHHHHHHHHHHh
Confidence            45788886653      36788999999999999877666655554

>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=93.27  E-value=0.11  Score=40.71  Aligned_cols=30  Identities=13%  Similarity=-0.085  Sum_probs=22.4

Q ss_pred             HHHHHHHHHhcC----CcEEEecCCCCCchHHHH
Q psy14273         38 FMKNLYYTLDNS----KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        38 ~m~~I~~~l~~~----~~~iiEaPTGtGKTls~L   67 (115)
                      +...++.++...    ..++|.||.|||||+.+.
T Consensus        89 ~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           89 AASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             HHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            445577777654    368999999999997654

>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=93.26  E-value=0.029  Score=45.75  Aligned_cols=44  Identities=23%  Similarity=0.286  Sum_probs=28.3

Q ss_pred             cccCC--CCCCHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      .|.|.  |.+...|.++.+.+..    .+.+|  ..++..|.||||||.+.+
T Consensus        68 ~F~FD~vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~  119 (373)
T 2wbe_C           68 KFTFDRSFGPESKQCDVYSVVVSPLIEEVLNGYNCTVFAYGQTGTGKTHTMV  119 (373)
T ss_dssp             EEECSEEECTTCCHHHHHHHHHHHHHHHHHHTCCEEEEEECSTTSSHHHHHT
T ss_pred             EEeccEEeccccchhHHHHHHHHHHHHHHhCCceEEEEeecCCCCCcceecc
Confidence            34444  3455678777765432    22345  346679999999999864

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=93.09  E-value=0.046  Score=44.24  Aligned_cols=43  Identities=16%  Similarity=0.247  Sum_probs=28.4

Q ss_pred             cccCC--CCCCHHHHHHHHHH----HHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I----~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      .|.|.  |.+...|.++.+.+    ...+.+|  ..++..|+||||||.+.
T Consensus        57 ~f~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           57 TFTFDAVYDQTSCNYGIFQASFKPLIDAVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             EEECSEEECTTCCHHHHHHHTTHHHHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             EeeCCEEECCCcchhHHHHHHHHHHHHHHhCCCceeEEeecCCCCCCCEEe
Confidence            34454  44667787777653    2333355  34667999999999987

>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=92.99  E-value=0.028  Score=45.98  Aligned_cols=44  Identities=20%  Similarity=0.259  Sum_probs=28.7

Q ss_pred             cccCC--CCCCHHHHHHHHHHH----HHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~----~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      .|.|.  |.+...|.++.+.+.    ..+.+|  ..++..|+||||||.+..
T Consensus        69 ~F~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM~  120 (372)
T 3b6u_A           69 TFTFDAVYDWNAKQFELYDETFRPLVDSVLQGFNGTIFAYGQTGTGKTYTME  120 (372)
T ss_dssp             EEECSEEECTTCCHHHHHHHTHHHHHHHHHTTCCEEEEEEESTTSSHHHHHT
T ss_pred             EEEcCeEeCCcCchHHHHHHHHHHHHHHHhCCCeeeEEeecCCCCCCCEeEe
Confidence            34444  446677887776543    233355  346679999999999864

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=92.93  E-value=0.031  Score=45.25  Aligned_cols=45  Identities=27%  Similarity=0.276  Sum_probs=28.8

Q ss_pred             cccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L~   68 (115)
                      .|.|.  |.+...|.++.+.+.    ..+.+|.  .++..|+||||||.+.+-
T Consensus        48 ~f~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~G  100 (355)
T 1goj_A           48 SFTFDRVFDMSCKQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMMG  100 (355)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             EEeeCeEECCCCccHHHHHHHHHHHHHHHhCCCcceEEEECCCCCCcceEeec
Confidence            34444  446667877776432    2333453  466799999999998743

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=92.91  E-value=0.048  Score=38.25  Aligned_cols=19  Identities=26%  Similarity=0.552  Sum_probs=16.0

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..++|.||+|+|||.-
T Consensus         5 ~~g~ii~l~Gp~GsGKSTl   23 (205)
T 3tr0_A            5 NKANLFIISAPSGAGKTSL   23 (205)
T ss_dssp             CCCCEEEEECCTTSCHHHH
T ss_pred             CCCcEEEEECcCCCCHHHH
Confidence            4577889999999999853

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.90  E-value=0.054  Score=41.34  Aligned_cols=26  Identities=27%  Similarity=0.358  Sum_probs=20.1

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .++.+.  +..+..++|.||||+|||..
T Consensus        16 vl~~i~--i~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           16 KVLELC--HRKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             HHHHGG--GCSSEEEEEECSTTCSHHHH
T ss_pred             HHHHHh--hCCCCEEEEECCCCccHHHH
Confidence            344544  66778899999999999964

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=92.88  E-value=0.2  Score=36.57  Aligned_cols=15  Identities=27%  Similarity=0.366  Sum_probs=13.0

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||+|+|||..
T Consensus        51 g~ll~G~~G~GKTtl   65 (254)
T 1ixz_A           51 GVLLVGPPGVGKTHL   65 (254)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            478999999999954

>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=92.88  E-value=0.14  Score=51.06  Aligned_cols=37  Identities=22%  Similarity=0.198  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +-|...-..+...+..++..++.+++.||||||||+.
T Consensus      1247 iVpT~DT~R~~~ll~~~l~~~~~vLL~GPpGtGKT~l 1283 (2695)
T 4akg_A         1247 VIPTIDTIKHEKIFYDLLNSKRGIILCGPPGSGKTMI 1283 (2695)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHTCEEEEECSTTSSHHHH
T ss_pred             eEeccchHHHHHHHHHHHHCCCeEEEECCCCCCHHHH
Confidence            3366666677777778888999999999999999975

>4h1g_A Maltose binding protein-cakar3 motor domain fusio; kinesin motor domain, motor protein, chimera; HET: MTT ADP EDO; 2.15A {Escherichia coli}

Probab=92.84  E-value=0.047  Score=47.15  Aligned_cols=38  Identities=16%  Similarity=0.215  Sum_probs=24.7

Q ss_pred             CCCCHHHHHHHHHHHH---HHhcCC--cEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNLYY---TLDNSK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~---~l~~~~--~~iiEaPTGtGKTls~   66 (115)
                      |.+...|.++.+.|..   .+.+|.  .++..|.||||||.+.
T Consensus       438 f~~~~~q~~v~~~~~~~v~~~~~G~n~~i~ayGqtgsGKT~Tm  480 (715)
T 4h1g_A          438 FEREQSNDLVFEELSQLIQCSLDGTNVCVFAYGQTGSGKTFTM  480 (715)
T ss_dssp             ECSSCCHHHHGGGTHHHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             eCCCCCHHHHHHHHHHHHHHHhCCceEEEEccCCCCCchhhcc
Confidence            3455667776554432   223453  4566899999999986

>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=92.81  E-value=0.042  Score=45.24  Aligned_cols=38  Identities=18%  Similarity=0.273  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHHHH----HHHHhcCC--cEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I----~~~l~~~~--~~iiEaPTGtGKTls~   66 (115)
                      |.+...|.++.+.+    ...+.+|.  .++..|+||||||.+.
T Consensus        73 f~~~~tQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           73 YGERSTQQDIYAGSVQPILRHLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             ECTTCCHHHHHHHHTGGGHHHHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             ecCCCCHhHHHHHHHHHHHHHhhcCceeeEeeecCCCCCCCeEe
Confidence            34667788877753    23333553  4667999999999987

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=92.80  E-value=0.078  Score=37.31  Aligned_cols=25  Identities=20%  Similarity=0.228  Sum_probs=18.7

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .+..|..+++.||+|+|||.-+.+-
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l   43 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHF   43 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHH
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHH
Confidence            3455678999999999999654443

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=92.79  E-value=0.046  Score=38.52  Aligned_cols=18  Identities=17%  Similarity=0.167  Sum_probs=15.1

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|.||+|+|||.-
T Consensus         4 ~g~~i~i~GpsGsGKSTL   21 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHI   21 (180)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467889999999999953

>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=92.79  E-value=0.024  Score=45.82  Aligned_cols=43  Identities=26%  Similarity=0.365  Sum_probs=28.5

Q ss_pred             ccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         25 FPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        25 ~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      |.|.  |.+...|.++.+.+.    ..+-+|.  .++..|+||||||.+.+
T Consensus        74 F~FD~vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~  124 (355)
T 3lre_A           74 FVFDAVFDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTML  124 (355)
T ss_dssp             EECSEEECTTCCHHHHHHTTHHHHHHHHTTTCCEEEEEECCTTSSHHHHHT
T ss_pred             EEeceEECCCCChHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCceeeec
Confidence            4444  446667888776543    3333553  46679999999999873

>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=92.76  E-value=0.035  Score=45.89  Aligned_cols=43  Identities=21%  Similarity=0.287  Sum_probs=27.5

Q ss_pred             cccCC--CCCCHHHHHHHHHHHH---HHhcC--CcEEEecCCCCCchHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLYY---TLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~~---~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      .|.|.  |.+...|.++.+.|..   .+.+|  ..++..|+||||||.+.
T Consensus       107 ~F~FD~VF~~~~~Q~~Vf~~v~plv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          107 IFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             EEECSEEECTTCCHHHHHTTTHHHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             EEeeCeEcCCCCCHHHHHHHHHHHHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            34454  4466677776654432   22345  34667999999999986

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=92.70  E-value=0.065  Score=42.67  Aligned_cols=31  Identities=23%  Similarity=0.093  Sum_probs=21.2

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ..|+++-||||+|||.++ -.++..+...+..
T Consensus        53 ~~h~~i~G~tGsGKs~~~-~~li~~~~~~g~~   83 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLL-RELAYTGLLRGDR   83 (437)
T ss_dssp             GGCEEEEECTTSSHHHHH-HHHHHHHHHTTCE
T ss_pred             cceEEEECCCCCCHHHHH-HHHHHHHHHCCCc
Confidence            468999999999999974 3334444344433

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=92.63  E-value=0.056  Score=37.85  Aligned_cols=19  Identities=21%  Similarity=0.503  Sum_probs=16.0

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..+..++|.||+|+|||..
T Consensus         4 ~~g~~i~l~G~~GsGKSTl   22 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTV   22 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            4677899999999999853

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.55  E-value=0.074  Score=38.04  Aligned_cols=29  Identities=14%  Similarity=0.140  Sum_probs=21.3

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +..|..+++.||+|+|||.-.+.-+...+
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~~~~~~~~   48 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQQFLWNGL   48 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45567899999999999976554444444

>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=92.50  E-value=0.049  Score=36.43  Aligned_cols=15  Identities=33%  Similarity=0.399  Sum_probs=13.1

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..++|.||+|+|||.
T Consensus         2 ~~I~l~G~~GsGKsT   16 (179)
T 3lw7_A            2 KVILITGMPGSGKSE   16 (179)
T ss_dssp             CEEEEECCTTSCHHH
T ss_pred             cEEEEECCCCCCHHH
Confidence            368899999999995

>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=92.48  E-value=0.069  Score=45.69  Aligned_cols=38  Identities=13%  Similarity=0.110  Sum_probs=27.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      |++.-++.+.++.+.+.+..  +.+++|.||+|+|||...
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~la  224 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIA  224 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHHH
Confidence            33333455666677777765  467999999999999654

>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=92.33  E-value=0.063  Score=40.45  Aligned_cols=40  Identities=18%  Similarity=0.208  Sum_probs=27.3

Q ss_pred             HHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        39 m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ++.+.-.+..|..++|.||+|+|||.-+++-+.......+
T Consensus        25 Ld~i~~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G   64 (296)
T 1cr0_A           25 INDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMG   64 (296)
T ss_dssp             HHHHHCSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSC
T ss_pred             HHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcC
Confidence            4455555677889999999999999765554444443334

>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=92.32  E-value=0.068  Score=38.55  Aligned_cols=18  Identities=22%  Similarity=0.471  Sum_probs=15.4

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|.||+|+|||..
T Consensus         7 ~g~~i~l~GpsGsGKsTl   24 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTV   24 (208)
T ss_dssp             CCCEEEEECCTTSCHHHH
T ss_pred             CCcEEEEECcCCCCHHHH
Confidence            567899999999999954

>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=92.27  E-value=0.034  Score=46.09  Aligned_cols=40  Identities=18%  Similarity=0.107  Sum_probs=27.1

Q ss_pred             CCCCHHHHHHHHHH----HHHHhcCC--cEEEecCCCCCchHHHHH
Q psy14273         29 FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        29 f~~r~~Q~e~m~~I----~~~l~~~~--~~iiEaPTGtGKTls~L~   68 (115)
                      |.+...|.++.+.+    ...+.+|.  .++..|.||||||.+..-
T Consensus       129 F~~~~tQ~~Vy~~~~~plV~~~l~G~N~tifAYGQTGSGKTyTM~G  174 (410)
T 1v8k_A          129 FDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGG  174 (410)
T ss_dssp             ECTTCCHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHHC
T ss_pred             EecCCChhhhhHHHHHHHHHHHhcCCceeEEeecCCCCCCCeEeec
Confidence            44666787777653    23333553  466799999999999754

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=92.26  E-value=0.22  Score=50.40  Aligned_cols=37  Identities=19%  Similarity=0.184  Sum_probs=30.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +-|...-..+...+..++..++.+++.||||||||..
T Consensus      1284 lVPT~DTvR~~~ll~~ll~~~~pvLL~GptGtGKT~l 1320 (3245)
T 3vkg_A         1284 VIPTVDTTRHVDVLHAWLSEHRPLILCGPPGSGKTMT 1320 (3245)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTTCCCEEESSTTSSHHHH
T ss_pred             eecchHHHHHHHHHHHHHHCCCcEEEECCCCCCHHHH
Confidence            4466666666777778888999999999999999954

>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=92.25  E-value=0.16  Score=43.53  Aligned_cols=43  Identities=21%  Similarity=0.325  Sum_probs=36.0

Q ss_pred             cccCCCCCCHHHHHHHHHHHHHHhcCC-cEEEecCCCCCchHHH
Q psy14273         24 EFPFPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSL   66 (115)
Q Consensus        24 ~~~fpf~~r~~Q~e~m~~I~~~l~~~~-~~iiEaPTGtGKTls~   66 (115)
                      .+.-||.|+..|...+..+...+.++. ..++.+.||+|||+.+
T Consensus         6 ~~~~~~~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~   49 (661)
T 2d7d_A            6 ELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTV   49 (661)
T ss_dssp             CCCCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH
T ss_pred             eeecCCCCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHH
Confidence            445689999999999999998988875 5678899999999753

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.20  E-value=0.2  Score=41.65  Aligned_cols=35  Identities=29%  Similarity=0.314  Sum_probs=23.6

Q ss_pred             CHHHHHHHHHHHHH-Hhc-----------CCcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYT-LDN-----------SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~-l~~-----------~~~~iiEaPTGtGKTls~   66 (115)
                      .+.|.+-+..+... +..           .+-+++.||+|||||+.+
T Consensus       186 l~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          186 LTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHH
Confidence            46676666555544 222           146889999999999753

>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=92.09  E-value=0.11  Score=43.22  Aligned_cols=17  Identities=35%  Similarity=0.392  Sum_probs=14.6

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      .++++.||+|+|||...
T Consensus        51 ~~iLl~GppGtGKT~la   67 (444)
T 1g41_A           51 KNILMIGPTGVGKTEIA   67 (444)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            57999999999999653

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=92.03  E-value=0.3  Score=36.40  Aligned_cols=35  Identities=23%  Similarity=0.261  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHHHHHHHhc-----------CCcEEEecCCCCCchHH
Q psy14273         31 AYDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~-----------~~~~iiEaPTGtGKTls   65 (115)
                      -.+.+..-++.+...+..           ...++|.||+|+|||..
T Consensus        44 g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl   89 (278)
T 1iy2_A           44 GAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHL   89 (278)
T ss_dssp             SCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHH
T ss_pred             ChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHH
Confidence            345555555555555432           13488999999999964

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.02  E-value=0.22  Score=41.15  Aligned_cols=35  Identities=20%  Similarity=0.247  Sum_probs=22.9

Q ss_pred             CHHHHHHHHHHHHHHhc--------C----CcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYTLDN--------S----KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~--------~----~~~iiEaPTGtGKTls~   66 (115)
                      ...|.+-+.........        |    +-+++.||+|||||+.+
T Consensus       177 l~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          177 LDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHH
Confidence            46666665554443222        1    34889999999999653

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=91.99  E-value=0.043  Score=46.69  Aligned_cols=31  Identities=19%  Similarity=0.105  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHhcCC-------------cEEEecCCCCCchHH
Q psy14273         35 QSNFMKNLYYTLDNSK-------------FGIFESPTGTGKSLS   65 (115)
Q Consensus        35 Q~e~m~~I~~~l~~~~-------------~~iiEaPTGtGKTls   65 (115)
                      |.++...+..++..+.             ++++.||+|||||..
T Consensus       300 ~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~L  343 (595)
T 3f9v_A          300 HWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQM  343 (595)
T ss_dssp             CHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHH
T ss_pred             hHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHH
Confidence            4445555555555553             899999999999963

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=91.96  E-value=0.061  Score=37.41  Aligned_cols=20  Identities=25%  Similarity=0.330  Sum_probs=16.3

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..+..++|+||.|+|||..
T Consensus         9 ~~~~~~I~l~G~~GsGKsT~   28 (199)
T 2bwj_A            9 LRKCKIIFIIGGPGSGKGTQ   28 (199)
T ss_dssp             HHHSCEEEEEECTTSSHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHH
Confidence            34567899999999999853

>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=91.95  E-value=0.14  Score=42.55  Aligned_cols=17  Identities=35%  Similarity=0.483  Sum_probs=14.7

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      ..++|.||+|||||+.+
T Consensus       239 ~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CcEEEECcCCCCHHHHH
Confidence            56999999999999753

>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=91.93  E-value=0.097  Score=45.84  Aligned_cols=38  Identities=13%  Similarity=0.144  Sum_probs=28.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      |++.-++.+.++.+...+..+  .+++|.||+|+|||..+
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHHH
Confidence            344445567777888877664  57999999999999643

>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=91.92  E-value=0.17  Score=43.54  Aligned_cols=40  Identities=15%  Similarity=0.133  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .-+.|.+.+..      .++.++|.|+.|||||.++..=+...+..
T Consensus        12 Ln~~Q~~av~~------~~g~~lV~AgAGSGKT~vL~~ri~~ll~~   51 (724)
T 1pjr_A           12 LNKEQQEAVRT------TEGPLLIMAGAGSGKTRVLTHRIAYLMAE   51 (724)
T ss_dssp             SCHHHHHHHHC------CSSCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHhC------CCCCEEEEEcCCCCHHHHHHHHHHHHHHh
Confidence            56889886552      35788899999999999876665555543

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=91.87  E-value=0.084  Score=40.37  Aligned_cols=16  Identities=25%  Similarity=0.136  Sum_probs=13.3

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..+++.||+|||||..
T Consensus        37 ~~lLl~GppGtGKT~l   52 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQ   52 (293)
T ss_dssp             SEEEEEECTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            3577899999999964

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.85  E-value=0.09  Score=43.66  Aligned_cols=17  Identities=41%  Similarity=0.577  Sum_probs=14.4

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      +.+++.||+|||||+.+
T Consensus       216 rGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeeEEECcCCCCHHHHH
Confidence            46889999999999653

>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=91.84  E-value=0.092  Score=43.15  Aligned_cols=40  Identities=18%  Similarity=0.113  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHHHH----HHHHhcC--CcEEEecCCCCCchHHHHH
Q psy14273         29 FDAYDIQSNFMKNL----YYTLDNS--KFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        29 f~~r~~Q~e~m~~I----~~~l~~~--~~~iiEaPTGtGKTls~L~   68 (115)
                      |.+...|.++.+.+    ...+.+|  ..++..|.||||||.+..-
T Consensus       109 F~~~~sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM~G  154 (387)
T 2heh_A          109 FDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGG  154 (387)
T ss_dssp             ECTTCCHHHHHHHTTHHHHHHHHTTCEEEEEEESCTTSSHHHHHC-
T ss_pred             EecCCCceeehhhhHHHHHHHHhcCCceEEEEecCCCCCCCeEecc
Confidence            44666787777653    3333355  3466799999999998754

>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=91.82  E-value=0.11  Score=40.39  Aligned_cols=33  Identities=21%  Similarity=0.127  Sum_probs=22.0

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +..+++-||+|+|||.....-+..+....+++|
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V  137 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKI  137 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEE
Confidence            457888999999999775555444443345444

>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=91.76  E-value=0.075  Score=36.53  Aligned_cols=16  Identities=19%  Similarity=0.339  Sum_probs=14.2

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..++|+||.|+|||.
T Consensus         3 ~~~I~i~G~~GsGKsT   18 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTT   18 (192)
T ss_dssp             CCEEEEECCTTSCHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            5678999999999995

>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=91.71  E-value=0.13  Score=41.11  Aligned_cols=30  Identities=23%  Similarity=0.500  Sum_probs=20.9

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ..+..++|.||||+|||.. |-.++.++...
T Consensus       121 ~~~g~i~I~GptGSGKTTl-L~~l~g~~~~~  150 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTT-LAAMLDYLNNT  150 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHH-HHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH-HHHHHhcccCC
Confidence            4556889999999999964 33445555443

>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=91.62  E-value=0.13  Score=43.54  Aligned_cols=27  Identities=22%  Similarity=0.273  Sum_probs=20.9

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+.|+++-|+||+|||..+-+-++..+
T Consensus       166 ~~pHlLIaG~TGSGKSt~L~~li~sLl  192 (512)
T 2ius_A          166 KMPHLLVAGTTGSGASVGVNAMILSML  192 (512)
T ss_dssp             GSCSEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHH
Confidence            468999999999999987655544443

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=91.57  E-value=0.082  Score=37.60  Aligned_cols=20  Identities=15%  Similarity=0.064  Sum_probs=15.8

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..+..++|.||+|+|||..
T Consensus        22 ~~~~~~i~l~G~~GsGKsTl   41 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTTL   41 (199)
T ss_dssp             --CCCEEEEECCTTSCHHHH
T ss_pred             cCCCCEEEEEcCCCCCHHHH
Confidence            34577899999999999964

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=91.53  E-value=0.15  Score=36.59  Aligned_cols=27  Identities=19%  Similarity=0.290  Sum_probs=21.1

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +...++.||.|+|||..++--+..+..
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~~~   29 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIYKL   29 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            567889999999999887766555543

>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=91.29  E-value=0.1  Score=37.32  Aligned_cols=27  Identities=11%  Similarity=0.015  Sum_probs=20.2

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      +..|..++|.||+|+|||.-++.-+..
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~~   47 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAVT   47 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            445678999999999999765554443

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=91.28  E-value=0.099  Score=37.57  Aligned_cols=18  Identities=28%  Similarity=0.501  Sum_probs=14.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|-||+|+|||.-
T Consensus         3 ~g~~i~lvGpsGaGKSTL   20 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTL   20 (198)
T ss_dssp             --CCEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            467899999999999853

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.22  E-value=0.29  Score=41.04  Aligned_cols=35  Identities=26%  Similarity=0.121  Sum_probs=23.9

Q ss_pred             CHHHHHHHHHHHHHHhc------------CCcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYTLDN------------SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~------------~~~~iiEaPTGtGKTls~   66 (115)
                      .+.|.+-+.++......            .+-+++.||.|||||+.+
T Consensus       187 ld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLA  233 (437)
T 4b4t_I          187 LESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLA  233 (437)
T ss_dssp             CHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHH
Confidence            46777766665554221            145889999999999753

>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=91.22  E-value=0.11  Score=40.01  Aligned_cols=36  Identities=17%  Similarity=0.198  Sum_probs=22.2

Q ss_pred             CCHHHHHHHHHHH-H-HHhc----CCcEEE--ecCCCCCchHHH
Q psy14273         31 AYDIQSNFMKNLY-Y-TLDN----SKFGIF--ESPTGTGKSLSL   66 (115)
Q Consensus        31 ~r~~Q~e~m~~I~-~-~l~~----~~~~ii--EaPTGtGKTls~   66 (115)
                      -|..+.+.+.... . ++..    ...++|  .||.|+|||..+
T Consensus        26 gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           26 VRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             SSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHH
T ss_pred             ChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHH
Confidence            4555555444433 2 2222    357888  999999999654

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=91.20  E-value=0.089  Score=36.44  Aligned_cols=17  Identities=18%  Similarity=0.040  Sum_probs=14.5

