Psyllid ID: psy14272

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190----
Protein Sequence
MASKTPNEDKEFNEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDESR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHcccccHHHHHHHHHccccHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHcHHHcccccccccccccccccHHHHccccHHHHHHHccc
Coil and Loop (DISEMBL)
masktpnedkefneqrplaevpsefpfpfdaydiQSNFMKNLYYtldnskfgifesptgtgksLSLICGILKWYYDHKIVGLEKIEAKIKDLeisknetvseDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRnrmdeknskeKRKEEERDGLENETQELDESR
Flexible Loop (DISEMBL)
masktpnedkefneqrplaevpsefPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIKdleisknetvsedWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKqnekrkkslrndqevkvhaltyrnrmdeknskekrkeeerdglenetqeldesr
Low Complexity Region (SEG)
MASKTPNEDKEFNEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDeknskekrkeeerDGLENETQELDESR
Disordered region (IsUnstruct)
************************FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFEL**********************************************************************************
Disordered Region (DISOPRED)
*******************EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH*******************************************LKDALK********************************************************************
Disordered Region (DISEMBL)
*****************LAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQN*********DQEVKVHALTYRNRM****************************
Disordered Region (DISPRO)
**********************SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIK*********VSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRK*********K***L**********************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASKTPNEDKEFNEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGxxxxxxxxxxxxxxxxxxxxxDWIEQQSFELKMRNQIDALKDxxxxxxxxxxxxxxxxxxxxxxxxxxxxDQEVKVHALTYRNRxxxxxxxxxxxxxxxxxxxxxxxxxxxxR
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	194	2.2.26 [Sep-21-2011]
O14147	844	ATP-dependent RNA helicas	yes	N/A	0.608	0.139	0.406	7e-17
A8MPP1	907	Putative ATP-dependent RN	yes	N/A	0.824	0.176	0.333	4e-16
Q1E5T3	861	ATP-dependent RNA helicas	N/A	N/A	0.319	0.072	0.619	2e-15
Q96FC9	970	Probable ATP-dependent RN	yes	N/A	0.690	0.138	0.333	1e-14
A1D8E4	861	ATP-dependent RNA helicas	N/A	N/A	0.293	0.066	0.561	5e-14
A2QY22	874	ATP-dependent RNA helicas	yes	N/A	0.283	0.062	0.581	7e-14
A5DUW8	892	ATP-dependent RNA helicas	N/A	N/A	0.319	0.069	0.523	3e-12
Q6CAX3	803	ATP-dependent RNA helicas	yes	N/A	0.412	0.099	0.415	3e-12
A7ERG1	902	ATP-dependent RNA helicas	N/A	N/A	0.283	0.060	0.563	5e-12
Q6CIF0	807	ATP-dependent RNA helicas	yes	N/A	0.319	0.076	0.5	1e-11

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

 Score = 87.0 bits (214), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 79/133 (59%), Gaps = 15/133 (11%)

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

Query: 83  EKIEAKIKDLEISKNETVSE--DWIEQQSFELKMRNQIDALKDALK-SQKTYDELIENIR 139
           E  E K  D   +K+ T S+  DW+ +Q  +++        KD +K +    ++ +E IR
Sbjct: 71  EDNE-KSND---NKSNTSSKIPDWVLEQDLKIQ--------KDLVKETHARLEQRLEEIR 118

Query: 140 KQNEKRKKSLRND 152
           K+N+ RK  + N+
Sbjct: 119 KRNQSRKNQMSNN 131

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: 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 = 84.3 bits (207), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 61/183 (33%), Positives = 86/183 (46%), Gaps = 23/183 (12%)

Query: 25  FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEK 84
           FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D +    E+
Sbjct: 13  FPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALSWLRDFEQKKREE 72