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ...+++.||+|+|||..
T Consensus         5 ~~~i~l~G~~GsGKst~   21 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSV   21 (185)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            46789999999999953

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=91.05  E-value=0.076  Score=37.93  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=16.1

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..+..++|.||+|+|||.
T Consensus         9 ~~~~~~i~l~G~sGsGKsT   27 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGT   27 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHH
T ss_pred             cccCCEEEEECCCCCCHHH
Confidence            4467889999999999985

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=91.04  E-value=0.16  Score=37.24  Aligned_cols=33  Identities=24%  Similarity=0.096  Sum_probs=24.8

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+...++.||.|+|||.++|--+..+. ..+.++
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~-~~g~kV   39 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAK-IAKQKI   39 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHH-HTTCCE
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHH-HCCCEE
Confidence            456788999999999988877766665 445554

>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=91.02  E-value=0.053  Score=37.70  Aligned_cols=19  Identities=21%  Similarity=0.237  Sum_probs=16.1

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+++.||+|+|||.
T Consensus         6 i~~g~~i~l~G~~GsGKST   24 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKST   24 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHH
T ss_pred             CCCCeEEEEECCCCCCHHH
Confidence            4567789999999999985

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=90.97  E-value=0.12  Score=36.31  Aligned_cols=23  Identities=13%  Similarity=0.163  Sum_probs=18.0

Q ss_pred             HhcCCcEEEecCCCCCchHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~   68 (115)
                      +..|..+++.||+|+|||.-.+.
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~~   39 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLALQ   39 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHHH
T ss_pred             CcCCEEEEEECCCCCCHHHHHHH
Confidence            44567899999999999965443

>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=90.94  E-value=0.25  Score=40.09  Aligned_cols=29  Identities=14%  Similarity=0.027  Sum_probs=20.3

Q ss_pred             HHHHHHHHHhcC---CcEEEecCCCCCchHHH
Q psy14273         38 FMKNLYYTLDNS---KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        38 ~m~~I~~~l~~~---~~~iiEaPTGtGKTls~   66 (115)
                      ....+.......   ..++|.||+|+|||..+
T Consensus       116 a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa  147 (440)
T 2z4s_A          116 AYHAALEVAKHPGRYNPLFIYGGVGLGKTHLL  147 (440)
T ss_dssp             HHHHHHHHHHSTTSSCCEEEECSSSSSHHHHH
T ss_pred             HHHHHHHHHhCCCCCCeEEEECCCCCCHHHHH
Confidence            444555555443   47999999999999653

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=90.87  E-value=0.069  Score=38.78  Aligned_cols=19  Identities=26%  Similarity=0.445  Sum_probs=11.8

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.|.||+|+|||..
T Consensus        25 ~~G~ii~l~Gp~GsGKSTl   43 (231)
T 3lnc_A           25 SVGVILVLSSPSGCGKTTV   43 (231)
T ss_dssp             ECCCEEEEECSCC----CH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3467888999999999854

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.87  E-value=0.13  Score=42.50  Aligned_cols=34  Identities=29%  Similarity=0.312  Sum_probs=23.2

Q ss_pred             CHHHHHHHHHHHHH-Hhc-----------CCcEEEecCCCCCchHH
Q psy14273         32 YDIQSNFMKNLYYT-LDN-----------SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        32 r~~Q~e~m~~I~~~-l~~-----------~~~~iiEaPTGtGKTls   65 (115)
                      ...|.+-++++... +..           .+-+++.||.|||||+.
T Consensus       153 l~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          153 LTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLL  198 (405)
T ss_dssp             CHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHH
Confidence            46676666655544 221           24689999999999975

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=90.82  E-value=0.12  Score=41.87  Aligned_cols=42  Identities=10%  Similarity=-0.003  Sum_probs=27.8

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.+...+..|..++|.|++|+|||.-.+.-+...+...+.+|
T Consensus       194 D~~~gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~V  235 (454)
T 2r6a_A          194 DRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENV  235 (454)
T ss_dssp             HHHHSSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCE
T ss_pred             HhhcCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcE
Confidence            333334556678999999999999766655555554444343

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=90.79  E-value=0.13  Score=37.56  Aligned_cols=24  Identities=21%  Similarity=0.196  Sum_probs=15.6

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchH
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .|.=.+..|..++|-||+|+|||.
T Consensus        15 ~isl~i~~G~~~~lvGpsGsGKST   38 (218)
T 1z6g_A           15 VPRGSMNNIYPLVICGPSGVGKGT   38 (218)
T ss_dssp             -------CCCCEEEECSTTSSHHH
T ss_pred             CCceecCCCCEEEEECCCCCCHHH
Confidence            333445678899999999999985

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=90.67  E-value=0.15  Score=35.33  Aligned_cols=19  Identities=21%  Similarity=0.338  Sum_probs=15.9

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..+..++|+||.|+|||.
T Consensus         6 m~~~~~I~l~G~~GsGKsT   24 (196)
T 2c95_A            6 LKKTNIIFVVGGPGSGKGT   24 (196)
T ss_dssp             HTTSCEEEEEECTTSSHHH
T ss_pred             CcCCCEEEEECCCCCCHHH
Confidence            3456789999999999995

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=90.65  E-value=0.084  Score=42.24  Aligned_cols=30  Identities=20%  Similarity=0.467  Sum_probs=20.6

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..+..++|.||||+|||..+ -.++.++..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll-~~l~~~~~~  162 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTI-ASMIDYINQ  162 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHH-HHHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHH-HHHHhhcCc
Confidence            456678999999999999643 333444443

>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=90.56  E-value=0.11  Score=42.06  Aligned_cols=35  Identities=17%  Similarity=0.153  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      ..|.++.+.+.    ..+.+|.  .++..|+||||||.+.+
T Consensus        68 asQ~~Vy~~~~~plv~~~l~G~N~tifAYGqTGSGKTyTm~  108 (366)
T 2zfi_A           68 ASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMM  108 (366)
T ss_dssp             CCHHHHHHHTHHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHHHhcCCeeEEEEeCCCCCCCceEee
Confidence            46877776553    2333553  46679999999999874

>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=90.51  E-value=0.12  Score=36.08  Aligned_cols=18  Identities=22%  Similarity=0.375  Sum_probs=15.3

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|+||.|+|||..
T Consensus         3 ~~~~I~l~G~~GsGKsT~   20 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQ   20 (204)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            467899999999999953

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=90.36  E-value=0.3  Score=48.71  Aligned_cols=40  Identities=18%  Similarity=0.222  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~   68 (115)
                      +.+-+.+..-+-.+++++.....+++.||||+|||.++=+
T Consensus       903 l~~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~~~  942 (2695)
T 4akg_A          903 FSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKT  942 (2695)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHHHH
Confidence            4445556555666777777788899999999999987543

>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=90.34  E-value=0.14  Score=34.61  Aligned_cols=15  Identities=33%  Similarity=0.235  Sum_probs=12.9

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|+|||..
T Consensus         3 ~i~l~G~~GsGKsT~   17 (173)
T 3kb2_A            3 LIILEGPDCCFKSTV   17 (173)
T ss_dssp             EEEEECSSSSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999953

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=90.33  E-value=0.16  Score=35.15  Aligned_cols=18  Identities=17%  Similarity=0.123  Sum_probs=15.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|.|+.|+|||..
T Consensus        10 ~~~~i~i~G~~GsGKst~   27 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTL   27 (180)
T ss_dssp             CCCCEEEECSTTSSHHHH
T ss_pred             cCCeEEEEeCCCCCHHHH
Confidence            456799999999999964

>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=90.28  E-value=0.12  Score=38.44  Aligned_cols=17  Identities=24%  Similarity=0.346  Sum_probs=15.0

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .++.++|.||+|+|||.
T Consensus        18 ~g~~ivl~GPSGaGKsT   34 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSH   34 (197)
T ss_dssp             SCCEEEEECCTTSSHHH
T ss_pred             CCCEEEEECcCCCCHHH
Confidence            46789999999999995

>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=90.25  E-value=0.1  Score=42.13  Aligned_cols=35  Identities=26%  Similarity=0.172  Sum_probs=23.8

Q ss_pred             CHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~   66 (115)
                      +..|.++.+.+.    ..+.+|.  .++..|+||||||.+.
T Consensus        70 ~a~Q~~vy~~~~~~lv~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           70 YAGQDIVFKCLGENILQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             BCCHHHHHHHHHHHHHHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             cccHHHHHHHhhHHHHHHHhCCceeEEEeeCCCCCCCceEE
Confidence            445777765543    3333553  4667999999999997

>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=90.21  E-value=0.11  Score=36.76  Aligned_cols=25  Identities=12%  Similarity=0.045  Sum_probs=18.8

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .+..|..+.|.||+|+|||.-+.+-
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l   45 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTL   45 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHH
Confidence            3445678999999999999654443

>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=90.16  E-value=0.16  Score=36.43  Aligned_cols=21  Identities=19%  Similarity=0.340  Sum_probs=16.1

Q ss_pred             HHhcCCcEEEecCCCCCchHH
Q psy14273         45 TLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .+..|..+.|-||+|+|||.-
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTL   36 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTV   36 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHH
T ss_pred             CCCCCCEEEEECCCCCCHHHH
Confidence            457788999999999999954

>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=90.15  E-value=0.33  Score=36.12  Aligned_cols=31  Identities=19%  Similarity=0.043  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      --|+.+.+   .+.+ +.. ..++|.||.|+|||.-
T Consensus        16 ~gR~~el~---~L~~-l~~-~~v~i~G~~G~GKT~L   46 (357)
T 2fna_A           16 FDREKEIE---KLKG-LRA-PITLVLGLRRTGKSSI   46 (357)
T ss_dssp             CCCHHHHH---HHHH-TCS-SEEEEEESTTSSHHHH
T ss_pred             cChHHHHH---HHHH-hcC-CcEEEECCCCCCHHHH
Confidence            34655544   4445 555 6899999999999964

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=90.15  E-value=0.087  Score=36.43  Aligned_cols=18  Identities=33%  Similarity=0.495  Sum_probs=14.8

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++++||.|+|||..
T Consensus         3 ~g~~I~l~G~~GsGKST~   20 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGTQ   20 (186)
T ss_dssp             CEEEEEEECCTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            356789999999999953

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=90.10  E-value=0.17  Score=41.06  Aligned_cols=35  Identities=14%  Similarity=0.135  Sum_probs=23.7

Q ss_pred             HHHHHHHHHHH----HHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~----~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.++.+.+.    ..+.+|  ..++..|.||||||.+.+
T Consensus        83 ~sQ~~Vy~~~~~plv~~~l~G~N~tifAYGQTGSGKTyTM~  123 (359)
T 3nwn_A           83 ASQDLVYETVAKDVVSQALDGYNGTIMCYGQTGAGKTYTMM  123 (359)
T ss_dssp             CCHHHHHHHHTHHHHHHHHTTCCEEEEEEESTTSSHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCEEEEEeCCCCCCccEEeC
Confidence            35777666543    333355  346679999999999875

>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=90.09  E-value=0.22  Score=34.37  Aligned_cols=23  Identities=22%  Similarity=0.278  Sum_probs=17.5

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ..+|.||+|+|||.-  +-+|.++.
T Consensus        28 ~~~i~G~NGsGKStl--l~ai~~~l   50 (182)
T 3kta_A           28 FTAIVGANGSGKSNI--GDAILFVL   50 (182)
T ss_dssp             EEEEEECTTSSHHHH--HHHHHHHT
T ss_pred             cEEEECCCCCCHHHH--HHHHHHHH
Confidence            678999999999953  45566654

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=90.07  E-value=0.16  Score=42.33  Aligned_cols=36  Identities=22%  Similarity=0.219  Sum_probs=24.6

Q ss_pred             CHHHHHHHHHHHH----HHhcC--CcEEEecCCCCCchHHHH
Q psy14273         32 YDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        32 r~~Q~e~m~~I~~----~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      +..|.++.+.+..    .+.+|  ..++..|.||||||.+.+
T Consensus       114 ~asQ~~Vy~~~~~plv~~~l~GyN~tIfAYGQTGSGKTyTM~  155 (443)
T 2owm_A          114 YATQEHVYDSLGEEFLDHNFEGYHTCIFAYGQTGSGKSYTMM  155 (443)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTCCEEEEEESSTTSSHHHHHT
T ss_pred             CCCHHHHHHhhhhhHHHHhhcCCceEEEEeCCCCCCCCEEee
Confidence            3567777765533    23355  346679999999999873

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=90.06  E-value=0.092  Score=36.81  Aligned_cols=21  Identities=19%  Similarity=0.229  Sum_probs=16.7

Q ss_pred             hcCCcEEEecCCCCCchHHHH
Q psy14273         47 DNSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L   67 (115)
                      ..|..+++.||+|+|||.-+=
T Consensus         7 ~~gei~~l~G~nGsGKSTl~~   27 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTFAK   27 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHH
Confidence            456788999999999996543

>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=90.04  E-value=0.21  Score=34.65  Aligned_cols=24  Identities=17%  Similarity=0.111  Sum_probs=18.0

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ...+|.||+|+|||.-  +-|+.|+.
T Consensus        24 g~~~I~G~NGsGKSti--l~Ai~~~l   47 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSL--LDAILVGL   47 (149)
T ss_dssp             EEEEEECCTTSSHHHH--HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHH--HHHHHHHH
Confidence            4678899999999954  55566654

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=90.01  E-value=0.12  Score=35.10  Aligned_cols=14  Identities=29%  Similarity=0.254  Sum_probs=12.6

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .+++.||.|+|||.
T Consensus         4 ~I~i~G~~GsGKST   17 (181)
T 1ly1_A            4 IILTIGCPGSGKST   17 (181)
T ss_dssp             EEEEECCTTSSHHH
T ss_pred             EEEEecCCCCCHHH
Confidence            57899999999985

>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=90.01  E-value=0.37  Score=40.24  Aligned_cols=17  Identities=41%  Similarity=0.503  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCchHHH
Q psy14273         50 KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~   66 (115)
                      +.++|.||+|||||+.+
T Consensus        50 ~gvLL~GppGtGKT~La   66 (476)
T 2ce7_A           50 KGILLVGPPGTGKTLLA   66 (476)
T ss_dssp             SEEEEECCTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            45889999999999753

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=89.88  E-value=0.33  Score=35.78  Aligned_cols=29  Identities=21%  Similarity=0.323  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|...++.    +..|..+.+-||+|+|||.-
T Consensus        10 ~g~~~~l~~----i~~Ge~~~liG~nGsGKSTL   38 (208)
T 3b85_A           10 LGQKHYVDA----IDTNTIVFGLGPAGSGKTYL   38 (208)
T ss_dssp             HHHHHHHHH----HHHCSEEEEECCTTSSTTHH
T ss_pred             HhHHHHHHh----ccCCCEEEEECCCCCCHHHH
Confidence            345554444    47888999999999999854

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=89.85  E-value=0.21  Score=37.00  Aligned_cols=28  Identities=25%  Similarity=0.341  Sum_probs=19.1

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+..++||||.|+|||.-. --+..++..
T Consensus         5 ~g~~i~~eG~~gsGKsT~~-~~l~~~l~~   32 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTNR-DYLAERLRE   32 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHH-HHHHHHHHT
T ss_pred             CceEEEEEcCCCCCHHHHH-HHHHHHHHH
Confidence            4678999999999998532 223345543

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=89.78  E-value=0.13  Score=35.70  Aligned_cols=14  Identities=29%  Similarity=0.166  Sum_probs=12.5

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+|+.|+|||.
T Consensus         2 ~I~i~G~~GsGKsT   15 (205)
T 2jaq_A            2 KIAIFGTVGAGKST   15 (205)
T ss_dssp             EEEEECCTTSCHHH
T ss_pred             EEEEECCCccCHHH
Confidence            57899999999995

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=89.74  E-value=0.29  Score=36.33  Aligned_cols=30  Identities=20%  Similarity=0.263  Sum_probs=20.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      .|..++|||+.|+|||.- +-.+..++...+
T Consensus         2 ~g~~i~~eG~~gsGKsT~-~~~l~~~l~~~~   31 (213)
T 4tmk_A            2 RSKYIVIEGLEGAGKTTA-RNVVVETLEQLG   31 (213)
T ss_dssp             CCCEEEEEECTTSCHHHH-HHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHH-HHHHHHHHHHcC
Confidence            367899999999999854 233345565544

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=89.70  E-value=0.12  Score=36.12  Aligned_cols=17  Identities=35%  Similarity=0.432  Sum_probs=14.4

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|+|+.|+|||.-
T Consensus         4 ~~~I~i~G~~GsGKsT~   20 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQ   20 (213)
T ss_dssp             CEEEEEECCTTSSHHHH
T ss_pred             CeEEEEEcCCCCCHHHH
Confidence            45789999999999853

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=89.65  E-value=0.15  Score=41.23  Aligned_cols=42  Identities=14%  Similarity=0.072  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.+..-+..|..++|.|++|+|||.-.+--+...+...+.++
T Consensus       191 D~~lgGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~v  232 (444)
T 2q6t_A          191 DQLIGTLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGV  232 (444)
T ss_dssp             HHHHCCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCE
T ss_pred             hhhcCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeE
Confidence            333334555678999999999999766655555554444444

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=89.63  E-value=0.18  Score=40.83  Aligned_cols=17  Identities=41%  Similarity=0.474  Sum_probs=14.1

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|.||||+|||.-
T Consensus        40 ~~lIvI~GPTgsGKTtL   56 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRL   56 (339)
T ss_dssp             CEEEEEECSTTSSHHHH
T ss_pred             CceEEEECCCCCCHHHH
Confidence            35789999999999953

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=89.58  E-value=0.13  Score=37.04  Aligned_cols=17  Identities=12%  Similarity=0.184  Sum_probs=14.4

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      ....++|+||.|+|||.
T Consensus         4 ~~~~I~l~G~~GsGKsT   20 (222)
T 1zak_A            4 DPLKVMISGAPASGKGT   20 (222)
T ss_dssp             CSCCEEEEESTTSSHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            34679999999999985

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=89.58  E-value=0.18  Score=34.50  Aligned_cols=17  Identities=24%  Similarity=0.302  Sum_probs=14.3

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..+++.|+.|+|||..
T Consensus         3 ~~~i~l~G~~GsGKST~   19 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            45789999999999854

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.55  E-value=0.16  Score=42.79  Aligned_cols=16  Identities=44%  Similarity=0.588  Sum_probs=14.0

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +-++|.||.|||||+.
T Consensus       244 rGILLyGPPGTGKTlL  259 (467)
T 4b4t_H          244 KGILLYGPPGTGKTLC  259 (467)
T ss_dssp             SEEEECSCTTSSHHHH
T ss_pred             CceEeeCCCCCcHHHH
Confidence            5688999999999965

>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=89.51  E-value=0.27  Score=35.70  Aligned_cols=31  Identities=10%  Similarity=-0.113  Sum_probs=21.1

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+.|.|+.|+|||. ++..++.++...+.++
T Consensus         5 ~~i~i~G~sGsGKTT-l~~~L~~~l~~~g~~v   35 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTT-LMEKWVAAAVREGWRV   35 (169)
T ss_dssp             CEEEEECCTTSSHHH-HHHHHHHHHHHTTCCE
T ss_pred             EEEEEECCCCCCHHH-HHHHHHHhhHhcCCee
Confidence            357789999999985 4445566665555444

>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=89.46  E-value=0.51  Score=39.65  Aligned_cols=49  Identities=12%  Similarity=0.172  Sum_probs=36.5

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ..||.++|.|..++..+    .....+++..|-|+|||.....-++.++...+
T Consensus       159 ~~~~~l~p~Q~~i~~~l----~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~  207 (592)
T 3cpe_A          159 VIKVQLRDYQRDMLKIM----SSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK  207 (592)
T ss_dssp             SBBCCCCHHHHHHHHHH----HHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS
T ss_pred             cccCcCCHHHHHHHHhh----ccccEEEEEEcCccChHHHHHHHHHHHHHhCC
Confidence            36788999999998876    24577999999999999876544444444433

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=89.46  E-value=0.33  Score=37.18  Aligned_cols=15  Identities=20%  Similarity=0.317  Sum_probs=13.0

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..+|+.||.|+|||.
T Consensus        34 ~livl~G~sGsGKST   48 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTS   48 (287)
T ss_dssp             EEEEEECCTTSCTHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            358899999999985

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=89.43  E-value=0.14  Score=37.10  Aligned_cols=18  Identities=17%  Similarity=0.230  Sum_probs=14.6

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      ....++|+||.|+|||.-
T Consensus         6 ~~~~I~l~G~~GsGKsT~   23 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTV   23 (227)
T ss_dssp             -CCEEEEEECTTSSHHHH
T ss_pred             cCcEEEEECCCCCCHHHH
Confidence            456799999999999953

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=89.38  E-value=0.28  Score=35.38  Aligned_cols=30  Identities=23%  Similarity=0.300  Sum_probs=19.7

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ..++|.||.|+|||. ++..++..+...+.+
T Consensus         7 ~~i~i~G~sGsGKTT-l~~~l~~~l~~~g~~   36 (174)
T 1np6_A            7 PLLAFAAWSGTGKTT-LLKKLIPALCARGIR   36 (174)
T ss_dssp             CEEEEECCTTSCHHH-HHHHHHHHHHHTTCC
T ss_pred             eEEEEEeCCCCCHHH-HHHHHHHhccccCCc
Confidence            467889999999985 444445555444333

>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=89.37  E-value=0.31  Score=38.26  Aligned_cols=26  Identities=19%  Similarity=0.155  Sum_probs=19.5

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      .+.++++-||||+|||..+-.-+..+
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~   59 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLRE   59 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHH
Confidence            56789999999999997654443333

>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=89.34  E-value=0.19  Score=40.57  Aligned_cols=17  Identities=29%  Similarity=0.434  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|.||||+|||.-
T Consensus         3 ~~~i~i~GptgsGKt~l   19 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKT   19 (322)
T ss_dssp             CEEEEEECCTTSCHHHH
T ss_pred             CcEEEEECCCcCCHHHH
Confidence            34678999999999953

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=89.28  E-value=0.22  Score=38.52  Aligned_cols=35  Identities=11%  Similarity=0.169  Sum_probs=24.3

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .+..-+..|..++|.|++|+|||.-.+.-+...+.
T Consensus        60 ~~lgGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~   94 (315)
T 3bh0_A           60 RMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSD   94 (315)
T ss_dssp             HHHSSBCTTCEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             hhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            33344556788999999999999655555555544

>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=89.20  E-value=0.43  Score=43.63  Aligned_cols=42  Identities=17%  Similarity=0.148  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ....+.|.+.+.      ..+++++|.|+-|||||.+++-=++..+..
T Consensus         9 ~~~t~eQ~~~i~------~~~~~~~v~a~AGSGKT~vl~~ri~~ll~~   50 (1232)
T 3u4q_A            9 STWTDDQWNAIV------STGQDILVAAAAGSGKTAVLVERMIRKITA   50 (1232)
T ss_dssp             -CCCHHHHHHHH------CCSSCEEEEECTTCCHHHHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHh------CCCCCEEEEecCCCcHHHHHHHHHHHHHhc
Confidence            345789998665      247799999999999999877766665554

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=89.10  E-value=0.14  Score=38.37  Aligned_cols=14  Identities=29%  Similarity=0.453  Sum_probs=12.3

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|.||||||||.
T Consensus         3 li~I~G~~GSGKST   16 (253)
T 2ze6_A            3 LHLIYGPTCSGKTD   16 (253)
T ss_dssp             EEEEECCTTSSHHH
T ss_pred             EEEEECCCCcCHHH
Confidence            47899999999985

>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=89.09  E-value=0.17  Score=37.62  Aligned_cols=20  Identities=30%  Similarity=0.551  Sum_probs=15.6

Q ss_pred             HHhcCCcEEEecCCCCCchH
Q psy14273         45 TLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTl   64 (115)
                      .+..|..++|.||+|+|||.
T Consensus        12 ~~~~G~ii~l~GpsGsGKST   31 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSS   31 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHH
T ss_pred             cCCCCcEEEEECCCCCCHHH
Confidence            45568899999999999995

>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=89.05  E-value=0.14  Score=35.41  Aligned_cols=17  Identities=24%  Similarity=0.233  Sum_probs=14.3

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|+|+.|+|||..
T Consensus         5 ~~~I~l~G~~GsGKST~   21 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTL   21 (193)
T ss_dssp             CEEEEEEESTTSSHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45789999999999953

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=88.98  E-value=0.21  Score=35.42  Aligned_cols=19  Identities=16%  Similarity=0.356  Sum_probs=15.4

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..+..++|.||.|+|||..
T Consensus        27 ~~g~~i~l~G~~GsGKSTl   45 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTI   45 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHH
T ss_pred             CCCcEEEEECCCCCCHHHH
Confidence            3567899999999999853

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=88.88  E-value=0.23  Score=33.84  Aligned_cols=17  Identities=29%  Similarity=0.389  Sum_probs=14.3

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|.||.|+|||..
T Consensus         4 ~~~i~l~G~~GsGKSTl   20 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTI   20 (173)
T ss_dssp             CCCEEEECCTTSCHHHH
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            46789999999999853

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=88.83  E-value=0.15  Score=34.95  Aligned_cols=17  Identities=18%  Similarity=0.171  Sum_probs=14.0

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|+|+.|||||..
T Consensus         3 ~~~I~l~G~~GsGKsT~   19 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQ   19 (196)
T ss_dssp             CEEEEEECCTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            34688999999999854

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=88.81  E-value=0.15  Score=34.92  Aligned_cols=14  Identities=43%  Similarity=0.639  Sum_probs=12.5

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+||.|+|||.
T Consensus         3 ~I~i~G~~GsGKsT   16 (194)
T 1nks_A            3 IGIVTGIPGVGKST   16 (194)
T ss_dssp             EEEEEECTTSCHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57899999999984

>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=88.79  E-value=0.25  Score=36.96  Aligned_cols=26  Identities=27%  Similarity=0.354  Sum_probs=19.8

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGIL   71 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al   71 (115)
                      +..|..++|.||+|+|||.-++.-+.
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHHHH
Confidence            45678899999999999976554443

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=88.76  E-value=0.32  Score=41.99  Aligned_cols=28  Identities=21%  Similarity=0.246  Sum_probs=22.1

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..|+++-|.||+|||..+-..++..+..
T Consensus       214 ~pHlLIaG~TGSGKS~~L~tlI~sLl~~  241 (574)
T 2iut_A          214 MPHLLVAGTTGSGKSVGVNAMLLSILFK  241 (574)
T ss_dssp             SCCEEEECCTTSSHHHHHHHHHHHHHTT
T ss_pred             CCeeEEECCCCCCHHHHHHHHHHHHHHh
Confidence            5799999999999998876666655543

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=88.74  E-value=0.38  Score=34.26  Aligned_cols=28  Identities=14%  Similarity=-0.001  Sum_probs=18.9

Q ss_pred             HHHHHHHHHhc-----CCcEEEecCCCCCchHH
Q psy14273         38 FMKNLYYTLDN-----SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        38 ~m~~I~~~l~~-----~~~~iiEaPTGtGKTls   65 (115)
                      .++.+...+.+     +..+.|.||+|+|||..
T Consensus         6 ~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl   38 (201)
T 1rz3_A            6 RIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTL   38 (201)
T ss_dssp             HHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHH
T ss_pred             HHHHHHHHHHHhccCCCeEEEEECCCCCCHHHH
Confidence            34455555543     34678899999999854

>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=88.73  E-value=0.28  Score=36.36  Aligned_cols=16  Identities=31%  Similarity=0.380  Sum_probs=13.7

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      ...++|.||.|+|||.
T Consensus        29 ~~~I~l~G~~GsGKsT   44 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGT   44 (243)
T ss_dssp             CEEEEEECCTTSSHHH
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4578999999999984

>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=88.69  E-value=0.22  Score=39.32  Aligned_cols=28  Identities=29%  Similarity=0.341  Sum_probs=22.8

Q ss_pred             HHHHHHHHHHhcCCcEEEecCCCCCchH
Q psy14273         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        37 e~m~~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      ..++.|.-.+..|..+.|-||+|+|||.
T Consensus       114 ~vL~~vsl~i~~Ge~vaIvGpsGsGKST  141 (305)
T 2v9p_A          114 NALKLWLKGIPKKNCLAFIGPPNTGKSM  141 (305)
T ss_dssp             HHHHHHHHTCTTCSEEEEECSSSSSHHH
T ss_pred             hhhccceEEecCCCEEEEECCCCCcHHH
Confidence            4566666667788999999999999984

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=88.65  E-value=0.17  Score=35.50  Aligned_cols=18  Identities=39%  Similarity=0.558  Sum_probs=15.1

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|+|+.|+|||..
T Consensus         9 ~~~~I~l~G~~GsGKST~   26 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQ   26 (212)
T ss_dssp             CSCEEEEEESTTSSHHHH
T ss_pred             cCCEEEEEcCCCCCHHHH
Confidence            456899999999999953

>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=88.53  E-value=0.24  Score=39.00  Aligned_cols=24  Identities=21%  Similarity=0.167  Sum_probs=18.8

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +.-+|.||||+|||.  |+=|+.|+.
T Consensus        26 gl~vi~G~NGaGKT~--ileAI~~~l   49 (371)
T 3auy_A           26 GIVAIIGENGSGKSS--IFEAVFFAL   49 (371)
T ss_dssp             EEEEEEECTTSSHHH--HHHHHHHHH
T ss_pred             CeEEEECCCCCCHHH--HHHHHHHHH
Confidence            467899999999995  366677754

>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=88.52  E-value=0.23  Score=35.53  Aligned_cols=19  Identities=16%  Similarity=0.041  Sum_probs=16.0

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..+..++|+|+.|+|||.
T Consensus        22 ~~~~~~i~~~G~~GsGKsT   40 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKST   40 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHH
T ss_pred             CCCCCEEEEECCCCCCHHH
Confidence            4566789999999999985

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=88.52  E-value=0.12  Score=37.15  Aligned_cols=27  Identities=22%  Similarity=0.396  Sum_probs=18.4

Q ss_pred             HHHHHHHHHh----cCCcEEEecCCCCCchH
Q psy14273         38 FMKNLYYTLD----NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        38 ~m~~I~~~l~----~~~~~iiEaPTGtGKTl   64 (115)
                      +++.|...+.    .+..+.|-||+|+|||.
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKST   37 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKST   37 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHH
Confidence            4444544443    34577899999999984

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=88.45  E-value=0.31  Score=35.84  Aligned_cols=24  Identities=17%  Similarity=0.382  Sum_probs=17.6

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      .+.++.|+.|||||+....-++..
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHH
Confidence            367899999999998654443343

>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=88.43  E-value=0.21  Score=35.78  Aligned_cols=16  Identities=31%  Similarity=0.418  Sum_probs=14.0

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..++|+||.|+|||.
T Consensus         4 ~~~I~l~G~~GsGKsT   19 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGT   19 (220)
T ss_dssp             CCEEEEECCTTSSHHH
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4678999999999985

>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=88.39  E-value=0.19  Score=35.28  Aligned_cols=18  Identities=22%  Similarity=0.290  Sum_probs=15.4

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|+|+.|+|||..
T Consensus         8 ~~~~I~l~G~~GsGKsT~   25 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQ   25 (215)
T ss_dssp             CCCEEEEEESTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            467899999999999953

>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=88.38  E-value=0.17  Score=36.96  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=14.3

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .|..+.|+||.|+|||.
T Consensus        19 ~g~~i~i~G~~GsGKST   35 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTT   35 (230)
T ss_dssp             CCEEEEEECSTTSCHHH
T ss_pred             CceEEEEECCCCCCHHH
Confidence            35678899999999985

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=88.37  E-value=0.28  Score=37.34  Aligned_cols=16  Identities=25%  Similarity=0.221  Sum_probs=13.3

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..++|.||||+|||.
T Consensus        34 g~~ilI~GpsGsGKSt   49 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSE   49 (205)
T ss_dssp             TEEEEEECCCTTTTHH
T ss_pred             CEEEEEECCCCCCHHH
Confidence            3458899999999984

>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=88.21  E-value=0.33  Score=35.21  Aligned_cols=26  Identities=15%  Similarity=0.056  Sum_probs=19.3

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ...+|.||+|+|||..  +-|+.|+...
T Consensus        24 ~~~~I~G~NgsGKSti--l~ai~~~l~g   49 (203)
T 3qks_A           24 GINLIIGQNGSGKSSL--LDAILVGLYW   49 (203)
T ss_dssp             EEEEEECCTTSSHHHH--HHHHHHHHHT
T ss_pred             CeEEEEcCCCCCHHHH--HHHHHHHhcC
Confidence            4678899999999954  5556776553

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=88.04  E-value=0.18  Score=37.48  Aligned_cols=32  Identities=16%  Similarity=-0.095  Sum_probs=14.7

Q ss_pred             HHHHHHHHHHHHHh-cCCcEEEecCCCCCchHH
Q psy14273         34 IQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~-~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++........ ++..++|||+.|+|||.-
T Consensus         8 ~~~~~~~~~~~~~~~~~~~I~ieG~~GsGKST~   40 (263)
T 1p5z_B            8 PKRSCPSFSASSEGTRIKKISIEGNIAAGKSTF   40 (263)
T ss_dssp             ---------------CCEEEEEECSTTSSHHHH
T ss_pred             hhccCCCCcccccccCceEEEEECCCCCCHHHH
Confidence            33334444333332 346789999999999953

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=88.01  E-value=0.22  Score=34.19  Aligned_cols=17  Identities=24%  Similarity=0.364  Sum_probs=14.3

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|.||.|+|||..
T Consensus         8 g~~i~l~G~~GsGKSTl   24 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAV   24 (175)
T ss_dssp             SEEEEEECSTTSCHHHH
T ss_pred             CcEEEEEcCCCCCHHHH
Confidence            45788999999999853

>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=87.96  E-value=0.27  Score=39.78  Aligned_cols=25  Identities=24%  Similarity=0.643  Sum_probs=18.2

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchH
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTl   64 (115)
                      +.+.-.+..+..+++.||+|+|||.
T Consensus       160 ~~~~~~i~~~~~i~l~G~~GsGKST  184 (377)
T 1svm_A          160 KCMVYNIPKKRYWLFKGPIDSGKTT  184 (377)
T ss_dssp             HHHHHCCTTCCEEEEECSTTSSHHH
T ss_pred             HhcccccCCCCEEEEECCCCCCHHH
Confidence            3333334566789999999999985

>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=87.91  E-value=0.21  Score=36.59  Aligned_cols=15  Identities=40%  Similarity=0.623  Sum_probs=13.0

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.+||.||.|+|||.
T Consensus         2 RpIVi~GPSG~GK~T   16 (186)
T 1ex7_A            2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CEEEEECCCCCCHHH
Confidence            458999999999985

>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=87.81  E-value=0.23  Score=34.35  Aligned_cols=18  Identities=17%  Similarity=0.156  Sum_probs=14.9

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|.|+.|+|||..
T Consensus         4 ~g~~i~l~G~~GsGKST~   21 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTV   21 (179)
T ss_dssp             CCEEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            456788999999999853

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=87.76  E-value=0.31  Score=37.02  Aligned_cols=15  Identities=33%  Similarity=0.527  Sum_probs=13.1

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .+++.||+|+|||+-
T Consensus        46 GvlL~Gp~GtGKTtL   60 (274)
T 2x8a_A           46 GVLLAGPPGCGKTLL   60 (274)
T ss_dssp             EEEEESSTTSCHHHH
T ss_pred             eEEEECCCCCcHHHH
Confidence            488999999999964

>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=87.74  E-value=0.29  Score=34.34  Aligned_cols=18  Identities=22%  Similarity=0.237  Sum_probs=15.1

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|.|+.|+|||..
T Consensus         9 ~~~~I~l~G~~GsGKSTv   26 (184)
T 1y63_A            9 KGINILITGTPGTGKTSM   26 (184)
T ss_dssp             SSCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            356799999999999954

>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=87.60  E-value=0.28  Score=34.74  Aligned_cols=19  Identities=16%  Similarity=0.305  Sum_probs=15.9

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+.+.||.|+|||.
T Consensus        30 i~~Ge~v~L~G~nGaGKTT   48 (158)
T 1htw_A           30 TEKAIMVYLNGDLGAGKTT   48 (158)
T ss_dssp             CSSCEEEEEECSTTSSHHH
T ss_pred             cCCCCEEEEECCCCCCHHH
Confidence            3567788899999999984

>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=87.35  E-value=0.25  Score=33.54  Aligned_cols=16  Identities=13%  Similarity=0.098  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.|+.|+|||..
T Consensus         3 ~~I~l~G~~GsGKsT~   18 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTV   18 (173)
T ss_dssp             CCEEEESCTTSSHHHH
T ss_pred             ceEEEECCCCCCHHHH
Confidence            3688999999999853

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=87.34  E-value=0.94  Score=37.97  Aligned_cols=35  Identities=23%  Similarity=0.245  Sum_probs=22.7

Q ss_pred             CHHHHHHHHHHHHHHhc-----------CCcEEEecCCCCCchHHH
Q psy14273         32 YDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~-----------~~~~iiEaPTGtGKTls~   66 (115)
                      .+.+..-+..+...+.+           .+.++|.||+|||||+.+
T Consensus        36 ~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLa   81 (499)
T 2dhr_A           36 AEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   81 (499)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHH
T ss_pred             cHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHH
Confidence            34555555555555543           134889999999999653

>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=87.33  E-value=0.35  Score=40.44  Aligned_cols=18  Identities=22%  Similarity=0.333  Sum_probs=15.4

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      +.+++|.||+|+|||..+
T Consensus       108 g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          108 GPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             SCEEEEESSSSSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            568999999999999653

>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=87.33  E-value=0.4  Score=33.96  Aligned_cols=19  Identities=21%  Similarity=0.167  Sum_probs=15.6

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..+..++|.||.|+|||..
T Consensus        23 ~~g~~i~l~G~sGsGKSTl   41 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTL   41 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHH
T ss_pred             CCCeEEEEECCCCCCHHHH
Confidence            4567888999999999853

>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=87.33  E-value=0.32  Score=39.07  Aligned_cols=16  Identities=31%  Similarity=0.374  Sum_probs=13.3

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||||+|||.-
T Consensus        11 ~~i~i~GptgsGKt~l   26 (316)
T 3foz_A           11 KAIFLMGPTASGKTAL   26 (316)
T ss_dssp             EEEEEECCTTSCHHHH
T ss_pred             cEEEEECCCccCHHHH
Confidence            4578899999999953

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=87.18  E-value=0.3  Score=34.41  Aligned_cols=16  Identities=25%  Similarity=0.208  Sum_probs=13.9

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||.|+|||..
T Consensus        19 ~~I~l~G~~GsGKSTl   34 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSV   34 (202)
T ss_dssp             SCEEEECSTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4789999999999953

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=87.16  E-value=0.23  Score=34.57  Aligned_cols=17  Identities=18%  Similarity=0.192  Sum_probs=14.3

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++++|+.|+|||..
T Consensus        13 ~~~i~l~G~~GsGKsT~   29 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTI   29 (186)
T ss_dssp             CEEEEEECCTTSSHHHH
T ss_pred             CcEEEEEcCCCCCHHHH
Confidence            45788999999999853

>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=87.12  E-value=0.23  Score=34.00  Aligned_cols=16  Identities=19%  Similarity=0.252  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|+|+.|+|||..
T Consensus         7 ~~I~l~G~~GsGKsT~   22 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQ   22 (194)
T ss_dssp             EEEEEEESTTSSHHHH
T ss_pred             cEEEEECCCCCCHHHH
Confidence            3688999999999963

>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=87.11  E-value=0.29  Score=34.48  Aligned_cols=16  Identities=25%  Similarity=0.387  Sum_probs=13.7

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|+||.|+|||..
T Consensus        21 ~~I~l~G~~GsGKST~   36 (201)
T 2cdn_A           21 MRVLLLGPPGAGKGTQ   36 (201)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4688999999999953

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=87.07  E-value=0.23  Score=37.43  Aligned_cols=19  Identities=37%  Similarity=0.543  Sum_probs=13.1

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..++||||.|+|||.-
T Consensus        23 ~~g~~I~~eG~~GsGKsT~   41 (227)
T 3v9p_A           23 ARGKFITFEGIDGAGKTTH   41 (227)
T ss_dssp             CCCCEEEEECCC---CHHH
T ss_pred             cCCeEEEEECCCCCCHHHH
Confidence            4578899999999999853

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=87.06  E-value=0.27  Score=33.75  Aligned_cols=14  Identities=36%  Similarity=0.553  Sum_probs=12.4

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+|+.|||||.
T Consensus         2 ~I~l~G~~GsGKsT   15 (195)
T 2pbr_A            2 LIAFEGIDGSGKTT   15 (195)
T ss_dssp             EEEEECSTTSCHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57899999999985

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=86.95  E-value=0.22  Score=34.16  Aligned_cols=17  Identities=29%  Similarity=0.423  Sum_probs=10.4

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|+|+.|+|||..
T Consensus         5 ~~~I~l~G~~GsGKST~   21 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHT   21 (183)
T ss_dssp             CCEEEEECCC----CHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            46789999999999953

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=86.79  E-value=0.35  Score=36.75  Aligned_cols=30  Identities=13%  Similarity=0.154  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHHhc---CCcEEEecCCCCCchHH
Q psy14273         36 SNFMKNLYYTLDN---SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        36 ~e~m~~I~~~l~~---~~~~iiEaPTGtGKTls   65 (115)
                      ...++.+.-.+..   +..++|.||.|+|||..
T Consensus        32 ~~~l~~~~~~i~~~l~g~~i~l~G~~GsGKSTl   64 (250)
T 3nwj_A           32 QQILKKKAEEVKPYLNGRSMYLVGMMGSGKTTV   64 (250)
T ss_dssp             CHHHHHHHHTTHHHHTTCCEEEECSTTSCHHHH
T ss_pred             chhhhhhhhhhhhhcCCCEEEEECCCCCCHHHH
Confidence            3466777666667   89999999999999864

>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=86.77  E-value=0.22  Score=34.65  Aligned_cols=16  Identities=44%  Similarity=0.698  Sum_probs=13.2

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||+|+|||..
T Consensus         3 ~ii~l~G~~GaGKSTl   18 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTT   18 (189)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECCCCCcHHHH
Confidence            4578899999999863

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=86.70  E-value=0.32  Score=39.87  Aligned_cols=40  Identities=10%  Similarity=0.112  Sum_probs=27.6

Q ss_pred             HHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        41 ~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+..-+..|..++|.|++|+|||.-.+--+...+.. +.++
T Consensus       189 ~~lgGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~-g~~v  228 (444)
T 3bgw_A          189 RMTYGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN-DDVV  228 (444)
T ss_dssp             HHHSSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT-TCEE
T ss_pred             hhcCCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc-CCEE
Confidence            333345566789999999999997666666666654 4343

>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=86.69  E-value=0.23  Score=37.06  Aligned_cols=18  Identities=33%  Similarity=0.597  Sum_probs=15.5

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.|-||+|+|||.
T Consensus        29 ~~Ge~~~iiG~nGsGKST   46 (235)
T 3tif_A           29 KEGEFVSIMGPSGSGKST   46 (235)
T ss_dssp             CTTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCcHHH
Confidence            457888999999999994

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=86.69  E-value=0.27  Score=34.52  Aligned_cols=16  Identities=19%  Similarity=0.194  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|+||.|+|||..
T Consensus        16 ~~I~l~G~~GsGKsT~   31 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQ   31 (203)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             cEEEEECCCCCCHHHH
Confidence            3688999999999953

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=86.60  E-value=0.27  Score=34.83  Aligned_cols=15  Identities=20%  Similarity=0.224  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|+|||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQ   16 (216)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999853

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=86.58  E-value=0.76  Score=36.41  Aligned_cols=32  Identities=13%  Similarity=0.123  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHhcCC------cEEEecCCCCCchHH
Q psy14273         34 IQSNFMKNLYYTLDNSK------FGIFESPTGTGKSLS   65 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~------~~iiEaPTGtGKTls   65 (115)
                      ...+.+..+...+..+.      .+.|.||+|+|||..
T Consensus        71 ~~~~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl  108 (321)
T 3tqc_A           71 TARQTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTT  108 (321)
T ss_dssp             HHHHHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHH
T ss_pred             cchHHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHH
Confidence            34444555555555553      577899999999954

>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=86.54  E-value=0.3  Score=35.55  Aligned_cols=16  Identities=25%  Similarity=0.470  Sum_probs=14.0

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      ...++|+|+.|+|||.
T Consensus        16 ~~~I~l~G~~GsGKsT   31 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGT   31 (233)
T ss_dssp             CCEEEEECCTTSSHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            4579999999999985

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=86.51  E-value=0.51  Score=34.23  Aligned_cols=29  Identities=28%  Similarity=0.362  Sum_probs=18.6

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .++|||+-|+|||.- +--...++...+..
T Consensus         2 fI~~EG~DGsGKsTq-~~~L~~~L~~~g~~   30 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQ-IQLLAQYLEKRGKK   30 (197)
T ss_dssp             EEEEECSTTSSHHHH-HHHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHH-HHHHHHHHHHCCCc
Confidence            478999999999853 22233566655443

>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=86.45  E-value=0.26  Score=36.54  Aligned_cols=18  Identities=44%  Similarity=0.687  Sum_probs=15.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..++|+||.|+|||.-
T Consensus        25 ~g~~i~i~G~~GsGKsT~   42 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTV   42 (229)
T ss_dssp             CCEEEEEECCTTSCHHHH
T ss_pred             CCeEEEEEcCCCCCHHHH
Confidence            467899999999999853

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=86.39  E-value=0.28  Score=34.63  Aligned_cols=17  Identities=18%  Similarity=0.067  Sum_probs=14.0

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .+..+.|.||+|+|||.
T Consensus         5 ~~~~i~i~G~~GsGKST   21 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTT   21 (211)
T ss_dssp             CCEEEEEEESTTSSHHH
T ss_pred             CcEEEEEECCCCCCHHH
Confidence            45567889999999985

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=86.21  E-value=0.43  Score=37.48  Aligned_cols=37  Identities=14%  Similarity=0.088  Sum_probs=22.7

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .++.+.-.+..+..+.|-||+|+|||.- |-.+..++.
T Consensus        44 ~l~~i~~~~~~g~~v~i~G~~GaGKSTL-l~~l~g~~~   80 (337)
T 2qm8_A           44 LIDAVLPQTGRAIRVGITGVPGVGKSTT-IDALGSLLT   80 (337)
T ss_dssp             HHHHHGGGCCCSEEEEEECCTTSCHHHH-HHHHHHHHH
T ss_pred             HHHhCCcccCCCeEEEEECCCCCCHHHH-HHHHHHhhh
Confidence            4444433344567788999999999953 333334443

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=86.01  E-value=0.69  Score=34.78  Aligned_cols=27  Identities=30%  Similarity=0.417  Sum_probs=18.3

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..++|||+.|+|||.- .-.+..++..
T Consensus        21 ~~~i~~~G~~g~GKst~-~~~l~~~l~~   47 (223)
T 3ld9_A           21 SMFITFEGIDGSGKTTQ-SHLLAEYLSE   47 (223)
T ss_dssp             CEEEEEECSTTSSHHHH-HHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHH-HHHHHHHHhh
Confidence            56789999999999854 2223344444

>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=85.99  E-value=0.31  Score=34.66  Aligned_cols=15  Identities=20%  Similarity=0.226  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|+|||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQ   16 (216)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999853

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=85.98  E-value=0.86  Score=46.32  Aligned_cols=41  Identities=17%  Similarity=0.073  Sum_probs=27.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      +.+-+.+..=+-.+++.+....-+++-||||+|||.++=+-
T Consensus       886 L~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~~L  926 (3245)
T 3vkg_A          886 LVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVY  926 (3245)
T ss_dssp             CCCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHHHH
Confidence            33445555544555666655666888999999999886443

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=85.94  E-value=0.87  Score=36.21  Aligned_cols=33  Identities=9%  Similarity=0.085  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      +.-.++++.+.+....+..+++.+++||||++.
T Consensus       144 ~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~l  176 (387)
T 1ny5_A          144 PKMKEILEKIKKISCAECPVLITGESGVGKEVV  176 (387)
T ss_dssp             HHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHH
T ss_pred             HHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHH
Confidence            455555666666555667899999999999964

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=85.91  E-value=0.34  Score=34.89  Aligned_cols=17  Identities=24%  Similarity=0.286  Sum_probs=14.2

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|+|+.|+|||..
T Consensus         5 ~~~I~l~G~~GsGKsT~   21 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQ   21 (217)
T ss_dssp             CCEEEEEECTTSSHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            45789999999999853