Query: 85  ----IEAKIKDLEISKNETV-----------------SEDWIEQQSFELKMRNQIDALKD 123
               +E     L   K+E++                    W+ Q   + + R+ +D LK 
Sbjct: 73  EARLLETGTGPLHDEKDESLCLSSSCEGAAGTPRPAGEPAWVTQFVQKKEERDLVDRLKV 132

Query: 124 ALKSQKTYDELIENI--RKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERD 181
               +K  +E ++ +  R Q +   K LR ++E   + L     M E   + +R E+   
Sbjct: 133 EQARRKQREERLQQLQHRVQLKYAAKRLRQEEEETENLLRLSREMLETGPEAERLEQLES 192

Query: 182 GLE 184
           G E
Sbjct: 193 GEE 195

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 = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 39/63 (61%), Positives = 44/63 (69%), Gaps = 1/63 (1%)

Query: 25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK-IVGLE 83
          F  P+  YDIQ  FM++LY  ++  K GIFESPTGTGKSLSLICG L W  DHK  V LE
Sbjct: 8  FYHPYSPYDIQVQFMRSLYTCIEECKVGIFESPTGTGKSLSLICGSLTWLRDHKRSVFLE 67

Query: 84 KIE 86
           IE
Sbjct: 68 DIE 70

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

 Score = 79.3 bits (194), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 56/168 (33%), Positives = 79/168 (47%), Gaps = 34/168 (20%)

Query: 13  NEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
           NE + +  +   FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L 
Sbjct: 3   NETQKVGAI--HFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALS 60

Query: 73  WYYDHKIVGLEK----IEAKIKDLEISKNETV-----------------SEDWIEQQSFE 111
           W  D +    E+    +E     L   K+E++                    W+ Q   +
Sbjct: 61  WLRDFEQKKREEEARLLETGTGPLHDEKDESLCLSSSCEGAAGTPRPAGEPAWVTQFVQK 120

Query: 112 LKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHA 159
            + R+ +D LK             +  RKQ E+R + L++  ++K  A
Sbjct: 121 KEERDLVDRLKAE-----------QARRKQREERLQQLQHRVQLKYAA 157

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: 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 = 77.8 bits (190), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 38/57 (66%)

Query: 22 PSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
          P  F  P+  YDIQ  FM+ LY  L+  K  +FESPTGTGKSLSLICG + W  +HK
Sbjct: 5  PQNFNHPYSPYDIQLQFMRALYTCLEEGKVAVFESPTGTGKSLSLICGSMTWLREHK 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.

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 = 77.0 bits (188), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 32/55 (58%), Positives = 37/55 (67%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
          +F  P+  YDIQ   M+ LY  L+  K  +FESPTGTGKSLSLICG L W  DHK
Sbjct: 7  DFHHPYSPYDIQLQLMRALYSCLEQGKVAVFESPTGTGKSLSLICGSLTWLRDHK 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.

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

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 = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 17 PLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYY 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|Q6CAX3|CHL1_YARLI ATP-dependent RNA helicase CHL1 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=CHL1 PE=3 SV=1

 Score = 71.6 bits (174), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/89 (41%), Positives = 53/89 (59%), Gaps = 9/89 (10%)

Query: 24  EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLE 83
           EF  P+  Y IQ +FM+ LY  +++ K GIFESPTGTGK+LSLICG + W        L 
Sbjct: 8   EFSHPYTPYPIQVDFMEALYDCIESYKVGIFESPTGTGKTLSLICGSMTW--------LR 59

Query: 84  KIEAKIKDLEISKNETVSEDWIEQQSFEL 112
           K +A++     S +E     W+ +Q+ +L
Sbjct: 60  KNKAQLAVSTASADEN-EPAWVLEQTIQL 87

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

 Score = 70.9 bits (172), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 31/55 (56%), Positives = 36/55 (65%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
          +F  P+  Y IQ  FM+ +Y  L+  K GI ESPTGTGKSLSLICG L W  D K
Sbjct: 18 DFHHPYTPYPIQEKFMQTVYDVLEQGKIGILESPTGTGKSLSLICGSLTWLRDFK 72