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=85.91  E-value=0.96  Score=31.79  Aligned_cols=40  Identities=18%  Similarity=0.159  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      +...+..+.+...+..  -..+++-|++|+|||. ++...+..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~i~i~G~~g~GKTT-l~~~l~~~   53 (221)
T 2wsm_A           12 AENKRLAEKNREALRESGTVAVNIMGAIGSGKTL-LIERTIER   53 (221)
T ss_dssp             HHHHHHHHHHHHHHHHHTCEEEEEEECTTSCHHH-HHHHHHHH
T ss_pred             hhcHHHHHHHHHhhcccCceEEEEEcCCCCCHHH-HHHHHHHH
Confidence            3444455555555433  2467889999999994 33343433

>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=85.83  E-value=0.27  Score=36.72  Aligned_cols=18  Identities=22%  Similarity=0.233  Sum_probs=15.5

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.|-||+|+|||.
T Consensus        29 ~~Ge~~~i~G~nGsGKST   46 (237)
T 2cbz_A           29 PEGALVAVVGQVGCGKSS   46 (237)
T ss_dssp             CTTCEEEEECSTTSSHHH
T ss_pred             CCCCEEEEECCCCCCHHH
Confidence            457889999999999984

>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=85.82  E-value=0.27  Score=36.69  Aligned_cols=17  Identities=29%  Similarity=0.255  Sum_probs=14.2

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ...++++|+.|+|||..
T Consensus         4 ~~lIvl~G~pGSGKSTl   20 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTF   20 (260)
T ss_dssp             CEEEEEECCTTSSHHHH
T ss_pred             CEEEEEEcCCCCCHHHH
Confidence            45789999999999953

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=85.71  E-value=0.33  Score=32.87  Aligned_cols=15  Identities=20%  Similarity=-0.084  Sum_probs=12.8

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|+|+.|+|||..
T Consensus         2 ~I~l~G~~GsGKsT~   16 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTV   16 (168)
T ss_dssp             EEEEESCTTSCHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            578999999999853

>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=85.66  E-value=0.36  Score=35.33  Aligned_cols=16  Identities=25%  Similarity=0.407  Sum_probs=14.0

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      ...++|.||+|+|||.
T Consensus        27 ~~~i~l~G~~GsGKST   42 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGT   42 (246)
T ss_dssp             CCEEEEECCTTSSHHH
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4689999999999985

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=85.66  E-value=0.44  Score=38.05  Aligned_cols=16  Identities=25%  Similarity=0.218  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||||+|||.-
T Consensus         6 ~~i~i~GptGsGKTtl   21 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDL   21 (323)
T ss_dssp             EEEEEECCTTSCHHHH
T ss_pred             cEEEEECCCCCCHHHH
Confidence            3688999999999954

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=85.63  E-value=0.31  Score=35.80  Aligned_cols=28  Identities=25%  Similarity=0.177  Sum_probs=15.6

Q ss_pred             HHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         38 FMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        38 ~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      .++.|.=.+..+..+.|.||+|+|||..
T Consensus        14 ~l~~isl~i~~g~iigI~G~~GsGKSTl   41 (245)
T 2jeo_A           14 GTENLYFQSMRPFLIGVSGGTASGKSTV   41 (245)
T ss_dssp             ---------CCSEEEEEECSTTSSHHHH
T ss_pred             eecceeccCCCCEEEEEECCCCCCHHHH
Confidence            3444444455666788999999999854

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=85.62  E-value=0.33  Score=33.09  Aligned_cols=15  Identities=27%  Similarity=0.299  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ++++|.|+.|||||.
T Consensus         8 ~~i~l~G~~GsGKST   22 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSS   22 (168)
T ss_dssp             CEEEEESCTTSSHHH
T ss_pred             ceEEEECCCCCCHHH
Confidence            578999999999985

>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=85.44  E-value=0.12  Score=36.45  Aligned_cols=14  Identities=29%  Similarity=0.368  Sum_probs=12.4

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+||.|+|||.
T Consensus         2 ~I~i~G~~GsGKsT   15 (214)
T 1gtv_A            2 LIAIEGVDGAGKRT   15 (214)
T ss_dssp             EEEEEEEEEEEHHH
T ss_pred             EEEEEcCCCCCHHH
Confidence            57899999999984

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=85.29  E-value=0.33  Score=36.27  Aligned_cols=18  Identities=28%  Similarity=0.346  Sum_probs=15.6

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .|..++|||+.|+|||.-
T Consensus         4 ~g~~i~~eG~~g~GKst~   21 (216)
T 3tmk_A            4 RGKLILIEGLDRTGKTTQ   21 (216)
T ss_dssp             CCCEEEEEECSSSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            578899999999999853

>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=85.28  E-value=0.27  Score=36.45  Aligned_cols=18  Identities=22%  Similarity=0.399  Sum_probs=15.5

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.|-||+|+|||.
T Consensus        32 ~~Ge~~~i~G~nGsGKST   49 (229)
T 2pze_A           32 ERGQLLAVAGSTGAGKTS   49 (229)
T ss_dssp             ETTCEEEEECCTTSSHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            457888999999999984

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=85.27  E-value=0.73  Score=34.47  Aligned_cols=33  Identities=15%  Similarity=0.068  Sum_probs=26.5

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ....+++-.++|.|||.+.+..++..+ .++.+|
T Consensus        27 ~~g~i~v~tG~GkGKTTaA~GlalRA~-g~G~rV   59 (196)
T 1g5t_A           27 ERGIIIVFTGNGKGKTTAAFGTAARAV-GHGKNV   59 (196)
T ss_dssp             CCCCEEEEESSSSCHHHHHHHHHHHHH-HTTCCE
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHH-HCCCeE
Confidence            456888889999999999999988777 445555

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=85.27  E-value=0.55  Score=37.20  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=16.9

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ..+|.||||+|||.-  +=+++|+.
T Consensus        25 ~~~i~G~NGaGKTTl--l~ai~~al   47 (365)
T 3qf7_A           25 ITVVEGPNGAGKSSL--FEAISFAL   47 (365)
T ss_dssp             EEEEECCTTSSHHHH--HHHHHHHH
T ss_pred             eEEEECCCCCCHHHH--HHHHHHHh
Confidence            677899999999943  34566663

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=85.27  E-value=0.7  Score=35.42  Aligned_cols=30  Identities=10%  Similarity=0.148  Sum_probs=22.2

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.++.|+|||...+.-+...+. .+.+|
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~~l~~-~G~~V   37 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAHAQLR-QGVRV   37 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHH-TTCCE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHH-CCCCE
Confidence            4888999999999887776665554 45444

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=85.26  E-value=0.57  Score=36.79  Aligned_cols=30  Identities=20%  Similarity=0.080  Sum_probs=19.9

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||+|+|||.....-+..+. ..+.+|
T Consensus       107 vI~ivG~~G~GKTT~~~~LA~~l~-~~g~kV  136 (320)
T 1zu4_A          107 IFMLVGVNGTGKTTSLAKMANYYA-ELGYKV  136 (320)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHH-HTTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HCCCeE
Confidence            577889999999977555544443 344444

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=85.12  E-value=0.51  Score=36.69  Aligned_cols=18  Identities=28%  Similarity=0.244  Sum_probs=14.3

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      ..+.+-||+|+|||..+-
T Consensus       101 ~vi~lvG~nGsGKTTll~  118 (302)
T 3b9q_A          101 AVIMIVGVNGGGKTTSLG  118 (302)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHH
Confidence            467789999999997543

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=85.03  E-value=0.44  Score=38.09  Aligned_cols=41  Identities=12%  Similarity=0.126  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        40 ~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.+..-+..|..++|.|++|+|||.-.+--+...+. .+.+|
T Consensus        37 D~~~gGl~~G~LiiIaG~pG~GKTt~al~ia~~~a~-~g~~V   77 (338)
T 4a1f_A           37 DNYTSGFNKGSLVIIGARPSMGKTSLMMNMVLSALN-DDRGV   77 (338)
T ss_dssp             HHHHCSBCTTCEEEEEECTTSCHHHHHHHHHHHHHH-TTCEE
T ss_pred             HHHhcCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHH-cCCeE
Confidence            344445666788999999999999766655555554 34443

>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=85.01  E-value=0.2  Score=40.94  Aligned_cols=37  Identities=14%  Similarity=0.029  Sum_probs=25.6

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -+..|..++|.|++|+|||.-.+--+...+..++.++
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~v  274 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKV  274 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCE
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcE
Confidence            3455678999999999999766655555554434443

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=84.96  E-value=0.38  Score=34.93  Aligned_cols=14  Identities=29%  Similarity=0.425  Sum_probs=12.5

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+||.|+|||.
T Consensus         2 ~I~l~G~~GsGKsT   15 (223)
T 2xb4_A            2 NILIFGPNGSGKGT   15 (223)
T ss_dssp             EEEEECCTTSCHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57899999999985

>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=84.90  E-value=0.65  Score=36.34  Aligned_cols=40  Identities=15%  Similarity=0.004  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHhc----------CCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDN----------SKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~----------~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      .+.-+.+.+.+.+..          +..+++.||+|+|||.....-+..+
T Consensus        79 ~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l  128 (306)
T 1vma_A           79 ALESLKEIILEILNFDTKLNVPPEPPFVIMVVGVNGTGKTTSCGKLAKMF  128 (306)
T ss_dssp             HHHHHHHHHHHHTCSCCCCCCCSSSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCCcccCCCCeEEEEEcCCCChHHHHHHHHHHHH
Confidence            455555555555532          2357789999999997654444333

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=84.81  E-value=0.28  Score=36.25  Aligned_cols=18  Identities=28%  Similarity=0.447  Sum_probs=15.4

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.+-||+|+|||.
T Consensus        28 ~~Ge~~~iiG~nGsGKST   45 (224)
T 2pcj_A           28 KKGEFVSIIGASGSGKST   45 (224)
T ss_dssp             ETTCEEEEEECTTSCHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            457788899999999994

>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=84.62  E-value=1.3  Score=35.97  Aligned_cols=46  Identities=11%  Similarity=0.147  Sum_probs=34.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .||.+.|.|..++..+.    ..+.+++..|-+.|||.....-++.++..
T Consensus       160 ~p~~L~p~Qk~il~~l~----~~R~~vi~~sRq~GKT~l~a~~~l~~a~~  205 (385)
T 2o0j_A          160 IKVQLRDYQRDMLKIMS----SKRMTVCNLSRQLGKTTVVAIFLAHFVCF  205 (385)
T ss_dssp             EECCCCHHHHHHHHHHH----HSSEEEEEECSSSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCHHHHHHHHhhc----cCcEEEEEEcCcCChhHHHHHHHHHHHHh
Confidence            67888999999988763    34679999999999998655555443433

>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=84.61  E-value=0.35  Score=34.55  Aligned_cols=14  Identities=21%  Similarity=0.062  Sum_probs=12.4

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|+||.|+|||.
T Consensus         2 ~I~l~G~~GsGKsT   15 (214)
T 1e4v_A            2 RIILLGAPVAGKGT   15 (214)
T ss_dssp             EEEEEESTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            47899999999985

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=84.56  E-value=0.53  Score=39.05  Aligned_cols=16  Identities=38%  Similarity=0.434  Sum_probs=13.2

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||||+|||.-
T Consensus         3 ~~i~i~GptgsGKttl   18 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQL   18 (409)
T ss_dssp             EEEEEEECSSSSHHHH
T ss_pred             cEEEEECcchhhHHHH
Confidence            3578999999999943

>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=84.43  E-value=0.35  Score=35.92  Aligned_cols=20  Identities=25%  Similarity=0.522  Sum_probs=16.4

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.|-||+|+|||.-
T Consensus        32 i~~Ge~~~iiG~NGsGKSTL   51 (214)
T 1sgw_A           32 IEKGNVVNFHGPNGIGKTTL   51 (214)
T ss_dssp             EETTCCEEEECCTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34678889999999999853

>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=84.33  E-value=0.34  Score=36.54  Aligned_cols=20  Identities=25%  Similarity=0.518  Sum_probs=16.3

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.+-||+|+|||.-
T Consensus        30 i~~Ge~~~liG~nGsGKSTL   49 (257)
T 1g6h_A           30 VNKGDVTLIIGPNGSGKSTL   49 (257)
T ss_dssp             EETTCEEEEECSTTSSHHHH
T ss_pred             EeCCCEEEEECCCCCCHHHH
Confidence            34578888999999999953

>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=84.33  E-value=0.34  Score=36.47  Aligned_cols=20  Identities=20%  Similarity=0.227  Sum_probs=16.5

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.|-||+|+|||.-
T Consensus        32 i~~Ge~~~i~G~nGsGKSTL   51 (247)
T 2ff7_A           32 IKQGEVIGIVGRSGSGKSTL   51 (247)
T ss_dssp             EETTCEEEEECSTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34678899999999999953

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=84.19  E-value=0.36  Score=36.62  Aligned_cols=20  Identities=25%  Similarity=0.292  Sum_probs=16.5

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.|-||+|+|||.-
T Consensus        43 i~~Ge~~~i~G~nGsGKSTL   62 (260)
T 2ghi_A           43 IPSGTTCALVGHTGSGKSTI   62 (260)
T ss_dssp             ECTTCEEEEECSTTSSHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHH
Confidence            34678899999999999953

>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=83.97  E-value=0.36  Score=36.03  Aligned_cols=19  Identities=16%  Similarity=0.314  Sum_probs=15.9

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.+-||+|+|||.-
T Consensus        30 ~~Ge~~~l~G~nGsGKSTL   48 (240)
T 1ji0_A           30 PRGQIVTLIGANGAGKTTT   48 (240)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4577888999999999853

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=83.97  E-value=0.34  Score=34.26  Aligned_cols=16  Identities=19%  Similarity=0.094  Sum_probs=13.5

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..+.|.||+|+|||.
T Consensus        21 ~~~i~i~G~~GsGKST   36 (207)
T 2qt1_A           21 TFIIGISGVTNSGKTT   36 (207)
T ss_dssp             CEEEEEEESTTSSHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            4567899999999985

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=83.96  E-value=0.49  Score=32.62  Aligned_cols=16  Identities=25%  Similarity=0.314  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.|+.|+|||..
T Consensus         3 ~~I~l~G~~GsGKsT~   18 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTI   18 (184)
T ss_dssp             CSEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4688999999999854

>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=83.90  E-value=0.28  Score=36.60  Aligned_cols=19  Identities=32%  Similarity=0.485  Sum_probs=15.8

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.|-||+|+|||.-
T Consensus        26 ~~Ge~~~i~G~nGsGKSTL   44 (243)
T 1mv5_A           26 QPNSIIAFAGPSGGGKSTI   44 (243)
T ss_dssp             CTTEEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4577888999999999953

>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=83.86  E-value=0.84  Score=35.55  Aligned_cols=20  Identities=15%  Similarity=0.290  Sum_probs=15.3

Q ss_pred             CCcEEEecCCCCCchHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~   68 (115)
                      +..+.+-||+|+|||..+-+
T Consensus       102 g~vi~lvG~nGsGKTTll~~  121 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAK  121 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            45777889999999965433

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=83.70  E-value=0.66  Score=37.32  Aligned_cols=16  Identities=25%  Similarity=0.320  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|.||||+|||.-
T Consensus         8 ~lI~I~GptgSGKTtl   23 (340)
T 3d3q_A            8 FLIVIVGPTASGKTEL   23 (340)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             ceEEEECCCcCcHHHH
Confidence            3688999999999953

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=83.63  E-value=0.44  Score=36.05  Aligned_cols=29  Identities=31%  Similarity=0.444  Sum_probs=19.6

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      .+..++|+||.|+|||.- +--+..++...
T Consensus        26 ~~~~i~~eG~~GsGKsT~-~~~l~~~l~~~   54 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTA-IQVVVETLQQN   54 (236)
T ss_dssp             CCCEEEEEESTTSCHHHH-HHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHH-HHHHHHHHHhc
Confidence            467899999999999953 22233444443

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=83.56  E-value=0.38  Score=35.27  Aligned_cols=16  Identities=50%  Similarity=0.839  Sum_probs=14.0

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      ++.++|||+-|+|||.
T Consensus         2 ~kFI~~EG~dGsGKsT   17 (205)
T 4hlc_A            2 SAFITFEGPEGSGKTT   17 (205)
T ss_dssp             CEEEEEECCTTSCHHH
T ss_pred             CCEEEEECCCCCcHHH
Confidence            4578999999999996

>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=83.56  E-value=0.45  Score=33.92  Aligned_cols=17  Identities=24%  Similarity=0.247  Sum_probs=14.0

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +..++|.|+.|+|||..
T Consensus         4 ~~~I~i~G~~GSGKST~   20 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTV   20 (218)
T ss_dssp             CEEEEEECCTTSCHHHH
T ss_pred             ceEEEEECCCCCCHHHH
Confidence            34688999999999953

>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=83.54  E-value=0.38  Score=36.09  Aligned_cols=19  Identities=26%  Similarity=0.420  Sum_probs=16.0

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.|-||+|+|||.-
T Consensus        27 ~~Ge~~~l~G~nGsGKSTL   45 (250)
T 2d2e_A           27 PKGEVHALMGPNGAGKSTL   45 (250)
T ss_dssp             ETTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            4578889999999999853

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=83.52  E-value=0.39  Score=36.43  Aligned_cols=19  Identities=26%  Similarity=0.372  Sum_probs=15.9

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.|-||+|+|||.-
T Consensus        31 ~~Ge~~~liG~nGsGKSTL   49 (266)
T 2yz2_A           31 NEGECLLVAGNTGSGKSTL   49 (266)
T ss_dssp             CTTCEEEEECSTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            4577888999999999953

>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=83.49  E-value=1  Score=34.48  Aligned_cols=18  Identities=17%  Similarity=0.089  Sum_probs=14.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..+.|.||+|+|||..
T Consensus        79 ~g~iigI~G~~GsGKSTl   96 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTT   96 (308)
T ss_dssp             CCEEEEEEECTTSSHHHH
T ss_pred             CCEEEEEECCCCCCHHHH
Confidence            345677899999999853

>1e69_A Chromosome segregation SMC protein; structural maintenance of chromosomes, coiled coil; 3.1A {Thermotoga maritima} SCOP: c.37.1.12

Probab=83.47  E-value=0.76  Score=35.35  Aligned_cols=24  Identities=33%  Similarity=0.613  Sum_probs=19.1

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +..+|.||||+|||.  |+-|+.|+.
T Consensus        25 g~~~i~G~NGsGKS~--ll~ai~~ll   48 (322)
T 1e69_A           25 RVTAIVGPNGSGKSN--IIDAIKWVF   48 (322)
T ss_dssp             SEEEEECCTTTCSTH--HHHHHHHTS
T ss_pred             CcEEEECCCCCcHHH--HHHHHHHHh
Confidence            378899999999995  466677764

>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=83.44  E-value=0.52  Score=36.42  Aligned_cols=27  Identities=15%  Similarity=0.065  Sum_probs=19.7

Q ss_pred             hcCCcEEEecCCCCCchHHHHHHHHHH
Q psy14273         47 DNSKFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      ..+..++|.||+|+|||.-.+.-+...
T Consensus       105 ~~G~i~~i~G~~GsGKT~la~~la~~~  131 (324)
T 2z43_A          105 ETRTMTEFFGEFGSGKTQLCHQLSVNV  131 (324)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCcEEEEECCCCCCHhHHHHHHHHHH
Confidence            345789999999999997655544443

>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=83.26  E-value=0.71  Score=36.60  Aligned_cols=29  Identities=14%  Similarity=0.173  Sum_probs=21.1

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +..+..++|.||+|+|||.-.+.-+...+
T Consensus        58 l~~G~iv~I~G~pGsGKTtLal~la~~~~   86 (349)
T 2zr9_A           58 LPRGRVIEIYGPESSGKTTVALHAVANAQ   86 (349)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            33567899999999999976555544444

>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=83.23  E-value=0.41  Score=36.43  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=16.4

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.|-||+|+|||.-
T Consensus        43 i~~Ge~~~l~G~NGsGKSTL   62 (267)
T 2zu0_C           43 VHPGEVHAIMGPNGSGKSTL   62 (267)
T ss_dssp             ECTTCEEEEECCTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34578899999999999953

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=83.06  E-value=0.42  Score=36.27  Aligned_cols=18  Identities=22%  Similarity=0.252  Sum_probs=15.4

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.|-||+|+|||.
T Consensus        30 ~~Ge~~~liG~nGsGKST   47 (262)
T 1b0u_A           30 RAGDVISIIGSSGSGKST   47 (262)
T ss_dssp             CTTCEEEEECCTTSSHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            457788899999999995

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=83.05  E-value=0.63  Score=32.99  Aligned_cols=16  Identities=25%  Similarity=0.518  Sum_probs=13.4

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..+.|.||+|+|||.
T Consensus         5 ~~~i~i~G~~GsGKST   20 (227)
T 1cke_A            5 APVITIDGPSGAGKGT   20 (227)
T ss_dssp             SCEEEEECCTTSSHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            3568899999999984

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=83.05  E-value=0.39  Score=35.01  Aligned_cols=16  Identities=25%  Similarity=0.177  Sum_probs=13.7

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      +..++|+|+.|+|||.
T Consensus         2 ~~~i~~~G~~g~GKtt   17 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKST   17 (241)
T ss_dssp             CEEEEEEECTTSSHHH
T ss_pred             CeEEEEEcCCCCCHHH
Confidence            3468999999999995

>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=83.03  E-value=0.6  Score=33.31  Aligned_cols=15  Identities=27%  Similarity=0.259  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      ++.|-||+|+|||.-
T Consensus         2 ~i~l~G~nGsGKTTL   16 (178)
T 1ye8_A            2 KIIITGEPGVGKTTL   16 (178)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            467899999999964

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=82.98  E-value=0.52  Score=32.39  Aligned_cols=14  Identities=36%  Similarity=0.349  Sum_probs=12.5

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|.||.|+|||.
T Consensus         6 ~i~i~G~~GsGKsT   19 (175)
T 1via_A            6 NIVFIGFMGSGKST   19 (175)
T ss_dssp             CEEEECCTTSCHHH
T ss_pred             EEEEEcCCCCCHHH
Confidence            58899999999985

>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=82.89  E-value=0.42  Score=36.21  Aligned_cols=19  Identities=26%  Similarity=0.349  Sum_probs=15.9

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.+-||+|+|||.-
T Consensus        24 ~~Ge~~~liG~NGsGKSTL   42 (249)
T 2qi9_C           24 RAGEILHLVGPNGAGKSTL   42 (249)
T ss_dssp             ETTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            4577889999999999953

>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=82.88  E-value=0.43  Score=36.28  Aligned_cols=20  Identities=20%  Similarity=0.431  Sum_probs=16.3

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.|-||+|+|||.-
T Consensus        38 i~~Gei~~l~G~NGsGKSTL   57 (256)
T 1vpl_A           38 IEEGEIFGLIGPNGAGKTTT   57 (256)
T ss_dssp             ECTTCEEEEECCTTSSHHHH
T ss_pred             EcCCcEEEEECCCCCCHHHH
Confidence            34578888999999999953

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=82.77  E-value=0.44  Score=36.40  Aligned_cols=19  Identities=37%  Similarity=0.518  Sum_probs=16.0

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+.|-||+|+|||.
T Consensus        42 i~~Ge~~~i~G~nGsGKST   60 (271)
T 2ixe_A           42 LYPGKVTALVGPNGSGKST   60 (271)
T ss_dssp             ECTTCEEEEECSTTSSHHH
T ss_pred             ECCCCEEEEECCCCCCHHH
Confidence            3467889999999999994

>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=82.77  E-value=0.42  Score=36.48  Aligned_cols=19  Identities=26%  Similarity=0.393  Sum_probs=15.9

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.|-||+|+|||.-
T Consensus        35 ~~Ge~~~liG~nGsGKSTL   53 (266)
T 4g1u_C           35 ASGEMVAIIGPNGAGKSTL   53 (266)
T ss_dssp             ETTCEEEEECCTTSCHHHH
T ss_pred             cCCCEEEEECCCCCcHHHH
Confidence            4578889999999999953

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=82.68  E-value=0.69  Score=33.51  Aligned_cols=17  Identities=24%  Similarity=0.509  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      |..+.+-||+|+|||..
T Consensus         1 G~~i~i~G~nG~GKTTl   17 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTL   17 (189)
T ss_dssp             CCCEEEESCCSSCHHHH
T ss_pred             CCEEEEECCCCChHHHH
Confidence            35678899999999964

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=82.68  E-value=0.42  Score=36.14  Aligned_cols=18  Identities=22%  Similarity=0.270  Sum_probs=15.5

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.+-||+|+|||.
T Consensus        29 ~~Ge~~~l~G~nGsGKST   46 (253)
T 2nq2_C           29 NKGDILAVLGQNGCGKST   46 (253)
T ss_dssp             ETTCEEEEECCSSSSHHH
T ss_pred             CCCCEEEEECCCCCCHHH
Confidence            457788899999999995

>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=82.40  E-value=0.87  Score=36.35  Aligned_cols=29  Identities=17%  Similarity=0.095  Sum_probs=21.3

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +..+..++|.||+|+|||.-.+.-+...+
T Consensus        60 l~~G~ii~I~G~pGsGKTtLal~la~~~~   88 (356)
T 1u94_A           60 LPMGRIVEIYGPESSGKTTLTLQVIAAAQ   88 (356)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34567899999999999976655544444

>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=82.33  E-value=0.84  Score=36.45  Aligned_cols=27  Identities=26%  Similarity=0.448  Sum_probs=20.3

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+...+|-||+|+|||.  |+-++.|+..
T Consensus        25 ~~~~~~i~G~nG~GKst--ll~ai~~~~~   51 (430)
T 1w1w_A           25 ESNFTSIIGPNGSGKSN--MMDAISFVLG   51 (430)
T ss_dssp             TCSEEEEECSTTSSHHH--HHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHHhhhc
Confidence            46788999999999995  3445666653

>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=82.26  E-value=1.7  Score=36.16  Aligned_cols=31  Identities=10%  Similarity=0.188  Sum_probs=21.4

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..+++.|++|+|||.+...-+ .++...+.++
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA-~~l~~~G~kV  131 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLA-RYFQKRGYKV  131 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH-HHHHTTTCCE
T ss_pred             eEEEEECcCCCCHHHHHHHHH-HHHHHCCCeE
Confidence            367889999999998755444 4444555554

>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=82.25  E-value=0.47  Score=36.28  Aligned_cols=19  Identities=26%  Similarity=0.440  Sum_probs=15.8

Q ss_pred             hcCCcEEEecCCCCCchHH
Q psy14273         47 DNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTls   65 (115)
                      ..|..+.|-||+|+|||.-
T Consensus        48 ~~Gei~~liG~NGsGKSTL   66 (263)
T 2olj_A           48 REGEVVVVIGPSGSGKSTF   66 (263)
T ss_dssp             CTTCEEEEECCTTSSHHHH
T ss_pred             cCCCEEEEEcCCCCcHHHH
Confidence            4577888999999999953

>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=82.24  E-value=2.4  Score=33.13  Aligned_cols=18  Identities=22%  Similarity=0.145  Sum_probs=14.2

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      ..++|.|++|+|||..+.
T Consensus        80 ~~I~i~G~~G~GKSTl~~   97 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIE   97 (355)
T ss_dssp             EEEEEECCTTSSHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHH
Confidence            357889999999996533

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=82.16  E-value=2  Score=33.78  Aligned_cols=25  Identities=28%  Similarity=0.173  Sum_probs=16.9

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      +..+.|-|++|+|||. +|-.++.++
T Consensus        74 ~~~v~lvG~pgaGKST-Lln~L~~~~   98 (349)
T 2www_A           74 AFRVGLSGPPGAGKST-FIEYFGKML   98 (349)
T ss_dssp             CEEEEEECCTTSSHHH-HHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHH-HHHHHHHHh
Confidence            3467889999999995 333334443

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=82.01  E-value=0.96  Score=36.87  Aligned_cols=34  Identities=21%  Similarity=0.236  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHHHHHHHHh----cCCcEEEecCCCCCchHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLD----NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~----~~~~~iiEaPTGtGKTls   65 (115)
                      |--|+...+   .|.+.+.    ....++|.||.|+|||.-
T Consensus       126 ~vGR~~~l~---~L~~~L~~~~~~~~~v~I~G~~GiGKTtL  163 (591)
T 1z6t_A          126 FVTRKKLVN---AIQQKLSKLKGEPGWVTIHGMAGCGKSVL  163 (591)
T ss_dssp             CCCCHHHHH---HHHHHHTTSTTSCEEEEEECCTTSSHHHH
T ss_pred             ecccHHHHH---HHHHHHhcccCCCceEEEEcCCCCCHHHH
Confidence            445665444   5555664    235688999999999953

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=81.92  E-value=0.47  Score=36.48  Aligned_cols=19  Identities=21%  Similarity=0.282  Sum_probs=15.9

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+.|-||+|+|||.
T Consensus        44 i~~Ge~~~liG~NGsGKST   62 (279)
T 2ihy_A           44 IAKGDKWILYGLNGAGKTT   62 (279)
T ss_dssp             EETTCEEEEECCTTSSHHH
T ss_pred             EcCCCEEEEECCCCCcHHH
Confidence            3457888899999999985

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=81.82  E-value=0.65  Score=32.52  Aligned_cols=15  Identities=27%  Similarity=0.100  Sum_probs=12.8

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|+|||..
T Consensus         3 ~i~i~G~~GsGKSTl   17 (204)
T 2if2_A            3 RIGLTGNIGCGKSTV   17 (204)
T ss_dssp             EEEEEECTTSSHHHH
T ss_pred             EEEEECCCCcCHHHH
Confidence            578899999999954

>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=81.74  E-value=0.86  Score=37.69  Aligned_cols=30  Identities=13%  Similarity=0.121  Sum_probs=20.5

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||+|+|||.+...-+. ++...+.+|
T Consensus        99 vI~lvG~~GsGKTTt~~kLA~-~l~~~G~kV  128 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAGKLAY-FYKKRGYKV  128 (433)
T ss_dssp             EEEECCCTTSCHHHHHHHHHH-HHHHTTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHHcCCeE
Confidence            577899999999977555443 444455554

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=81.41  E-value=0.85  Score=36.68  Aligned_cols=18  Identities=28%  Similarity=0.244  Sum_probs=14.4

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      ..+.+-||+|+|||..+-
T Consensus       158 ~vi~lvG~nGsGKTTll~  175 (359)
T 2og2_A          158 AVIMIVGVNGGGKTTSLG  175 (359)
T ss_dssp             EEEEEECCTTSCHHHHHH
T ss_pred             eEEEEEcCCCChHHHHHH
Confidence            467789999999997543

>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=81.32  E-value=1.1  Score=35.44  Aligned_cols=18  Identities=22%  Similarity=0.390  Sum_probs=14.6

Q ss_pred             CCcEEEecCCCCCchHHH
Q psy14273         49 SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~   66 (115)
                      +..+.+-||+|+|||..+
T Consensus       129 g~vi~lvG~nGaGKTTll  146 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTI  146 (328)
T ss_dssp             SEEEEEECCTTSSHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456889999999999653

>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=81.31  E-value=0.57  Score=36.06  Aligned_cols=20  Identities=20%  Similarity=0.270  Sum_probs=16.3

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.|-||+|+|||.-
T Consensus        31 i~~Ge~~~iiGpnGsGKSTL   50 (275)
T 3gfo_A           31 IKRGEVTAILGGNGVGKSTL   50 (275)
T ss_dssp             EETTSEEEEECCTTSSHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHH
Confidence            34578889999999999853

>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=81.02  E-value=0.78  Score=35.88  Aligned_cols=25  Identities=12%  Similarity=-0.150  Sum_probs=18.8

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      .|..++|.||+|+|||.-.+.-+..
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~  145 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVT  145 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4567899999999999765554444

>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=80.80  E-value=1  Score=34.98  Aligned_cols=24  Identities=17%  Similarity=0.111  Sum_probs=16.9

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +.-+|.||+|+|||.-  +=|+.|+.
T Consensus        24 ~~~~i~G~NGsGKS~l--leAi~~~l   47 (339)
T 3qkt_A           24 GINLIIGQNGSGKSSL--LDAILVGL   47 (339)
T ss_dssp             EEEEEECCTTSSHHHH--HHHHHHHH
T ss_pred             CeEEEECCCCCCHHHH--HHHHHHHh
Confidence            4567899999999964  34455543

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=80.65  E-value=2.2  Score=33.77  Aligned_cols=35  Identities=11%  Similarity=0.069  Sum_probs=25.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls   65 (115)
                      ..+...++.+.+.........+++.|++||||++.
T Consensus       134 ~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~l  168 (368)
T 3dzd_A          134 EHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIV  168 (368)
T ss_dssp             CSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHH
T ss_pred             cchHHHHHHhhhhhhhccchhheEEeCCCchHHHH
Confidence            34555556666666666677899999999999954

>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=80.60  E-value=0.73  Score=35.17  Aligned_cols=25  Identities=16%  Similarity=0.229  Sum_probs=18.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      .+..++|.||+|+|||.-.+.-+..
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4567899999999999765544443

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=80.45  E-value=1  Score=36.86  Aligned_cols=31  Identities=19%  Similarity=0.008  Sum_probs=20.0

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.+++|+|||.+..--+..+...++++|
T Consensus       102 vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kV  132 (433)
T 2xxa_A          102 VVLMAGLQGAGKTTSVGKLGKFLREKHKKKV  132 (433)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTSCCCE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhcCCeE
Confidence            4667799999999875555444443324444

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=80.45  E-value=0.87  Score=33.80  Aligned_cols=18  Identities=22%  Similarity=0.353  Sum_probs=14.9

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .+..+.|.||+|+|||..
T Consensus        26 ~g~~I~I~G~~GsGKSTl   43 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTL   43 (252)
T ss_dssp             TSCEEEEECCTTSSHHHH
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            456788999999999853

>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=80.44  E-value=0.72  Score=41.11  Aligned_cols=16  Identities=38%  Similarity=0.538  Sum_probs=13.8

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +.+++.||.|||||+-
T Consensus       239 ~GILL~GPPGTGKT~L  254 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLI  254 (806)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4689999999999964

>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=80.43  E-value=0.51  Score=36.61  Aligned_cols=18  Identities=22%  Similarity=0.311  Sum_probs=15.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .|..+.|-||+|+|||.-
T Consensus        63 ~Ge~~~i~G~NGsGKSTL   80 (290)
T 2bbs_A           63 RGQLLAVAGSTGAGKTSL   80 (290)
T ss_dssp             TTCEEEEEESTTSSHHHH
T ss_pred             CCCEEEEECCCCCcHHHH
Confidence            467888999999999954

>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=80.16  E-value=1.4  Score=34.06  Aligned_cols=16  Identities=44%  Similarity=0.837  Sum_probs=12.9

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..+.|.||+|+|||..
T Consensus        32 ~ii~I~G~sGsGKSTl   47 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFT   47 (290)
T ss_dssp             EEEEEECCTTSSHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            3567899999999853

>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=80.06  E-value=0.89  Score=37.48  Aligned_cols=31  Identities=23%  Similarity=0.245  Sum_probs=23.1

Q ss_pred             HHHHHHH-HHhcCCcEEEecCCCCCchHHHHH
Q psy14273         38 FMKNLYY-TLDNSKFGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        38 ~m~~I~~-~l~~~~~~iiEaPTGtGKTls~L~   68 (115)
                      .++.|.- .+..|..++|.||+|+|||.-+.+
T Consensus        27 ~Ld~i~~G~i~~Ge~~~l~G~nGsGKSTL~~~   58 (525)
T 1tf7_A           27 GFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQ   58 (525)
T ss_dssp             THHHHTTSSEETTSEEEEEESTTSSHHHHHHH
T ss_pred             hHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHH
Confidence            3455554 556788999999999999965544

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=80.05  E-value=0.86  Score=36.64  Aligned_cols=27  Identities=11%  Similarity=0.063  Sum_probs=19.3

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .|..++|.||+|+|||.-.+.-+....
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~   86 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQ   86 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            456788999999999975555444433

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	115
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.02
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.01
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.95
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.95
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.93
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	98.91
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.84
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.83
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.81
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.75
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	98.72
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.61
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	98.58
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.28
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.2
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.2
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	98.08
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.06
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.99
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.15
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.11
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.09
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.08
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.04
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.0
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.98
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.97
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.87
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	96.84
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.81
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.73
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.72
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.7
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.64
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.63
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.52
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	96.42
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.22
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.11
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.02
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	95.73
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.64
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	95.63
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	95.49
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	95.45
d1okkd2	207	GTPase domain of the signal recognition particle r	95.28
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	95.18
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	95.09
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	95.05
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	94.98
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	94.97
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	94.93
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.84
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	94.77
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	94.71
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	94.64
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.55
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	94.5
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	94.4
d1vmaa2	213	GTPase domain of the signal recognition particle r	94.4
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	94.32
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	94.27
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.26
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.24
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	94.15
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	94.1
d1ls1a2	207	GTPase domain of the signal sequence recognition p	93.99
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	93.96
d2qy9a2	211	GTPase domain of the signal recognition particle r	93.8
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	93.78
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	93.76
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	93.73
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	93.66
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	93.63
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	93.61
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	93.58
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	93.54
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	93.47
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.31
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	93.21
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	93.2
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	93.16
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	93.11
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	93.05
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	92.8
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	92.71
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	92.67
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	92.18
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	91.94
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	91.85
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	91.83
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	91.75
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	91.73
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	91.72
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	91.63
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.54
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	91.46
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	91.41
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	91.36
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	91.24
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	91.13
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	90.81
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	90.62
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	90.61
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	90.49
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	90.47
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	90.05
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	90.03
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	89.72
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	89.68
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	89.67
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	89.48
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	89.46
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	89.44
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	89.33
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	89.29
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	89.19
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	89.19
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	89.14
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	89.1
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	89.08
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.72
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	88.56
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	88.45
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	88.42
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	88.25
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	88.1
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	87.8
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	87.76
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	87.49
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	87.36
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	87.35
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	87.29
d1tuea_	205	Replication protein E1 helicase domain {Human papi	87.23
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	87.11
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	87.1
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	86.9
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	86.82
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	86.59
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	86.46
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	86.12
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.69
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	84.46
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	84.34
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	84.26
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	84.05
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	83.93
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	83.51
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	83.41
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	82.11
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	82.02
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	82.0
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	81.82
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	81.39
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	81.13
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	80.24

>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=99.02  E-value=1.5e-10  Score=84.44  Aligned_cols=51  Identities=18%  Similarity=0.132  Sum_probs=43.6

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      ..+|. |+|.|.+.+..+    .+|+++|+.||||||||++|++|++..+...+..
T Consensus        20 ~~g~~~pt~iQ~~aip~i----l~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~~   71 (206)
T d1veca_          20 EMGWEKPSPIQEESIPIA----LSGRDILARAKNGTGKSGAYLIPLLERLDLKKDN   71 (206)
T ss_dssp             TTTCCSCCHHHHHHHHHH----HTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSCS
T ss_pred             HCCCCCCCHHHHHHHHHH----HcCCCEEeeccCccccccccccchhhcccccccC
Confidence            46787 999999988764    5889999999999999999999999887665543

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.01  E-value=7.3e-11  Score=84.72  Aligned_cols=50  Identities=20%  Similarity=0.244  Sum_probs=42.2

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .++|. |++.|.+.+..+    .+|+++++.||||||||++|++|++..+.....
T Consensus        18 ~~g~~~pt~iQ~~aip~~----l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~   68 (209)
T d1q0ua_          18 TLRFYKPTEIQERIIPGA----LRGESMVGQSQTGTGKTHAYLLPIMEKIKPERA   68 (209)
T ss_dssp             HTTCCSCCHHHHHHHHHH----HHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSC
T ss_pred             HCCCCCCCHHHHHHHHHH----HCCCCeEeecccccccceeeeeeeccccccccc
Confidence            35677 999999988864    578999999999999999999999887765543

>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=98.95  E-value=2.9e-10  Score=82.96  Aligned_cols=49  Identities=12%  Similarity=0.139  Sum_probs=42.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .+|. |+|.|.+.+..+    .+|+++++.||||||||++|++|++..+.....
T Consensus        19 ~g~~~pt~iQ~~aip~i----l~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~~   68 (207)
T d1t6na_          19 CGFEHPSEVQHECIPQA----ILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTG   68 (207)
T ss_dssp             TTCCCCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHCCCCTT
T ss_pred             CCCCCCCHHHHHHHHHH----HcCCCeEEEeccccccccccccceeeeecccCC
Confidence            4677 999999988875    478999999999999999999999988766543

>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=98.95  E-value=5.9e-10  Score=83.11  Aligned_cols=49  Identities=16%  Similarity=0.209  Sum_probs=42.5

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhh
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDH   77 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~   77 (115)
                      ...+|. |.+.|..++..+    .+|+++++.||||||||+||++|++..+...
T Consensus        37 ~~~g~~~pt~iQ~~~ip~i----l~g~dvvi~a~TGsGKTlayllp~l~~l~~~   86 (238)
T d1wrba1          37 LLASYQRPTPIQKNAIPAI----LEHRDIMACAQTGSGKTAAFLIPIINHLVCQ   86 (238)
T ss_dssp             TTTTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             HHCCCCCCCHHHHHHhhhh----hCCCCEEEECCCCCCcceeeHHHHHHHHHhc
Confidence            356788 999999988875    4789999999999999999999999988543

>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=98.93  E-value=3.9e-10  Score=83.86  Aligned_cols=50  Identities=22%  Similarity=0.309  Sum_probs=43.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .+|. |++.|...+..+    .+|+++++.||||||||++|++|++..+......
T Consensus        35 ~g~~~pt~IQ~~aIp~i----l~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~   85 (222)
T d2j0sa1          35 YGFEKPSAIQQRAIKQI----IKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRE   85 (222)
T ss_dssp             HTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCS
T ss_pred             CCCCCCCHHHHHHHHHH----HCCCCeEEEcCcchhhhhhhcccccccccccccC
Confidence            4677 999999988875    4789999999999999999999999988766544

>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=98.91  E-value=2.4e-10  Score=81.57  Aligned_cols=44  Identities=23%  Similarity=0.227  Sum_probs=37.8

Q ss_pred             ccCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        25 ~~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      -.|+|+ +||.|.+.++.+    .+|+++++.+|||+|||++|.+|++.
T Consensus        19 ~~fg~~~~rp~Q~~ai~~~----l~g~~vlv~apTGsGKT~~~~~~~~~   63 (206)
T d1oywa2          19 ETFGYQQFRPGQEEIIDTV----LSGRDCLVVMPTGGGKSLCYQIPALL   63 (206)
T ss_dssp             HTTCCSSCCTTHHHHHHHH----HTTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HhcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCCCCcchhhhhhhh
Confidence            468887 899999988764    46789999999999999999999764

>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=98.84  E-value=1.5e-09  Score=79.56  Aligned_cols=50  Identities=16%  Similarity=0.192  Sum_probs=43.0

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      ..+|. |++.|...+..+    .+|+.+++.||||||||++|++|++..+.....
T Consensus        27 ~~g~~~pt~iQ~~aip~i----l~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~   77 (212)
T d1qdea_          27 GYGFEEPSAIQQRAIMPI----IEGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK   77 (212)
T ss_dssp             HHTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC
T ss_pred             HCCCCCCCHHHHHHHHHH----HcCCCEEeecccccchhhhhHhhhHhhhhccCC
Confidence            35777 999999988875    478999999999999999999999998865543

>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=98.83  E-value=1.7e-09  Score=79.70  Aligned_cols=49  Identities=20%  Similarity=0.203  Sum_probs=42.0

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ..+|. |++.|...+..+    .+|+++++.||||||||++|++|++..+....
T Consensus        29 ~~g~~~pt~iQ~~aip~i----l~g~dvl~~a~TGsGKTlayllp~l~~i~~~~   78 (218)
T d2g9na1          29 AYGFEKPSAIQQRAILPC----IKGYDVIAQAQSGTGKTATFAISILQQIELDL   78 (218)
T ss_dssp             HHTCCSCCHHHHHHHHHH----HHTCCEEEECCTTSSHHHHHHHHHHHHCCTTC
T ss_pred             HCCCCCCCHHHHHHHHHH----HcCCCEEEEcccchhhhhhhhhhhhheecccc
Confidence            46777 999999988765    47899999999999999999999998886543

>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=98.81  E-value=1.9e-09  Score=77.92  Aligned_cols=49  Identities=16%  Similarity=0.125  Sum_probs=41.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        27 fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .+|. |+|.|...+..+    .+|+++|+.||||||||++|++|++..+.....
T Consensus        19 ~g~~~pt~iQ~~aip~i----l~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~~   68 (206)
T d1s2ma1          19 AGFEKPSPIQEEAIPVA----ITGRDILARAKNGTGKTAAFVIPTLEKVKPKLN   68 (206)
T ss_dssp             TTCCSCCHHHHHHHHHH----HHTCCEEEECCTTSCHHHHHHHHHHHHCCTTSC
T ss_pred             CCCCCCCHHHHHHHHHH----HcCCCEEEecCCcchhhhhhccccccccccccc
Confidence            4677 999999988865    468899999999999999999999987755543

>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=98.75  E-value=2.6e-09  Score=75.07  Aligned_cols=48  Identities=15%  Similarity=-0.017  Sum_probs=37.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++||+.|.+.++.+   .  ++++|+.+|||+|||++++.++...+...+.++
T Consensus         8 ~~pr~~Q~~~~~~~---~--~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~i   55 (200)
T d1wp9a1           8 IQPRIYQEVIYAKC---K--ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKV   55 (200)
T ss_dssp             HCCCHHHHHHHHHG---G--GSCEEEECCTTSCHHHHHHHHHHHHHHHSCSCE
T ss_pred             CCCCHHHHHHHHHH---h--cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCcE
Confidence            46999999987754   2  456899999999999998888777776655543

>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=98.72  E-value=4.7e-09  Score=76.51  Aligned_cols=45  Identities=22%  Similarity=0.127  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        30 ~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      +|++.|.+.+..+    ..|+++++.||||+|||++++++++..+...+
T Consensus        43 ~p~~~Q~~~i~~~----l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~~   87 (237)
T d1gkub1          43 EPRAIQKMWAKRI----LRKESFAATAPTGVGKTSFGLAMSLFLALKGK   87 (237)
T ss_dssp             SCCHHHHHHHHHH----HTTCCEECCCCBTSCSHHHHHHHHHHHHTTSC
T ss_pred             CCCHHHHHHHHHH----HCCCCEEEEecCCChHHHHHHHHHHHHHHhcC
Confidence            3899999977764    47889999999999999999999887765543

>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=98.61  E-value=3.5e-09  Score=75.51  Aligned_cols=49  Identities=14%  Similarity=0.153  Sum_probs=37.1

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhh
Q psy14273         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIA   80 (115)
Q Consensus        28 pf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~   80 (115)
                      .|+ +||.|.+.+..+    .+++++|+.||||+|||++++++++..+...++-
T Consensus        22 g~~~l~~~Q~~ai~~l----~~~~~~il~apTGsGKT~~a~l~i~~~~~~~~~v   71 (202)
T d2p6ra3          22 GIEELFPPQAEAVEKV----FSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKS   71 (202)
T ss_dssp             ---CCCCCCHHHHHHH----TTCSCEEEECSSHHHHHHHHHHHHHHHHHTTCCE
T ss_pred             CCCCCCHHHHHHHHHH----HcCCCEEEEcCCCCchhHHHHHHHHHHhhccCcc
Confidence            454 888899977764    4788999999999999999988887766554433

>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=98.58  E-value=3.8e-08  Score=71.24  Aligned_cols=50  Identities=20%  Similarity=0.319  Sum_probs=39.7

Q ss_pred             cCCCC-CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        26 ~fpf~-~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      ..+|+ |+|.|.+.+..+   +..+..+|+.||||+|||++|+.|++.......
T Consensus        21 ~~g~~~pt~iQ~~~ip~~---l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~~~   71 (208)
T d1hv8a1          21 NKGFEKPTDIQMKVIPLF---LNDEYNIVAQARTGSGKTASFAIPLIELVNENN   71 (208)
T ss_dssp             HHTCCSCCHHHHHHHHHH---HHTCSEEEEECCSSSSHHHHHHHHHHHHSCSSS
T ss_pred             HCCCCCCCHHHHHHHHHH---HcCCCCeeeechhcccccceeeccccccccccc
Confidence            35676 999999987765   444468999999999999999999887655443

>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=98.28  E-value=1.5e-07  Score=61.01  Aligned_cols=36  Identities=17%  Similarity=0.278  Sum_probs=30.2

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      |++|+.+|+.||||+|||+.++..++..+...+..+
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~v   39 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRT   39 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCCE
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhcCcee
Confidence            567899999999999999999888888877766554

>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=98.20  E-value=1.5e-07  Score=68.94  Aligned_cols=37  Identities=14%  Similarity=0.258  Sum_probs=29.8