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|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 = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 33/66 (50%), Positives = 46/66 (69%), Gaps = 4/66 (6%)

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

Query: 84 KIEAKI 89
          K+ +K+
Sbjct: 62 KLNSKV 67

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	194
91081131	861	PREDICTED: similar to regulator of telom	0.618	0.139	0.450	8e-23
270006445	817	DEAD/H (Asp-Glu-Ala-Asp/His) box polypep	0.618	0.146	0.450	9e-23
307191862	862	Probable ATP-dependent RNA helicase DDX1	0.798	0.179	0.401	8e-21
332029639	857	Putative ATP-dependent RNA helicase DDX1	0.747	0.169	0.389	2e-20
383850034	861	PREDICTED: putative ATP-dependent RNA he	0.804	0.181	0.369	3e-20
242025010	852	conserved hypothetical protein [Pediculu	0.597	0.136	0.461	1e-19
340378232	886	PREDICTED: putative ATP-dependent RNA he	0.690	0.151	0.383	4e-19
193608349	890	PREDICTED: probable ATP-dependent RNA he	0.680	0.148	0.367	8e-19
443709796	875	hypothetical protein CAPTEDRAFT_175213 [	0.448	0.099	0.489	1e-17
198436769	907	PREDICTED: similar to DEAD/H (Asp-Glu-Al	0.422	0.090	0.505	7e-17

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

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 55/122 (45%), Positives = 80/122 (65%), Gaps = 2/122 (1%)

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

Query: 80  VGLEKIEAKIKDLEISKNETV--SEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIEN 137
              E ++ +I++LE+ K +    S DW+  Q+ E+ +  QI+ LK        YD+ IE+
Sbjct: 62  YERENLKLQIEELELKKRKVSGNSSDWLSAQAQEIDLNRQINELKIRQNKIDEYDKKIES 121

Query: 138 IR 139
           +R
Sbjct: 122 LR 123

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 =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 55/122 (45%), Positives = 80/122 (65%), Gaps = 2/122 (1%)

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

Query: 80  VGLEKIEAKIKDLEISKNETV--SEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIEN 137
              E ++ +I++LE+ K +    S DW+  Q+ E+ +  QI+ LK        YD+ IE+
Sbjct: 62  YERENLKLQIEELELKKRKVSGNSSDWLSAQAQEIDLNRQINELKIRQNKIDEYDKKIES 121

Query: 138 IR 139
           +R
Sbjct: 122 LR 123

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 =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 67/167 (40%), Positives = 97/167 (58%), Gaps = 12/167 (7%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI 79
           E+P EFPFPF AY+IQ  FMK LY  L+  K G+FESPTGTGKSLSLICG LKW  DH+ 
Sbjct: 2   ELPQEFPFPFPAYEIQKQFMKELYNCLEGGKLGLFESPTGTGKSLSLICGALKWLVDHEK 61

Query: 80  VGLEKIEAKIKDLE--ISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIEN 137
              +++ + I +++  I   E  S+DW   Q+ ++    Q++A K   K Q   + ++E 
Sbjct: 62  YKKQELSSVISEIDDKIKNCEKPSDDWFSVQTEQI----QLNAEKQ--KFQAKLNAILE- 114

Query: 138 IRKQNEKRKKSLRNDQEVKVHA---LTYRNRMDEKNSKEKRKEEERD 181
              + EK KK +  ++  K  A   +  + R+ +K S +  K EE D
Sbjct: 115 FESEKEKFKKIIELNKTSKTKATQKVRQQFRISQKKSTDHSKTEEVD 161

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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 65/167 (38%), Positives = 90/167 (53%), Gaps = 22/167 (13%)

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

Query: 79  ------IVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYD 132
                 I  + KI+ K+K       E +S++W   Q+ ++++  +   L+  L +   Y+
Sbjct: 62  WRKEELISTIAKIDDKLKSC-----EKLSDNWFTVQTEQIELNAEKQPLQAKLNALLEYE 116