Q ss_pred             HHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        45 ~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++.+++.+|+.||||+|||++||.+++..+...+.++
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~~~~   41 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRT   41 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHTCCE
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcCCEE
Confidence            4567899999999999999999888877665555443

>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=98.20  E-value=8.7e-07  Score=63.61  Aligned_cols=40  Identities=23%  Similarity=0.249  Sum_probs=30.9

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHH
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      ...+.+|+.|.+.++.+    .+++.+++.+|||+|||+..+..
T Consensus        66 ~~~~~Lr~yQ~eav~~~----~~~~~~ll~~~tG~GKT~~a~~~  105 (206)
T d2fz4a1          66 DAEISLRDYQEKALERW----LVDKRGCIVLPTGSGKTHVAMAA  105 (206)
T ss_dssp             CCCCCCCHHHHHHHHHH----TTTSEEEEEESSSTTHHHHHHHH
T ss_pred             CCCCCcCHHHHHHHHHH----HhCCCcEEEeCCCCCceehHHhH
Confidence            34567999999976643    35667889999999999876544

>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=98.08  E-value=3.8e-06  Score=63.14  Aligned_cols=51  Identities=14%  Similarity=0.167  Sum_probs=46.0

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .|||+..+.|...++.|.+.+.++.  ..+++|.||||||..|+.++...+..
T Consensus        51 ~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~  103 (233)
T d2eyqa3          51 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN  103 (233)
T ss_dssp             TCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT
T ss_pred             ccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc
Confidence            6999999999999999999999875  67999999999999999998777744

>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=98.06  E-value=1.5e-06  Score=65.85  Aligned_cols=46  Identities=20%  Similarity=0.137  Sum_probs=33.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++++|+.|.+.+..   ++.+ +.+++.+|||+|||+..++.+..+...
T Consensus       110 ~~~~~rdyQ~~av~~---~l~~-~~~il~~pTGsGKT~i~~~i~~~~~~~  155 (282)
T d1rifa_         110 KRIEPHWYQKDAVFE---GLVN-RRRILNLPTSAGRSLIQALLARYYLEN  155 (282)
T ss_dssp             EECCCCHHHHHHHHH---HHHH-SEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CccccchHHHHHHHH---HHhc-CCceeEEEcccCccHHHHHHHHHhhhc
Confidence            468899999995554   4544 578999999999999866544333333

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.99  E-value=6.2e-06  Score=62.94  Aligned_cols=54  Identities=19%  Similarity=0.270  Sum_probs=47.3

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHHHHHHHHHHhhh
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILKWYSDHK   78 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L~~al~~l~~~~   78 (115)
                      -.|||+..+.|...+++|.+-+.++.  ..++.|.||||||..|+.+++..+....
T Consensus        78 ~~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~  133 (264)
T d1gm5a3          78 KSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF  133 (264)
T ss_dssp             HHSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS
T ss_pred             hhccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc
Confidence            36999999999999999999998774  6799999999999999999887775543

>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=97.15  E-value=0.00014  Score=51.43  Aligned_cols=39  Identities=23%  Similarity=0.357  Sum_probs=31.1

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        29 f~~r~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      |+-.-+|.+..+.+..++.++  ++++|.||+|+|||..+-
T Consensus        23 ~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHH
Confidence            443346778888999999887  679999999999996644

>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=97.11  E-value=0.00026  Score=49.44  Aligned_cols=37  Identities=24%  Similarity=0.126  Sum_probs=23.8

Q ss_pred             CCCHHHHHH-HHHHHHHHhcC----CcEEEecCCCCCchHHH
Q psy14273         30 DAYDIQSNF-MKNLYYTLDNS----KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        30 ~~r~~Q~e~-m~~I~~~l~~~----~~~iiEaPTGtGKTls~   66 (115)
                      .-|+.|.+- +..|..++.+.    .+++|.||+|||||...
T Consensus        19 ~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          19 PHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             TTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHH
Confidence            356677543 33333333332    58999999999999654

>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=97.09  E-value=0.0002  Score=50.24  Aligned_cols=34  Identities=26%  Similarity=0.455  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      +|.+..+.+..++.++.  +++|.||+|+|||..+.
T Consensus        18 g~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~   53 (227)
T d1sxjc2          18 GQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIV   53 (227)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHH
Confidence            46677888889998874  69999999999996543

>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=97.08  E-value=0.00017  Score=51.03  Aligned_cols=35  Identities=26%  Similarity=0.291  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHHhc----C---CcEEEecCCCCCchHHHH
Q psy14273         33 DIQSNFMKNLYYTLDN----S---KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~----~---~~~iiEaPTGtGKTls~L   67 (115)
                      =+|.+..+.+..++..    +   ++++|.||+|||||..+-
T Consensus        12 vGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~   53 (238)
T d1in4a2          12 IGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAH   53 (238)
T ss_dssp             CSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHH
Confidence            3566777777666642    2   579999999999997643

>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=97.04  E-value=0.00013  Score=47.91  Aligned_cols=19  Identities=32%  Similarity=0.567  Sum_probs=15.6

Q ss_pred             cCCcEEEecCCCCCchHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~   66 (115)
                      ..+.+|+.+|||+|||+.+
T Consensus         7 ~~~~~ll~apTGsGKT~~~   25 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKV   25 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            3467899999999999753

>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=97.00  E-value=0.00022  Score=50.29  Aligned_cols=37  Identities=19%  Similarity=0.194  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~   69 (115)
                      =+|.+..+.+..++.++  .+++|.||.|+|||..+-+-
T Consensus        18 ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~l   56 (224)
T d1sxjb2          18 VGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCL   56 (224)
T ss_dssp             CSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHH
Confidence            35667778888999887  57999999999999765433

>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=96.98  E-value=0.00026  Score=50.22  Aligned_cols=37  Identities=19%  Similarity=0.113  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHHHHHhc-------CCcEEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~-------~~~~iiEaPTGtGKTls~L~~   69 (115)
                      =+|.+..+.+..++..       -++++|.||+|+|||..+-+-
T Consensus        12 vGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~l   55 (239)
T d1ixsb2          12 IGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVI   55 (239)
T ss_dssp             CSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHH
Confidence            3667777777666642       258999999999999765543

>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=96.97  E-value=0.0013  Score=46.69  Aligned_cols=44  Identities=14%  Similarity=-0.057  Sum_probs=36.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .||.|.+.++.++.....+..+|+.-..|+|||+..++-+..+.
T Consensus        13 L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~~~~   56 (230)
T d1z63a1          13 LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDAK   56 (230)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhhhhh
Confidence            78999999988887777778899999999999998766544333

>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=96.87  E-value=0.00067  Score=47.79  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=28.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC------CcEEEecCCCCCchHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLDNS------KFGIFESPTGTGKSLS   65 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~~~------~~~iiEaPTGtGKTls   65 (115)
                      ..|.++..|..+.+.+...+...      ..+++.||+|||||..
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~l   48 (273)
T d1gvnb_           4 VNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSL   48 (273)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHH
T ss_pred             cccChHHHHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHH
Confidence            34667788888887776554432      2478999999999964

>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=96.84  E-value=0.00081  Score=47.01  Aligned_cols=39  Identities=10%  Similarity=-0.058  Sum_probs=25.1

Q ss_pred             CCHHHHH-HHHHHHHHHhcCC-------cEEEecCCCCCchHHHHHH
Q psy14273         31 AYDIQSN-FMKNLYYTLDNSK-------FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        31 ~r~~Q~e-~m~~I~~~l~~~~-------~~iiEaPTGtGKTls~L~~   69 (115)
                      -|+.|.+ ++..+.+.+.++.       +++|.||+|||||...-.-
T Consensus        20 ~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l   66 (287)
T d1w5sa2          20 VRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFT   66 (287)
T ss_dssp             SSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHH
Confidence            4555544 4455566666552       3467899999999765443

>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=96.81  E-value=0.00021  Score=50.01  Aligned_cols=37  Identities=27%  Similarity=0.375  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHH
Q psy14273         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~a   70 (115)
                      +|.+..+.+..++.++  .+++|.||+|+|||....+-+
T Consensus        16 g~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~   54 (237)
T d1sxjd2          16 AQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALT   54 (237)
T ss_dssp             SCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHH
Confidence            4445566788888776  569999999999997655443

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.73  E-value=0.00074  Score=48.03  Aligned_cols=40  Identities=10%  Similarity=0.091  Sum_probs=32.8

Q ss_pred             CCHHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~a   70 (115)
                      .||.|....+.+.+.+.+++  + ++|.||.|+|||....+-+
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a   45 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALS   45 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHH
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHH
Confidence            46888888999999998874  3 8899999999998665543

>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=96.72  E-value=0.00054  Score=44.78  Aligned_cols=31  Identities=19%  Similarity=0.298  Sum_probs=22.6

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++++|.||+|||||. ++..++..+...+..+
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~~~~~v   32 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKSSGVPV   32 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHHTTCCC
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHHCCCEE
Confidence            579999999999997 4555566665555444

>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=96.70  E-value=0.00088  Score=48.04  Aligned_cols=39  Identities=13%  Similarity=0.040  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      -|.|.+.++.      ....++|.||.|||||.+++.-+...+..
T Consensus         3 ~~eQ~~av~~------~~~~~lI~g~aGTGKTt~l~~rv~~ll~~   41 (306)
T d1uaaa1           3 NPGQQQAVEF------VTGPCLVLAGAGSGKTRVITNKIAHLIRG   41 (306)
T ss_dssp             CHHHHHHHHC------CSSEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHhC------CCCCEEEEeeCCccHHHHHHHHHHHHHHh
Confidence            4788886642      24567888999999999877655444433

>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=96.64  E-value=0.00099  Score=48.50  Aligned_cols=40  Identities=15%  Similarity=0.133  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      ..+.|.+.++.      .++.++|.||.|||||.+++.-+...+..
T Consensus        12 L~~eQ~~~v~~------~~g~~lV~g~aGSGKTt~l~~ri~~ll~~   51 (318)
T d1pjra1          12 LNKEQQEAVRT------TEGPLLIMAGAGSGKTRVLTHRIAYLMAE   51 (318)
T ss_dssp             SCHHHHHHHHC------CSSCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHhC------CCCCEEEEecCCccHHHHHHHHHHHHHHc
Confidence            34788886653      24568888999999999987766555543

>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=96.63  E-value=0.00073  Score=50.90  Aligned_cols=19  Identities=32%  Similarity=0.316  Sum_probs=15.5

Q ss_pred             CCcEEEecCCCCCchHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L   67 (115)
                      .+.++|.||||||||+.+-
T Consensus        49 ~~~iLl~GPpG~GKT~lAk   67 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIAR   67 (309)
T ss_dssp             CCCEEEECCTTSSHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            3678899999999997543

>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=96.52  E-value=0.00044  Score=48.70  Aligned_cols=37  Identities=19%  Similarity=0.197  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHhcC---CcEEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~---~~~iiEaPTGtGKTls~L~~   69 (115)
                      -+|.+..+.+..++.++   .+++|.||.|+|||..+.+-
T Consensus        14 ig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~l   53 (252)
T d1sxje2          14 SHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMAL   53 (252)
T ss_dssp             CSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTH
T ss_pred             cCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHH
Confidence            34556666777777654   46899999999999775544

>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=96.42  E-value=0.0012  Score=46.42  Aligned_cols=18  Identities=22%  Similarity=0.455  Sum_probs=15.0

Q ss_pred             CcEEEecCCCCCchHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L   67 (115)
                      .+++|.||+|+|||..+-
T Consensus        53 ~~lll~GPpG~GKTt~a~   70 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAAH   70 (253)
T ss_dssp             SEEEEECSTTSSHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHH
Confidence            479999999999996543

>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=96.22  E-value=0.0018  Score=49.62  Aligned_cols=40  Identities=20%  Similarity=0.223  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         36 SNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        36 ~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .++...+..++..++++++.||||||||.. |-+.+.++..
T Consensus       153 ~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~~  192 (323)
T d1g6oa_         153 EQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIPK  192 (323)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSCT
T ss_pred             HHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhccc
Confidence            355667777888899999999999999964 4444555533

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=96.11  E-value=0.0019  Score=50.48  Aligned_cols=46  Identities=20%  Similarity=0.224  Sum_probs=31.6

Q ss_pred             CHHHHHHHHHHHHHHh-cCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         32 YDIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~-~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      -+.|.+.++.+   +. .++.+||.||||||||.++- .++.++....+++
T Consensus       143 ~~~~~~~l~~l---~~~~~GliLvtGpTGSGKSTTl~-~~l~~~~~~~~~i  189 (401)
T d1p9ra_         143 TAHNHDNFRRL---IKRPHGIILVTGPTGSGKSTTLY-AGLQELNSSERNI  189 (401)
T ss_dssp             CHHHHHHHHHH---HTSSSEEEEEECSTTSCHHHHHH-HHHHHHCCTTSCE
T ss_pred             cHHHHHHHHHH---HhhhhceEEEEcCCCCCccHHHH-HHhhhhcCCCceE
Confidence            36776655543   43 34789999999999998754 4577776655554

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.02  E-value=0.0026  Score=45.47  Aligned_cols=37  Identities=19%  Similarity=0.128  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-EEEecCCCCCchHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~--~-~iiEaPTGtGKTls~L~~   69 (115)
                      -+|.+.++.+..++.+++  + ++|.||.|+|||..+.+-
T Consensus        15 ig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~   54 (239)
T d1njfa_          15 VGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLL   54 (239)
T ss_dssp             CSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHH
T ss_pred             cChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHH
Confidence            457788888999998773  3 789999999999775543

>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=95.73  E-value=0.0015  Score=48.84  Aligned_cols=39  Identities=31%  Similarity=0.259  Sum_probs=26.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHh--cCCcEEEecCCCCCchHH
Q psy14273         27 FPFDAYDIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        27 fpf~~r~~Q~e~m~~I~~~l~--~~~~~iiEaPTGtGKTls   65 (115)
                      |||.-=-+|.++-+.+.-++-  .+.+++++||+|||||..
T Consensus         4 ~~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~l   44 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTA   44 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHH
T ss_pred             CChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHH
Confidence            566533567666554443332  446899999999999964

>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=95.64  E-value=0.0026  Score=45.63  Aligned_cols=38  Identities=18%  Similarity=0.155  Sum_probs=29.0

Q ss_pred             HHHhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        44 ~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .-+..|..++|.|+||+|||.-.+--++.++..++.+|
T Consensus        30 ~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v   67 (277)
T d1cr2a_          30 LGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKV   67 (277)
T ss_dssp             CSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCE
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccce
Confidence            34566789999999999999766666677776666554

>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=95.63  E-value=0.0028  Score=49.24  Aligned_cols=16  Identities=38%  Similarity=0.565  Sum_probs=13.8

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      .++++-||||+|||-.
T Consensus        69 ~niLfiGPTGvGKTEl   84 (364)
T d1um8a_          69 SNILLIGPTGSGKTLM   84 (364)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             cceeeeCCCCccHHHH
Confidence            5689999999999943

>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=95.49  E-value=0.012  Score=43.16  Aligned_cols=44  Identities=25%  Similarity=0.154  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHHHHhc-----CCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~-----~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .||.|.+.++-+++.+..     +..+|+.-..|+|||+..|+-+..++
T Consensus        56 Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia~l~~l~  104 (298)
T d1z3ix2          56 LRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLL  104 (298)
T ss_dssp             CCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHHHHHHHH
Confidence            789999999988877643     34588888999999998766443433

>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=95.45  E-value=0.0051  Score=39.98  Aligned_cols=31  Identities=23%  Similarity=0.304  Sum_probs=24.5

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.+.|.|+.||||| +++..++.++..++.++
T Consensus         3 Pvi~itG~~GSGKT-TL~~~L~~~l~~~g~~v   33 (170)
T d1np6a_           3 PLLAFAAWSGTGKT-TLLKKLIPALCARGIRP   33 (170)
T ss_dssp             CEEEEECCTTSCHH-HHHHHHHHHHHHTTCCE
T ss_pred             CEEEEEcCCCCCHH-HHHHHHHHHHHHCCCeE
Confidence            35788999999999 46777778887777665

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=95.28  E-value=0.0057  Score=44.36  Aligned_cols=32  Identities=13%  Similarity=0.175  Sum_probs=22.3

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ++.+++.||||+|||.+..=-| .|+..++++|
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA-~~~~~~g~kV   37 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLG-RYYQNLGKKV   37 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHH-HHHHTTTCCE
T ss_pred             CEEEEEECCCCCCHHHHHHHHH-HHHHHCCCcE
Confidence            4567889999999998754333 3555556665

>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=95.09  E-value=0.014  Score=42.67  Aligned_cols=34  Identities=24%  Similarity=0.263  Sum_probs=23.5

Q ss_pred             CHHHHHHHHHHHHHHhc-----------CCcEEEecCCCCCchHH
Q psy14273         32 YDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        32 r~~Q~e~m~~I~~~l~~-----------~~~~iiEaPTGtGKTls   65 (115)
                      .+.+++.++.+...+.+           ...+++.||.|||||+.
T Consensus        14 ~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~l   58 (247)
T d1ixza_          14 AEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             CHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             HHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHH
Confidence            45666666666555433           13589999999999965

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=95.05  E-value=0.004  Score=49.65  Aligned_cols=15  Identities=40%  Similarity=0.510  Sum_probs=13.7

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      .++++-||||+|||+
T Consensus        50 sNILliGPTGvGKTl   64 (443)
T d1g41a_          50 KNILMIGPTGVGKTE   64 (443)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             ccEEEECCCCCCHHH
Confidence            579999999999995

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=94.98  E-value=0.005  Score=39.04  Aligned_cols=16  Identities=31%  Similarity=0.451  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      .+.++|.||.|+|||.
T Consensus         2 ~k~I~l~G~~GsGKST   17 (169)
T d1kaga_           2 KRNIFLVGPMGAGKST   17 (169)
T ss_dssp             CCCEEEECCTTSCHHH
T ss_pred             CCeEEEECCCCCCHHH
Confidence            4678999999999995

>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=94.97  E-value=0.015  Score=44.77  Aligned_cols=33  Identities=18%  Similarity=0.301  Sum_probs=24.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L   67 (115)
                      .-+.|...+.   .++ .++..||.||.|||||.+..
T Consensus       149 ~~~~Q~~A~~---~al-~~~~~vI~G~pGTGKTt~i~  181 (359)
T d1w36d1         149 EINWQKVAAA---VAL-TRRISVISGGPGTGKTTTVA  181 (359)
T ss_dssp             SCCHHHHHHH---HHH-TBSEEEEECCTTSTHHHHHH
T ss_pred             cccHHHHHHH---HHH-cCCeEEEEcCCCCCceehHH
Confidence            3467888444   445 46799999999999998753

>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=94.93  E-value=0.0029  Score=41.07  Aligned_cols=15  Identities=27%  Similarity=0.213  Sum_probs=13.3

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.++|+||+|||||.
T Consensus         8 K~I~i~G~~GsGKTT   22 (192)
T d1lw7a2           8 KTVAILGGESSGKSV   22 (192)
T ss_dssp             EEEEEECCTTSHHHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            468999999999994

>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=94.84  E-value=0.014  Score=42.46  Aligned_cols=38  Identities=8%  Similarity=0.160  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~   72 (115)
                      +.-+++.+.+.++...+..++|.|++||||++  ++-++.
T Consensus         7 ~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~--~A~~ih   44 (247)
T d1ny5a2           7 PKMKEILEKIKKISCAECPVLITGESGVGKEV--VARLIH   44 (247)
T ss_dssp             HHHHHHHHHHHHHTTCCSCEEEECSTTSSHHH--HHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCcCHHH--HHHHHH
Confidence            45566777777777778899999999999985  344443

>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=94.77  E-value=0.0073  Score=45.67  Aligned_cols=45  Identities=22%  Similarity=0.245  Sum_probs=30.0

Q ss_pred             cccCC--CCCCHHHHHHHHHH-----HHHHhcCCc--EEEecCCCCCchHHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNL-----YYTLDNSKF--GIFESPTGTGKSLSLIC   68 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I-----~~~l~~~~~--~iiEaPTGtGKTls~L~   68 (115)
                      .|.|.  |.+-..|.++.+.+     ..++.+|.+  ++..|+||||||.+.+-
T Consensus        51 ~F~fD~Vf~~~~~q~~vy~~~~~plv~~~~~~G~n~~i~aYGqTGSGKTyTm~G  104 (330)
T d1ry6a_          51 EFIVDKVFDDTVDNFTVYENTIKPLIIDLYENGCVCSCFAYGQTGSGKTYTMLG  104 (330)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHHHHHHCCEEEEEEECCTTSSHHHHHHB
T ss_pred             eEeCCeecCCCCCHHHHHHHHHHHHHHHHHhcCCCeEEEeeeccccccceeeec
Confidence            34444  44566777777653     345555643  66789999999999754

>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=94.71  E-value=0.0058  Score=39.82  Aligned_cols=17  Identities=24%  Similarity=0.362  Sum_probs=14.4

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ++.++|+||.|+|||..
T Consensus         1 ~kiI~i~G~~GsGKsT~   17 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTS   17 (190)
T ss_dssp             CCEEEEECCTTSCHHHH
T ss_pred             CCEEEEECCCCCCHHHH
Confidence            46789999999999953

>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=94.64  E-value=0.0095  Score=44.87  Aligned_cols=40  Identities=23%  Similarity=0.127  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHhc--------C---CcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         33 DIQSNFMKNLYYTLDN--------S---KFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~--------~---~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      -+|.+.++.|..++..        +   ...+|.||||+|||..  +-+|+-+
T Consensus        25 iGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~l--ak~la~~   75 (315)
T d1r6bx3          25 FGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEV--TVQLSKA   75 (315)
T ss_dssp             CSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHH--HHHHHHH
T ss_pred             cChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHH--HHHHHhh
Confidence            3577777777666631        1   2578899999999954  4444433

>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=94.55  E-value=0.0084  Score=39.00  Aligned_cols=27  Identities=11%  Similarity=-0.086  Sum_probs=19.3

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .|...+|.||+|+|||.-.+--+..++
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            457899999999999965444444433

>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=94.50  E-value=0.018  Score=41.87  Aligned_cols=15  Identities=27%  Similarity=0.412  Sum_probs=13.3

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .+++.||+|||||+.
T Consensus        42 ~vLL~GppGtGKT~l   56 (246)
T d1d2na_          42 SVLLEGPPHSGKTAL   56 (246)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECcCCCCHHHH
Confidence            489999999999965

>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=94.40  E-value=0.0099  Score=38.89  Aligned_cols=15  Identities=40%  Similarity=0.574  Sum_probs=12.8

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .+||+|+.|+|||..
T Consensus         3 iivi~G~~GsGKTT~   17 (194)
T d1nksa_           3 IGIVTGIPGVGKSTV   17 (194)
T ss_dssp             EEEEEECTTSCHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            578999999999943

>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=94.40  E-value=0.012  Score=42.76  Aligned_cols=30  Identities=23%  Similarity=0.099  Sum_probs=20.4

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++.||||+|||.+..=-| .|+..++++|
T Consensus        13 vi~lvGptGvGKTTTiAKLA-a~~~~~~~kV   42 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLA-KMFVDEGKSV   42 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHH-HHHHHTTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHHCCCce
Confidence            46789999999998754333 3445555664

>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=94.32  E-value=0.011  Score=39.89  Aligned_cols=36  Identities=22%  Similarity=0.234  Sum_probs=24.0

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +..|...+|.|++|+|||.-.+--+..++...+..+
T Consensus        23 i~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~   58 (242)
T d1tf7a1          23 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPG   58 (242)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCE
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCc
Confidence            345678999999999999655444444555544333

>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=94.27  E-value=0.0087  Score=45.32  Aligned_cols=33  Identities=21%  Similarity=0.233  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHhc---------CC--cEEEecCCCCCchHHH
Q psy14273         34 IQSNFMKNLYYTLDN---------SK--FGIFESPTGTGKSLSL   66 (115)
Q Consensus        34 ~Q~e~m~~I~~~l~~---------~~--~~iiEaPTGtGKTls~   66 (115)
                      +|.++++.|..++..         ..  ..++.||||+|||..+
T Consensus        27 GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~la   70 (315)
T d1qvra3          27 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELA   70 (315)
T ss_dssp             SCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHH
Confidence            577777777666642         11  4678999999999653

>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=94.26  E-value=0.013  Score=42.57  Aligned_cols=30  Identities=17%  Similarity=0.113  Sum_probs=16.2

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .++|-||||+|||.+..=-| .|+...+++|
T Consensus        14 vi~lvGptGvGKTTTiAKLA-~~~~~~g~kV   43 (211)
T d1j8yf2          14 VIMLVGVQGTGKATTAGKLA-YFYKKKGFKV   43 (211)
T ss_dssp             EEEEECSCCC----HHHHHH-HHHHHTTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHHCCCce
Confidence            46678999999998754333 3444555554

>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=94.24  E-value=0.021  Score=44.14  Aligned_cols=17  Identities=24%  Similarity=0.624  Sum_probs=14.6

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ++.++|.||+|||||+.
T Consensus       154 ~~~~~~~g~~~~gk~~~  170 (362)
T d1svma_         154 KRYWLFKGPIDSGKTTL  170 (362)
T ss_dssp             CCEEEEECSTTSSHHHH
T ss_pred             cCeEEEECCCCCCHHHH
Confidence            36799999999999964

>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=94.15  E-value=0.0083  Score=39.12  Aligned_cols=18  Identities=22%  Similarity=0.364  Sum_probs=15.2

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .|+.++|.||+|||||..
T Consensus         3 ~g~iI~l~G~~GsGKSTi   20 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTI   20 (176)
T ss_dssp             TTEEEEEEECTTSCHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            466789999999999963

>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=94.10  E-value=0.0096  Score=38.33  Aligned_cols=15  Identities=33%  Similarity=0.308  Sum_probs=12.9

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.+++.||+|+|||.
T Consensus         3 klIii~G~pGsGKTT   17 (152)
T d1ly1a_           3 KIILTIGCPGSGKST   17 (152)
T ss_dssp             EEEEEECCTTSSHHH
T ss_pred             EEEEEECCCCCCHHH
Confidence            357889999999985

>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=93.99  E-value=0.014  Score=42.13  Aligned_cols=32  Identities=16%  Similarity=0.193  Sum_probs=20.3

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ...+++-||||+|||.+..=-|. ++..++++|
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~-~~~~~g~kV   41 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLAL-YYKGKGRRP   41 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHH-HHHHTTCCE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH-HHHHCCCcE
Confidence            34567799999999876443333 334455554

>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=93.96  E-value=0.0099  Score=38.16  Aligned_cols=16  Identities=44%  Similarity=0.698  Sum_probs=13.5

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +.++|.||+|||||.-
T Consensus         3 klI~i~G~~GsGKTTv   18 (176)
T d2bdta1           3 KLYIITGPAGVGKSTT   18 (176)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            3588999999999953

>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=93.80  E-value=0.018  Score=41.89  Aligned_cols=30  Identities=10%  Similarity=0.087  Sum_probs=20.4

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+++-||||+|||.+..=-| .++...+++|
T Consensus        11 vi~lvGptGvGKTTTiAKLA-~~~~~~g~kV   40 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGKLA-RQFEQQGKSV   40 (211)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HHHHTTTCCE
T ss_pred             EEEEECCCCCCHHHHHHHHH-HHHHHCCCcE
Confidence            46679999999998754444 3444555665

>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=93.78  E-value=0.016  Score=44.52  Aligned_cols=41  Identities=17%  Similarity=0.105  Sum_probs=27.2

Q ss_pred             CCCCHHHHHHHHHH----HHHHhcCC--cEEEecCCCCCchHHHHHH
Q psy14273         29 FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        29 f~~r~~Q~e~m~~I----~~~l~~~~--~~iiEaPTGtGKTls~L~~   69 (115)
                      |.+...|.++.+.+    ...+-+|.  .++..|+||||||.+.+-+
T Consensus        88 f~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifaYGqTGSGKTyTm~G~  134 (362)
T d1v8ka_          88 FDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGD  134 (362)
T ss_dssp             ECTTCCHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHHCB
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHHhccCceEEeeccCCCCCceeeeec
Confidence            33556677776653    33334553  4666899999999997653

>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=93.76  E-value=0.011  Score=40.70  Aligned_cols=19  Identities=21%  Similarity=0.197  Sum_probs=15.6

Q ss_pred             cCCcEEEecCCCCCchHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~   66 (115)
                      .+++++|.||.|+|||.-+
T Consensus        28 ~~~~i~i~G~~G~GKTsLl   46 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSII   46 (283)
T ss_dssp             CSSEEEEEESTTSSHHHHH
T ss_pred             cCCEEEEEcCCCCcHHHHH
Confidence            4578889999999999543

>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=93.73  E-value=0.0098  Score=45.73  Aligned_cols=45  Identities=16%  Similarity=0.266  Sum_probs=29.0

Q ss_pred             ccccCC--CCCCHHHHHHHHHHH---HHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLY---YTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~---~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+-..|.++.+.|.   ..+-+|  ..++..|+||||||.+.+
T Consensus        42 ~~f~FD~vf~~~~~q~~vy~~v~~lv~~~l~G~n~~i~aYGqTGSGKTyTm~   93 (364)
T d1sdma_          42 KQHMYDRVFDGNATQDDVFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTIY   93 (364)
T ss_dssp             EEEECSEEECTTCCHHHHHHTTTHHHHHHHTTCEEEEEEECSTTSSHHHHHT
T ss_pred             eEEECCeecCCCCCHHHHHHHHHHHHHHHhcCCceeeeccccCCCCcccccc
Confidence            344454  335566777776653   333345  346679999999999973

>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=93.66  E-value=0.026  Score=37.20  Aligned_cols=16  Identities=13%  Similarity=0.385  Sum_probs=12.4

Q ss_pred             CCcEE-EecCCCCCchH
Q psy14273         49 SKFGI-FESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~i-iEaPTGtGKTl   64 (115)
                      ++.+| |.||+|||||.
T Consensus        21 ~~~iIgI~G~~GSGKST   37 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTT   37 (198)
T ss_dssp             SSEEEEEEECTTSSHHH
T ss_pred             CCEEEEEECCCCCCHHH
Confidence            34445 89999999994

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=93.63  E-value=0.013  Score=37.90  Aligned_cols=15  Identities=20%  Similarity=0.306  Sum_probs=13.2

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..++|.||.|||||.
T Consensus         5 ~~I~i~G~pGsGKTT   19 (173)
T d1rkba_           5 PNILLTGTPGVGKTT   19 (173)
T ss_dssp             CCEEEECSTTSSHHH
T ss_pred             CEEEEECCCCCCHHH
Confidence            468899999999995

>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=93.61  E-value=0.017  Score=37.22  Aligned_cols=18  Identities=22%  Similarity=0.294  Sum_probs=14.9

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      ..+.++|.||.|+|||..
T Consensus         2 ~~kiI~l~G~~GsGKsTv   19 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGI   19 (178)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            356789999999999943

>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=93.58  E-value=0.011  Score=38.55  Aligned_cols=17  Identities=24%  Similarity=0.364  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ++.+||.||.|||||.-
T Consensus         6 ~~iivl~G~~GsGKsT~   22 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAV   22 (171)
T ss_dssp             SEEEEEECSTTSCHHHH
T ss_pred             CeEEEEECCCCCCHHHH
Confidence            45688899999999953

>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=93.54  E-value=0.0091  Score=44.89  Aligned_cols=45  Identities=13%  Similarity=0.144  Sum_probs=30.3

Q ss_pred             ccccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+-..|.++.+.+.    ..+-+|.  .++..|+||||||.+.+
T Consensus        42 ~~f~FD~vf~~~~~q~~vf~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          42 KPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             EEEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             ceeECCEEECCCCCHHHHHHHHHHHHHHHHHcCCCcceeeecccCCCCceecc
Confidence            445566  446667777766543    3334553  56779999999999975

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=93.47  E-value=0.019  Score=37.37  Aligned_cols=17  Identities=24%  Similarity=0.235  Sum_probs=14.4

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      +.+++|.||.|+|||..
T Consensus         5 ~~~I~i~G~~GsGKTT~   21 (174)
T d1y63a_           5 GINILITGTPGTGKTSM   21 (174)
T ss_dssp             SCEEEEECSTTSSHHHH
T ss_pred             CCEEEEEeCCCCCHHHH
Confidence            45799999999999953

>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=93.31  E-value=0.015  Score=39.20  Aligned_cols=31  Identities=16%  Similarity=0.233  Sum_probs=22.6

Q ss_pred             HhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         46 LDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      +..|...+|.|++|+|||.-.+--+...+..
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~   61 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNLQNP   61 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHTTCG
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            3345789999999999997666665555443

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=93.21  E-value=0.026  Score=42.45  Aligned_cols=32  Identities=22%  Similarity=0.051  Sum_probs=21.3

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      ..|++|-|+||+|||.++. ..+..+...+..+
T Consensus        50 ~~H~~I~G~tGsGKT~~l~-~li~~~~~~g~~~   81 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLR-ELAYTGLLRGDRM   81 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHH-HHHHHHHHTTCEE
T ss_pred             cceEEEEeCCCCcHHHHHH-HHHHHHHhCCCCE
Confidence            4689999999999997643 3344444444443

>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=93.20  E-value=0.032  Score=36.92  Aligned_cols=30  Identities=10%  Similarity=-0.126  Sum_probs=23.5

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .+-|.|+.|||||. ++.-.+.++...+.++
T Consensus         3 ii~I~G~~gSGKTT-li~~l~~~L~~~g~~v   32 (165)
T d1xjca_           3 VWQVVGYKHSGKTT-LMEKWVAAAVREGWRV   32 (165)
T ss_dssp             EEEEECCTTSSHHH-HHHHHHHHHHHTTCCE
T ss_pred             EEEEEeCCCCCHHH-HHHHHHHHHHhCCCeE
Confidence            34589999999994 6667788888877776

>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=93.16  E-value=0.025  Score=42.76  Aligned_cols=44  Identities=25%  Similarity=0.439  Sum_probs=30.1

Q ss_pred             cccCC--CCCCHHHHHHHHHHHHHHh---cCC--cEEEecCCCCCchHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLYYTLD---NSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~~~l~---~~~--~~iiEaPTGtGKTls~L   67 (115)
                      .|.|.  |.+-..|.++.+.|...+.   +|.  .++..|+||||||.+.+
T Consensus        51 ~f~FD~vf~~~~~q~~vy~~v~~~v~~~l~G~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          51 EFKFDKIFDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             EEEESEEECTTCCHHHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             EeecCeEeCCCCCHHHHHHHhhhhhcchhcccccceeeeeccCCccccccc
Confidence            34454  3355668888887655443   343  46679999999999985

>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=93.11  E-value=0.01  Score=45.66  Aligned_cols=45  Identities=20%  Similarity=0.256  Sum_probs=29.0

Q ss_pred             ccccCC--CCCCHHHHHHHHHHHHHH---hcC--CcEEEecCCCCCchHHHH
Q psy14273         23 SEFPFP--FDAYDIQSNFMKNLYYTL---DNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        23 ~~~~fp--f~~r~~Q~e~m~~I~~~l---~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      ..|.|.  |.+-..|.++.+.|...+   -+|  ..++..|+||||||.+..
T Consensus        92 ~~F~FD~vf~~~~~Q~~Vy~~v~plv~~vl~G~n~ti~aYGqtGSGKT~Tm~  143 (368)
T d2ncda_          92 QIFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMD  143 (368)
T ss_dssp             CEEECSEEECTTCCHHHHHTTTHHHHHHHHTTCEEEEEEECSTTSSHHHHHT
T ss_pred             eeeECCeEECCCCCccchHHHHHHHHHHHhcccceeEEeeccCCCccceEec
Confidence            344555  445556888766543322   345  357779999999999864

>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=93.05  E-value=0.062  Score=39.31  Aligned_cols=33  Identities=30%  Similarity=0.324  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHhc-----------CCcEEEecCCCCCchHH
Q psy14273         33 DIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        33 ~~Q~e~m~~I~~~l~~-----------~~~~iiEaPTGtGKTls   65 (115)
                      +.+.+.+.++...+..           .+.+++.||+|||||+.
T Consensus        18 ~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_          18 DEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             HHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHH
T ss_pred             HHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHH
Confidence            4555555555444432           24589999999999965

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.80  E-value=0.068  Score=37.79  Aligned_cols=34  Identities=18%  Similarity=0.055  Sum_probs=22.4

Q ss_pred             CCHHHHHHHHHHHHHHhcC----CcEEEecCCCCCchH
Q psy14273         31 AYDIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSL   64 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~~----~~~iiEaPTGtGKTl   64 (115)
                      .-+........+.++++.-    ..+++.||+|+|||.
T Consensus        14 vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTH   51 (213)
T d1l8qa2          14 VGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTH   51 (213)
T ss_dssp             CCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHH
T ss_pred             CCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHH
Confidence            3344555555555555432    348999999999995

>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=92.71  E-value=0.023  Score=41.15  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=16.5

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKW   73 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~   73 (115)
                      +.+++.||.|||||+.  +-++++
T Consensus        39 ~giLL~GppGtGKT~l--~~ala~   60 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI--ARAVAN   60 (258)
T ss_dssp             CEEEEECCTTSSHHHH--HHHHHH
T ss_pred             ceeEEecCCCCCchHH--HHHHHH
Confidence            4588999999999964  444444

>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=92.67  E-value=0.016  Score=43.81  Aligned_cols=43  Identities=21%  Similarity=0.254  Sum_probs=28.1

Q ss_pred             ccCC--CCCCHHHHHHHHHH----HHHHhcCC--cEEEecCCCCCchHHHH
Q psy14273         25 FPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLI   67 (115)
Q Consensus        25 ~~fp--f~~r~~Q~e~m~~I----~~~l~~~~--~~iiEaPTGtGKTls~L   67 (115)
                      |.|.  |.+...|.++.+.+    ...+-+|.  .++..|+||||||.+.+
T Consensus        49 f~FD~vf~~~~~q~~vy~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyTm~   99 (345)
T d1x88a1          49 YTFDMVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTME   99 (345)
T ss_dssp             EECSEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHHT
T ss_pred             EecCEEeCCCCCHHHHHHHHHHHhHHHHhccCCceEEeeeeccccceEEee
Confidence            4444  33556677766554    33444563  46679999999998864

>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=92.18  E-value=0.028  Score=37.91  Aligned_cols=16  Identities=25%  Similarity=0.540  Sum_probs=14.4

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      |+.+||.||.|+|||.
T Consensus         2 G~iivl~GpsG~GK~t   17 (182)
T d1znwa1           2 GRVVVLSGPSAVGKST   17 (182)
T ss_dssp             CCEEEEECSTTSSHHH
T ss_pred             CeEEEEECCCCCCHHH
Confidence            6789999999999995

>d1nn5a_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.94  E-value=0.051  Score=38.14  Aligned_cols=31  Identities=13%  Similarity=0.093  Sum_probs=20.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHHHhhhh
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWYSDHKI   79 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l~~~~~   79 (115)
                      .|..++|||+-|+|||.- .-.+..++...+.
T Consensus         2 rG~lI~ieG~dGsGKsT~-~~~L~~~L~~~g~   32 (209)
T d1nn5a_           2 RGALIVLEGVDRAGKSTQ-SRKLVEALCAAGH   32 (209)
T ss_dssp             CCCEEEEEESTTSSHHHH-HHHHHHHHHHTTC
T ss_pred             CeeEEEEECCCCCCHHHH-HHHHHHHHHHCCC
Confidence            467899999999999852 1223455555443

>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=91.85  E-value=0.047  Score=35.64  Aligned_cols=14  Identities=29%  Similarity=0.328  Sum_probs=12.6

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|.||+|+|||.
T Consensus         2 ki~I~G~~G~GKST   15 (178)
T d1ye8a1           2 KIIITGEPGVGKTT   15 (178)
T ss_dssp             EEEEECCTTSSHHH
T ss_pred             EEEEECCCCcHHHH
Confidence            47899999999996

>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=91.83  E-value=0.033  Score=37.81  Aligned_cols=19  Identities=32%  Similarity=0.392  Sum_probs=16.4

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +.+.+.++|.||+|||||.
T Consensus         5 ~~~~~iI~l~G~pGSGKsT   23 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGT   23 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHH
T ss_pred             ccCCcEEEEECCCCCCHHH
Confidence            4567889999999999985

>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=91.75  E-value=0.033  Score=39.35  Aligned_cols=17  Identities=35%  Similarity=0.604  Sum_probs=15.0

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      +|..+||.||+|+|||.
T Consensus         1 ~G~livi~GPSG~GK~t   17 (205)
T d1s96a_           1 QGTLYIVSAPSGAGKSS   17 (205)
T ss_dssp             CCCEEEEECCTTSCHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            47789999999999995

>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=91.73  E-value=0.033  Score=38.30  Aligned_cols=17  Identities=35%  Similarity=0.573  Sum_probs=15.1

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .|+.++|||+-|+|||.
T Consensus         1 rgkfIviEG~dGsGKsT   17 (210)
T d4tmka_           1 RSKYIVIEGLEGAGKTT   17 (210)
T ss_dssp             CCCEEEEEECTTSCHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            37889999999999985

>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=91.72  E-value=0.064  Score=39.81  Aligned_cols=27  Identities=22%  Similarity=0.358  Sum_probs=21.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ++..||+|+-|||||.++..=++..+.
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~   42 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLL   42 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHh
Confidence            467899999999999887766666654

>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=91.63  E-value=0.064  Score=37.69  Aligned_cols=27  Identities=26%  Similarity=0.311  Sum_probs=20.9

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+...+|.|++|+|||.-.+--+++++
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~~ia   54 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAAQIA   54 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            367899999999999976666555544

>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=91.54  E-value=0.048  Score=37.56  Aligned_cols=27  Identities=22%  Similarity=0.167  Sum_probs=19.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .+...+|.||+|+|||.-.+--+...+
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~   51 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENAC   51 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            457899999999999975544444443

>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=91.46  E-value=0.032  Score=35.85  Aligned_cols=18  Identities=11%  Similarity=0.001  Sum_probs=14.6

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      +|..++|.|+.|+|||..
T Consensus         5 ~g~~I~l~G~~GsGKTTi   22 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAI   22 (183)
T ss_dssp             CCEEEEEECSTTSSHHHH
T ss_pred             CCeEEEEECCCCCCHHHH
Confidence            456677999999999954

>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=91.41  E-value=0.033  Score=37.57  Aligned_cols=20  Identities=20%  Similarity=0.004  Sum_probs=16.0

Q ss_pred             cCCcEEEecCCCCCchHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L   67 (115)
                      .|..++|.||+|+|||.-.+
T Consensus        33 ~G~~~li~G~pGsGKT~l~l   52 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCH   52 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHH
Confidence            45689999999999996433

>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=91.36  E-value=0.035  Score=38.09  Aligned_cols=22  Identities=14%  Similarity=-0.016  Sum_probs=16.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .|..++|.||+|+|||.-.+--
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~   56 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTL   56 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHH
Confidence            3467999999999999654433

>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=91.24  E-value=0.039  Score=37.62  Aligned_cols=15  Identities=40%  Similarity=0.623  Sum_probs=13.1

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.+||.||+|+|||.
T Consensus         2 rpIvl~GpsG~GK~t   16 (186)
T d1gkya_           2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            358999999999995

>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=91.13  E-value=0.035  Score=37.43  Aligned_cols=15  Identities=13%  Similarity=0.151  Sum_probs=12.9

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..++|.||.|||||.
T Consensus         4 m~I~i~GppGsGKsT   18 (189)
T d1zaka1           4 LKVMISGAPASGKGT   18 (189)
T ss_dssp             CCEEEEESTTSSHHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            468899999999975

>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=90.81  E-value=0.091  Score=41.40  Aligned_cols=41  Identities=24%  Similarity=0.357  Sum_probs=34.9

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHhcC-CcEEEecCCCCCchHH
Q psy14273         25 FPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLS   65 (115)
Q Consensus        25 ~~fpf~~r~~Q~e~m~~I~~~l~~~-~~~iiEaPTGtGKTls   65 (115)
                      +.=||.|---|=+.++.+...|.+| +..++.|-||||||+.
T Consensus         6 ~~~~~~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~   47 (413)
T d1t5la1           6 LVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFT   47 (413)
T ss_dssp             CCCSSCCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHH
T ss_pred             EecCCCCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHH
Confidence            3457888888989999999999887 5688999999999954

>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=90.62  E-value=0.074  Score=40.15  Aligned_cols=34  Identities=18%  Similarity=0.204  Sum_probs=23.1

Q ss_pred             HHHHHHHHH----HHHHhcC--CcEEEecCCCCCchHHHH
Q psy14273         34 IQSNFMKNL----YYTLDNS--KFGIFESPTGTGKSLSLI   67 (115)
Q Consensus        34 ~Q~e~m~~I----~~~l~~~--~~~iiEaPTGtGKTls~L   67 (115)
                      -|.++.+.+    ...+-+|  ..++..|+||||||.+.+
T Consensus        66 sQ~~vy~~~~~plv~~~l~G~n~ti~aYGqTgSGKT~Tm~  105 (349)
T d2zfia1          66 SQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMM  105 (349)
T ss_dssp             CHHHHHHHTHHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             cHHHHHHHhhHHHHHHHHhccCceeeeeccCCCCCceeec
Confidence            366665543    3344456  346779999999999974

>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=90.61  E-value=0.069  Score=40.39  Aligned_cols=45  Identities=27%  Similarity=0.276  Sum_probs=28.2

Q ss_pred             cccCC--CCCCHHHHHHHHHHH----HHHhcCC--cEEEecCCCCCchHHHHH
Q psy14273         24 EFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLIC   68 (115)
Q Consensus        24 ~~~fp--f~~r~~Q~e~m~~I~----~~l~~~~--~~iiEaPTGtGKTls~L~   68 (115)
                      .|.|.  |.+-..|.++.+.+.    ..+-+|.  .++..|+||||||.+.+-
T Consensus        47 ~f~FD~vf~~~~~q~~vy~~~~~plv~~~l~G~n~ti~aYG~tgSGKT~Tm~G   99 (354)
T d1goja_          47 SFTFDRVFDMSCKQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMMG   99 (354)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHTB
T ss_pred             eEECCeEcCCCCCHHHHHHHHHHHHHHHhhccCceeEEecccCCCCcceeeec
Confidence            34444  334456777665443    2333553  466799999999998653

>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=90.47  E-value=0.069  Score=38.82  Aligned_cols=16  Identities=44%  Similarity=0.609  Sum_probs=14.0

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +.+++.||.|||||+.
T Consensus        42 ~giLL~Gp~GtGKT~l   57 (265)
T d1r7ra3          42 KGVLFYGPPGCGKTLL   57 (265)
T ss_dssp             CEEEEBCCTTSSHHHH
T ss_pred             CeEEEECCCCCcchhH
Confidence            4689999999999965

>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=90.05  E-value=0.091  Score=38.38  Aligned_cols=25  Identities=28%  Similarity=0.470  Sum_probs=18.6

Q ss_pred             CCcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         49 SKFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ++.-+|-||||+|||.  |+=|++|+.
T Consensus        25 ~~l~~i~G~NGsGKS~--ileAi~~~l   49 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSN--MMDAISFVL   49 (427)
T ss_dssp             CSEEEEECSTTSSHHH--HHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHH--HHHHHHHHh
Confidence            3456788999999995  355677764

>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=90.03  E-value=0.066  Score=35.91  Aligned_cols=17  Identities=24%  Similarity=0.446  Sum_probs=13.7

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      |..+||-||+|||||.-
T Consensus         3 ~~riil~G~pGSGKsT~   19 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQ   19 (190)
T ss_dssp             CCEEEEECCTTSSHHHH
T ss_pred             ccEEEEECCCCCCHHHH
Confidence            45677889999999863

>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=89.72  E-value=0.17  Score=38.33  Aligned_cols=45  Identities=20%  Similarity=0.152  Sum_probs=30.5

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCCcEEEecCCCCCchHHHHHHHHHHHHh
Q psy14273         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSD   76 (115)
Q Consensus        26 ~fpf~~r~~Q~e~m~~I~~~l~~~~~~iiEaPTGtGKTls~L~~al~~l~~   76 (115)
                      .+...+|++|.--  .+  +|.+|  -|.|+.||=||||+.-+|+.-.+..
T Consensus        76 tlG~RhyDVQLiG--gi--~L~~G--~iaem~TGEGKTL~a~l~a~l~al~  120 (273)
T d1tf5a3          76 VTGMFPFKVQLMG--GV--ALHDG--NIAEMKTGEGKTLTSTLPVYLNALT  120 (273)
T ss_dssp             HHSCCCCHHHHHH--HH--HHHTT--SEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             hhceEEehhHHHH--HH--HHHhh--hheeecCCCcchhHHHHHHHHHHhc
Confidence            3456677887653  22  23444  5889999999999988886544433