Query: 133 ELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEE 179
                   Q EK KK +   +  K+   T + R   K   E  K EE
Sbjct: 117 -------GQREKLKKMIVESKRAKI---TRKMRQQFKRVPESDKTEE 153

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 61/165 (36%), Positives = 92/165 (55%), Gaps = 9/165 (5%)

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

Query: 84  KIEAKIKDLE--ISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYD-------EL 134
           ++   I D E  I K    S +W   Q+ ++++ ++   L+  L S   Y+       E 
Sbjct: 66  QLTKAISDFEEKIKKCTNSSTNWFSVQTEQIQLNSEKQILQTKLNSILQYERKKNGLKEA 125

Query: 135 IENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEE 179
           ++N+ K+ ++   S  N  + +    T +N   ++++K+   EEE
Sbjct: 126 VKNVDKKKKRFGPSKPNQGKTQTETQTEKNAPVDEDNKDTIIEEE 170

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 54/117 (46%), Positives = 75/117 (64%), Gaps = 1/117 (0%)

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

Query: 82  LEKIEAKIKDL-EISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIEN 137
              +E  IK+L +  KN ++  +W+E+ S   K+R++ D L++ L      +  IEN
Sbjct: 71  KNDLELNIKNLNDELKNTSLGSNWLEEHSSLTKLRHKRDQLQNELNRVLNMENRIEN 127

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 56/146 (38%), Positives = 90/146 (61%), Gaps = 12/146 (8%)

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

Query: 80  VGLEKIEAKIK-DLEI----SKNE--TVSEDWIEQQSFELKMRNQIDALKDALKSQKTYD 132
              ++ EA +  D+ +     KNE  +V +DW  +     ++R++   +K A   +K   
Sbjct: 65  KETKRCEAILSGDVSVLPLSDKNEKKSVVDDWFAEYDQRKRLRDEAFKMKLAADKRKQRQ 124

Query: 133 ELIENIRKQN-----EKRKKSLRNDQ 153
           E I  ++++       KR+ +++N++
Sbjct: 125 ERISLLKERYGTSLFSKRQATVKNEK 150

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|193608349|ref|XP_001949260.1| PREDICTED: probable ATP-dependent RNA helicase DDX11-like [Acyrthosiphon pisum]

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/136 (36%), Positives = 82/136 (60%), Gaps = 4/136 (2%)

Query: 20  EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI 79
           E PS FPFPF  Y IQ +FM  +Y  ++  K GIFESPTGTGK+LS+ICG ++W  DH+ 
Sbjct: 17  ETPSTFPFPFTPYGIQHDFMTEIYSAIEGRKLGIFESPTGTGKTLSIICGAVRWLLDHEN 76

Query: 80  VGLEKIEAKIKDLEISKNET----VSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELI 135
               +++  ++ L +   ET      +DWI  Q+  ++ + ++  +   LKS + ++  I
Sbjct: 77  REWNQLKLALESLTMKNGETNDDDDDDDWIAGQAKLVEQQRKVYEINKMLKSLEEFNNNI 136

Query: 136 ENIRKQNEKRKKSLRN 151
           E I+K+ E +K  +++
Sbjct: 137 EKIKKEQEFKKNKVKS 152

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 46/94 (48%), Positives = 60/94 (63%), Gaps = 7/94 (7%)

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

Query: 78  ----KIVGLEKIEAKIKDLEISKNETVSEDWIEQ 107
               ++  L  I+ +IK   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|198436769|ref|XP_002122486.1| PREDICTED: similar to DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 [Ciona intestinalis]

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 47/93 (50%), Positives = 63/93 (67%), Gaps = 11/93 (11%)