>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=89.68  E-value=0.062  Score=35.78  Aligned_cols=14  Identities=29%  Similarity=0.470  Sum_probs=12.4

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|.||.|||||.
T Consensus         2 ~I~i~G~pGsGKsT   15 (181)
T d2cdna1           2 RVLLLGPPGAGKGT   15 (181)
T ss_dssp             EEEEECCTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57889999999985

>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=89.67  E-value=0.072  Score=35.65  Aligned_cols=14  Identities=29%  Similarity=0.451  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|||+.|+|||.
T Consensus        11 ~I~ieG~~GsGKTT   24 (197)
T d2vp4a1          11 TVLIEGNIGSGKTT   24 (197)
T ss_dssp             EEEEECSTTSCHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            68899999999995

>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=89.48  E-value=0.068  Score=36.62  Aligned_cols=14  Identities=36%  Similarity=0.610  Sum_probs=12.6

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .+||.||+|+|||.
T Consensus         2 pIvl~GPsGsGK~t   15 (190)
T d1lvga_           2 PVVLSGPSGAGKST   15 (190)
T ss_dssp             CEEEECCTTSSHHH
T ss_pred             eEEEECCCCCCHHH
Confidence            47899999999995

>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=89.46  E-value=0.063  Score=36.50  Aligned_cols=22  Identities=14%  Similarity=-0.183  Sum_probs=16.7

Q ss_pred             cCCcEEEecCCCCCchHHHHHH
Q psy14273         48 NSKFGIFESPTGTGKSLSLICG   69 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls~L~~   69 (115)
                      .|..++|.||+|+|||.-.+.-
T Consensus        36 ~G~~~~i~G~~GsGKT~lalq~   57 (258)
T d1v5wa_          36 SMAITEAFGEFRTGKTQLSHTL   57 (258)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHH
Confidence            3467999999999999654433

>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=89.44  E-value=0.061  Score=35.76  Aligned_cols=15  Identities=20%  Similarity=0.062  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|||||.-
T Consensus         2 ~I~i~G~pGSGKsT~   16 (179)
T d1e4va1           2 RIILLGAPVAGKGTQ   16 (179)
T ss_dssp             EEEEEESTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478899999999953

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.33  E-value=0.066  Score=35.22  Aligned_cols=15  Identities=20%  Similarity=0.226  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|||||.-
T Consensus         2 ~I~i~G~pGSGKsT~   16 (182)
T d1zina1           2 NLVLMGLPGAGKGTQ   16 (182)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999853

>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=89.29  E-value=0.025  Score=36.33  Aligned_cols=23  Identities=17%  Similarity=0.156  Sum_probs=16.8

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      ..||.||+|+|||.-  +-||.|+.
T Consensus        26 ~tvi~G~NGsGKSti--l~Ai~~~L   48 (222)
T d1qhla_          26 VTTLSGGNGAGKSTT--MAAFVTAL   48 (222)
T ss_dssp             HHHHHSCCSHHHHHH--HHHHHHHH
T ss_pred             eEEEECCCCCCHHHH--HHHHHHHh
Confidence            456789999999953  55566664

>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=89.19  E-value=0.068  Score=35.71  Aligned_cols=15  Identities=20%  Similarity=0.224  Sum_probs=12.8

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|||||.-
T Consensus         2 ~I~i~G~pGSGKsT~   16 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQ   16 (182)
T ss_dssp             EEEEECSTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999853

>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=89.19  E-value=0.066  Score=41.02  Aligned_cols=17  Identities=24%  Similarity=0.216  Sum_probs=13.8

Q ss_pred             CCcEEEecCCCCCchHH
Q psy14273         49 SKFGIFESPTGTGKSLS   65 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTls   65 (115)
                      ++++++.||.|||||+.
T Consensus       123 ~g~~l~~G~pG~GKT~l  139 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPL  139 (321)
T ss_dssp             SEEEEEECSSSSCHHHH
T ss_pred             CceEEEECCCCccHHHH
Confidence            35677799999999965

>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=89.14  E-value=0.21  Score=35.00  Aligned_cols=40  Identities=10%  Similarity=0.043  Sum_probs=26.6

Q ss_pred             HHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         41 NLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        41 ~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      .|...+..+  +.+++.|-.|+|||.....-+..++.. +++|
T Consensus        10 ~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~-G~rV   51 (279)
T d1ihua2          10 ALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADM-GFDV   51 (279)
T ss_dssp             HHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             HHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCcE
Confidence            344444444  567789999999998866666666543 4554

>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=89.10  E-value=0.086  Score=35.27  Aligned_cols=16  Identities=25%  Similarity=0.376  Sum_probs=13.2

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..+||.||.|||||.-
T Consensus         3 mrIvl~G~pGSGKtT~   18 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQ   18 (180)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            4578899999999853

>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=89.08  E-value=0.08  Score=36.17  Aligned_cols=16  Identities=31%  Similarity=0.150  Sum_probs=13.9

Q ss_pred             CCcEEEecCCCCCchH
Q psy14273         49 SKFGIFESPTGTGKSL   64 (115)
Q Consensus        49 ~~~~iiEaPTGtGKTl   64 (115)
                      .+.++|||+-|+|||.
T Consensus         2 ~k~I~ieG~dGsGKST   17 (241)
T d1p5zb_           2 IKKISIEGNIAAGKST   17 (241)
T ss_dssp             CEEEEEECSTTSSHHH
T ss_pred             CCEEEEECCCCCCHHH
Confidence            3578999999999995

>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=88.56  E-value=0.032  Score=36.85  Aligned_cols=15  Identities=20%  Similarity=0.193  Sum_probs=12.5

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..++|.|+.|+|||.
T Consensus        20 ~vI~L~G~pGSGKTT   34 (195)
T d1x6va3          20 CTVWLTGLSGAGKTT   34 (195)
T ss_dssp             EEEEEESSCHHHHHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            356689999999985

>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=88.45  E-value=0.091  Score=35.95  Aligned_cols=15  Identities=20%  Similarity=0.293  Sum_probs=13.4

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.+||.||+|+||+.
T Consensus         4 k~ivl~Gpsg~GK~t   18 (178)
T d1kgda_           4 KTLVLLGAHGVGRRH   18 (178)
T ss_dssp             CEEEEECCTTSSHHH
T ss_pred             CcEEEECCCCCCHHH
Confidence            578999999999995

>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=88.42  E-value=0.09  Score=34.88  Aligned_cols=16  Identities=38%  Similarity=0.329  Sum_probs=13.0

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ++++|.||.|+|||..
T Consensus         1 k~I~liG~~GsGKsTi   16 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTL   16 (161)
T ss_dssp             CCEEEECCTTSCHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            3578889999999953

>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=88.25  E-value=0.096  Score=35.07  Aligned_cols=16  Identities=25%  Similarity=0.451  Sum_probs=13.1

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +.++|.||.|||||.-
T Consensus         4 piI~I~GppGSGKgT~   19 (225)
T d1ckea_           4 PVITIDGPSGAGKGTL   19 (225)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             CEEEEECCCCCCHHHH
Confidence            4677899999999853

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.80  E-value=0.099  Score=35.48  Aligned_cols=15  Identities=27%  Similarity=0.257  Sum_probs=13.1

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..+|+.|++|+|||.
T Consensus        15 ~liil~G~pGsGKST   29 (172)
T d1yj5a2          15 EVVVAVGFPGAGKST   29 (172)
T ss_dssp             CEEEEECCTTSSHHH
T ss_pred             EEEEEECCCCCCHHH
Confidence            468899999999994

>d1gsia_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=87.76  E-value=0.19  Score=33.62  Aligned_cols=14  Identities=29%  Similarity=0.368  Sum_probs=12.3

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|||+-|+|||.
T Consensus         2 lI~ieG~dGsGKST   15 (208)
T d1gsia_           2 LIAIEGVDGAGKRT   15 (208)
T ss_dssp             EEEEECSTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            47899999999985

>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=87.49  E-value=0.081  Score=36.50  Aligned_cols=15  Identities=27%  Similarity=0.180  Sum_probs=13.3

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.++|||+-|+|||.
T Consensus         3 k~IviEG~~GsGKST   17 (241)
T d2ocpa1           3 RRLSIEGNIAVGKST   17 (241)
T ss_dssp             EEEEEEECTTSSHHH
T ss_pred             eEEEEECCCCCcHHH
Confidence            468999999999996

>d1tmka_ c.37.1.1 (A:) Thymidylate 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: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.36  E-value=0.12  Score=36.18  Aligned_cols=18  Identities=28%  Similarity=0.346  Sum_probs=15.5

Q ss_pred             cCCcEEEecCCCCCchHH
Q psy14273         48 NSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTls   65 (115)
                      .|..++|||+-|+|||.-
T Consensus         2 kGk~I~iEG~DGsGKST~   19 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQ   19 (214)
T ss_dssp             CCCEEEEEESTTSSHHHH
T ss_pred             CeEEEEEECCCCCcHHHH
Confidence            468899999999999853

>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=87.35  E-value=0.2  Score=34.89  Aligned_cols=37  Identities=8%  Similarity=-0.085  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHhcC--CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         35 QSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        35 Q~e~m~~I~~~l~~~--~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      |.++++   +.+.++  .+.+++||.|+|||-..+.-+ .++.
T Consensus         2 ~~~~l~---~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~   40 (198)
T d2gnoa2           2 QLETLK---RIIEKSEGISILINGEDLSYPREVSLELP-EYVE   40 (198)
T ss_dssp             HHHHHH---HHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHH
T ss_pred             HHHHHH---HHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHh
Confidence            555444   445544  679999999999997665543 4443

>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=87.29  E-value=0.091  Score=37.00  Aligned_cols=20  Identities=25%  Similarity=0.522  Sum_probs=16.6

Q ss_pred             HhcCCcEEEecCCCCCchHH
Q psy14273         46 LDNSKFGIFESPTGTGKSLS   65 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTls   65 (115)
                      +..|..+.+-||+|+|||.-
T Consensus        24 i~~Gei~~l~G~NGsGKSTL   43 (200)
T d1sgwa_          24 IEKGNVVNFHGPNGIGKTTL   43 (200)
T ss_dssp             EETTCCEEEECCTTSSHHHH
T ss_pred             EcCCCEEEEECCCCChHHHH
Confidence            35678899999999999953

>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=87.23  E-value=0.34  Score=35.11  Aligned_cols=29  Identities=31%  Similarity=0.421  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHhcC---CcEEEecCCCCCchHH
Q psy14273         37 NFMKNLYYTLDNS---KFGIFESPTGTGKSLS   65 (115)
Q Consensus        37 e~m~~I~~~l~~~---~~~iiEaPTGtGKTls   65 (115)
                      .++..+...+...   ..++|.||.+||||+-
T Consensus        38 ~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f   69 (205)
T d1tuea_          38 TFLGALKSFLKGTPKKNCLVFCGPANTGKSYF   69 (205)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHHH
T ss_pred             HHHHHHHHHHcCCCCceEEEEECCCCccHHHH
Confidence            4666777777543   5688999999999953

>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=87.11  E-value=0.21  Score=33.81  Aligned_cols=24  Identities=21%  Similarity=0.408  Sum_probs=16.7

Q ss_pred             cEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         51 FGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        51 ~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      .++|-||.|+|||. ++-.++.++.
T Consensus         2 vi~v~G~~GsGKTT-Ll~~ll~~~~   25 (244)
T d1yrba1           2 IVVFVGTAGSGKTT-LTGEFGRYLE   25 (244)
T ss_dssp             EEEEECSTTSSHHH-HHHHHHHHHT
T ss_pred             EEEEEcCCCCcHHH-HHHHHHHHHh
Confidence            46789999999984 4444555543

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.10  E-value=0.11  Score=34.93  Aligned_cols=15  Identities=20%  Similarity=0.202  Sum_probs=12.5

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      ..++|-||.|||||.
T Consensus         9 ~iI~i~GppGSGKsT   23 (196)
T d1ukza_           9 SVIFVLGGPGAGKGT   23 (196)
T ss_dssp             EEEEEECSTTSSHHH
T ss_pred             cEEEEECCCCCCHHH
Confidence            467888999999973

>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=86.90  E-value=0.1  Score=34.91  Aligned_cols=14  Identities=21%  Similarity=0.264  Sum_probs=12.3

Q ss_pred             cEEEecCCCCCchH
Q psy14273         51 FGIFESPTGTGKSL   64 (115)
Q Consensus        51 ~~iiEaPTGtGKTl   64 (115)
                      .++|.||.|||||.
T Consensus         8 iI~i~G~pGSGKsT   21 (194)
T d1qf9a_           8 VVFVLGGPGSGKGT   21 (194)
T ss_dssp             EEEEEESTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57889999999995

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.82  E-value=0.13  Score=33.83  Aligned_cols=16  Identities=25%  Similarity=0.314  Sum_probs=12.7

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      +.+||.|+.|+|||..
T Consensus         2 p~IvliG~~G~GKSTi   17 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTI   17 (165)
T ss_dssp             CSEEEECSTTSSHHHH
T ss_pred             CcEEEECCCCCCHHHH
Confidence            3567779999999954

>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=86.59  E-value=0.14  Score=33.78  Aligned_cols=15  Identities=13%  Similarity=0.127  Sum_probs=12.2

Q ss_pred             CcEEEecCCCCCchH
Q psy14273         50 KFGIFESPTGTGKSL   64 (115)
Q Consensus        50 ~~~iiEaPTGtGKTl   64 (115)
                      +.+++-||.|+|||.
T Consensus         3 ~~Iil~G~~GsGKST   17 (170)
T d1e6ca_           3 EPIFMVGARGCGMTT   17 (170)
T ss_dssp             CCEEEESCTTSSHHH
T ss_pred             CCEEEECCCCCCHHH
Confidence            457778999999974

>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=86.46  E-value=0.13  Score=34.28  Aligned_cols=15  Identities=20%  Similarity=0.231  Sum_probs=12.7

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .++|.||.|||||.-
T Consensus         3 iI~i~GppGSGKsT~   17 (194)
T d1teva_           3 VVFVLGGPGAGKGTQ   17 (194)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            478999999999854

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=86.12  E-value=0.57  Score=34.22  Aligned_cols=36  Identities=14%  Similarity=-0.007  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHhcC----CcEEEecCCCCCchHHHHHHHHHHH
Q psy14273         37 NFMKNLYYTLDNS----KFGIFESPTGTGKSLSLICGILKWY   74 (115)
Q Consensus        37 e~m~~I~~~l~~~----~~~iiEaPTGtGKTls~L~~al~~l   74 (115)
                      .++..++.+|..+    ..+++.||.++|||+  ++-++..+
T Consensus        88 ~f~~~l~~~L~~~~~k~n~~~l~G~~~tGKS~--f~~~i~~~  127 (267)
T d1u0ja_          88 YAASVFLGWATKKFGKRNTIWLFGPATTGKTN--IAEAIAHT  127 (267)
T ss_dssp             HHHHHHHHHHTTCSTTCCEEEEECSTTSSHHH--HHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCccEEEEEEcCCCCCHHH--HHHHHHHH
Confidence            3556677777533    457889999999995  44445444

>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=84.46  E-value=0.15  Score=37.21  Aligned_cols=18  Identities=22%  Similarity=0.239  Sum_probs=15.6

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.|.||+|+|||.
T Consensus        27 ~~Ge~vaIvG~sGsGKST   44 (241)
T d2pmka1          27 KQGEVIGIVGRSGSGKST   44 (241)
T ss_dssp             ETTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCCHHH
Confidence            457889999999999984

>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=84.34  E-value=0.34  Score=33.86  Aligned_cols=31  Identities=13%  Similarity=0.139  Sum_probs=23.1

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +.+++.+..|+|||.....-|..++.. +++|
T Consensus         9 ~~i~~sGKGGVGKTTvaa~lA~~lA~~-G~rV   39 (296)
T d1ihua1           9 PYLFFTGKGGVGKTSISCATAIRLAEQ-GKRV   39 (296)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHT-TCCE
T ss_pred             eEEEEECCCcChHHHHHHHHHHHHHHC-CCCE
Confidence            467889999999998877766666644 4554

>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=84.26  E-value=0.27  Score=34.68  Aligned_cols=24  Identities=29%  Similarity=0.533  Sum_probs=17.8

Q ss_pred             CcEEEecCCCCCchHHHHHHHHHHHH
Q psy14273         50 KFGIFESPTGTGKSLSLICGILKWYS   75 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls~L~~al~~l~   75 (115)
                      +.-||.||+|+|||..  +=|+.|+.
T Consensus        25 ~lnvlvG~NgsGKS~i--L~Ai~~~l   48 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNI--IDAIKWVF   48 (308)
T ss_dssp             SEEEEECCTTTCSTHH--HHHHHHTS
T ss_pred             CeEEEECCCCCcHHHH--HHHHHHHh
Confidence            3568999999999964  45566653

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.05  E-value=0.2  Score=34.00  Aligned_cols=13  Identities=31%  Similarity=0.118  Sum_probs=10.8

Q ss_pred             EEEecCCCCCchH
Q psy14273         52 GIFESPTGTGKSL   64 (115)
Q Consensus        52 ~iiEaPTGtGKTl   64 (115)
                      +-|.||+|||||.
T Consensus         5 IgI~G~~gSGKST   17 (213)
T d1uj2a_           5 IGVSGGTASGKSS   17 (213)
T ss_dssp             EEEECSTTSSHHH
T ss_pred             EEEECCCCCCHHH
Confidence            3479999999984

>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=83.93  E-value=0.45  Score=33.85  Aligned_cols=33  Identities=15%  Similarity=0.251  Sum_probs=23.5

Q ss_pred             CCHHHHHHHHHHHHHHhc--CCcEEEecCCCCCchHHH
Q psy14273         31 AYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (115)
Q Consensus        31 ~r~~Q~e~m~~I~~~l~~--~~~~iiEaPTGtGKTls~   66 (115)
                      -|+..   ++.+...|..  ..++++-||.|+|||.-.
T Consensus        26 gRd~E---i~~l~~iL~r~~k~n~lLvG~pGVGKTalv   60 (195)
T d1jbka_          26 GRDEE---IRRTIQVLQRRTKNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCHHH---HHHHHHHHTSSSSCEEEEECCTTSCHHHHH
T ss_pred             CcHHH---HHHHHHHHhccCCCCeEEEecCCcccHHHH
Confidence            45443   4466667764  368999999999999643

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=83.51  E-value=0.17  Score=37.13  Aligned_cols=19  Identities=26%  Similarity=0.394  Sum_probs=16.1

Q ss_pred             HhcCCcEEEecCCCCCchH
Q psy14273         46 LDNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        46 l~~~~~~iiEaPTGtGKTl   64 (115)
                      +..|..+.|.||+|+|||.
T Consensus        41 i~~Ge~vaivG~sGsGKST   59 (255)
T d2hyda1          41 IEKGETVAFVGMSGGGKST   59 (255)
T ss_dssp             ECTTCEEEEECSTTSSHHH
T ss_pred             EcCCCEEEEECCCCCcHHH
Confidence            4467899999999999984

>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=83.41  E-value=0.84  Score=33.60  Aligned_cols=28  Identities=14%  Similarity=0.189  Sum_probs=21.4

Q ss_pred             HHHHHHHHhcC--CcEEEecCCCCCchHHH
Q psy14273         39 MKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (115)
Q Consensus        39 m~~I~~~l~~~--~~~iiEaPTGtGKTls~   66 (115)
                      ++.+..+|...  .++++-||.|+|||.-.
T Consensus        27 i~~l~~iL~r~~k~n~lLVG~~GvGKTalv   56 (268)
T d1r6bx2          27 LERAIQVLCRRRKNNPLLVGESGVGKTAIA   56 (268)
T ss_dssp             HHHHHHHHTSSSSCEEEEECCTTSSHHHHH
T ss_pred             HHHHHHHHhcCccCCcEEECCCCCcHHHHH
Confidence            45667777643  68999999999999543

>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=82.11  E-value=0.25  Score=33.66  Aligned_cols=16  Identities=19%  Similarity=0.214  Sum_probs=12.9

Q ss_pred             CcEEEecCCCCCchHH
Q psy14273         50 KFGIFESPTGTGKSLS   65 (115)
Q Consensus        50 ~~~iiEaPTGtGKTls   65 (115)
                      ..++|-||.|||||.-
T Consensus         7 mrIiliG~PGSGKtT~   22 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTV   22 (189)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             eeEEEECCCCCCHHHH
Confidence            4577889999999853

>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=82.02  E-value=0.3  Score=35.55  Aligned_cols=18  Identities=28%  Similarity=0.482  Sum_probs=15.6

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.|.||+|+|||.
T Consensus        38 ~~Ge~vaivG~sGsGKST   55 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKST   55 (251)
T ss_dssp             CTTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCcHHH
Confidence            457889999999999984

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=82.00  E-value=0.22  Score=36.21  Aligned_cols=18  Identities=33%  Similarity=0.597  Sum_probs=15.5

Q ss_pred             hcCCcEEEecCCCCCchH
Q psy14273         47 DNSKFGIFESPTGTGKSL   64 (115)
Q Consensus        47 ~~~~~~iiEaPTGtGKTl   64 (115)
                      ..|..+.+-||+|+|||.
T Consensus        29 ~~Ge~~~iiG~sGsGKST   46 (230)
T d1l2ta_          29 KEGEFVSIMGPSGSGKST   46 (230)
T ss_dssp             CTTCEEEEECSTTSSHHH
T ss_pred             cCCCEEEEECCCCCCcch
Confidence            457889999999999993

>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=81.82  E-value=0.26  Score=33.19  Aligned_cols=15  Identities=27%  Similarity=0.357  Sum_probs=12.0

Q ss_pred             cEEEecCCCCCchHH
Q psy14273         51 FGIFESPTGTGKSLS   65 (115)
Q Consensus        51 ~~iiEaPTGtGKTls   65 (115)
                      .+.|.||.|+|||..
T Consensus         5 ~IaIdGp~GsGKgT~   19 (223)
T d1q3ta_           5 QIAIDGPASSGKSTV   19 (223)
T ss_dssp             EEEEECSSCSSHHHH
T ss_pred             EEEEECCCCCCHHHH
Confidence            356789999999853

>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=81.39  E-value=0.4  Score=36.18  Aligned_cols=29  Identities=14%  Similarity=0.033  Sum_probs=19.5

Q ss_pred             EEEecCCCCCchHHHHHHHHHHHHhhhhhh
Q psy14273         52 GIFESPTGTGKSLSLICGILKWYSDHKIAG   81 (115)
Q Consensus        52 ~iiEaPTGtGKTls~L~~al~~l~~~~~~v   81 (115)
                      +-|.||+|+|||. ++-..+.++...+.+|
T Consensus        57 IgitG~pGaGKST-Li~~l~~~~~~~g~~v   85 (327)
T d2p67a1          57 LGVTGTPGAGKST-FLEAFGMLLIREGLKV   85 (327)
T ss_dssp             EEEEECTTSCHHH-HHHHHHHHHHHTTCCE
T ss_pred             EEeeCCCCCCHHH-HHHHHHHHHHhcCCce
Confidence            5578999999994 4444455555556554

>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=81.13  E-value=0.76  Score=34.24  Aligned_cols=10  Identities=60%  Similarity=1.175  Sum_probs=9.5

Q ss_pred             EecCCCCCch
Q psy14273         54 FESPTGTGKS   63 (115)
Q Consensus        54 iEaPTGtGKT   63 (115)
                      |.||+|||||
T Consensus        32 i~G~qGSGKS   41 (286)
T d1odfa_          32 FSGPQGSGKS   41 (286)
T ss_dssp             EECCTTSSHH
T ss_pred             eECCCCCCHH
Confidence            7999999999

>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=80.24  E-value=0.3  Score=36.16  Aligned_cols=17  Identities=24%  Similarity=0.399  Sum_probs=14.4

Q ss_pred             cCCcEEEecCCCCCchH
Q psy14273         48 NSKFGIFESPTGTGKSL   64 (115)
Q Consensus        48 ~~~~~iiEaPTGtGKTl   64 (115)
                      .|..+.|-||+|+|||.
T Consensus        61 ~Ge~vaivG~nGsGKST   77 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTS   77 (281)
T ss_dssp             TTCEEEEEESTTSSHHH
T ss_pred             CCCEEEEECCCCChHHH
Confidence            36788899999999984