Query: 21  VPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV 80
            PS+F FPF+ Y IQ +FMK+LY+ +++ K GIFESPTGTGKSLSLICG L W  DH+  
Sbjct: 13  APSKFAFPFEPYSIQVDFMKSLYHAIEDKKIGIFESPTGTGKSLSLICGSLTWLKDHE-- 70

Query: 81  GLEKIEAKIKDL------EISKNETVSEDWIEQ 107
             E+ E + +++      E SK ET   DWI++
Sbjct: 71  --EREEKRCQEITNKLTTEKSK-ETCDFDWIQE 100

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

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	194
POMBASE|SPAC3G6.11	844	chl1 "ATP-dependent DNA helica	0.685	0.157	0.401	3e-18
ZFIN|ZDB-GENE-041114-191	890	ddx11 "DEAD/H (Asp-Glu-Ala-Asp	0.701	0.152	0.386	3.3e-18
UNIPROTKB|F5GXL6	192	DDX11 "Probable ATP-dependent	0.381	0.385	0.519	2.3e-17
UNIPROTKB|F5GYY1	171	DDX11 "Probable ATP-dependent	0.381	0.432	0.519	2.3e-17
UNIPROTKB|E1BL06	913	E1BL06 "Uncharacterized protei	0.268	0.056	0.673	8.7e-17
UNIPROTKB|C9K0E8	302	DDX11 "Probable ATP-dependent	0.690	0.443	0.359	1.8e-15
FB|FBgn0026876	861	CG11403 [Drosophila melanogast	0.737	0.166	0.335	3.1e-15
UNIPROTKB|F5H235	297	DDX11 "Probable ATP-dependent	0.762	0.498	0.351	6.3e-15
UNIPROTKB|F1SK82	210	F1SK82 "Uncharacterized protei	0.695	0.642	0.346	6.9e-15
UNIPROTKB|B4DMS8	304	DDX11 "Probable ATP-dependent	0.762	0.486	0.351	7.5e-15

POMBASE|SPAC3G6.11 chl1 "ATP-dependent DNA helicase Chl1 (predicted)" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 232 (86.7 bits), Expect = 3.0e-18, P = 3.0e-18
 Identities = 59/147 (40%), Positives = 86/147 (58%)

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

Query:    83 EKIEAKIKDLEISKNETVSE--DWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRK 140
             E  E K  D   +K+ T S+  DW+ +Q  +LK+  Q D +K+   +    ++ +E IRK
Sbjct:    71 EDNE-KSND---NKSNTSSKIPDWVLEQ--DLKI--QKDLVKE---THARLEQRLEEIRK 119

Query:   141 QNEKRKKSLRNDQEVKVHALTYRNRMD 167
             +N+ RK  + N+     H  T R  ++
Sbjct:   120 RNQSRKNQMSNNSTT-YHRETKRRNIN 145

GO:0000790 "nuclear chromatin" evidence=IC

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0005829 "cytosol" evidence=IDA

GO:0006342 "chromatin silencing" evidence=NAS

GO:0007064 "mitotic sister chromatid cohesion" evidence=ISO

GO:0032508 "DNA duplex unwinding" evidence=IEA

GO:0045910 "negative regulation of DNA recombination" evidence=ISO

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

 Score = 232 (86.7 bits), Expect = 3.3e-18, P = 3.3e-18
 Identities = 58/150 (38%), Positives = 83/150 (55%)

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

Query:    81 GLEKIEAKIKDLEISKNETVSE-----DWIEQQSFELKMRNQIDALKDALKSQKTYDELI 135
                 +E + KD ++ K +  +      DW+ +   +   R+ ++ LKD    +K  +E +
Sbjct:    68 AARLLEGQ-KDSDVVKEKNSNSGPPEPDWVSEFVQKKAERDMVNKLKDEELKRKKREERL 126

Query:   136 ENIRKQNEKR----KKSLRNDQEVKVHALT 161
             E IR   + R    +K+  +D+ VK+  L+
Sbjct:   127 EMIRHNAQLRYAMKRKADEDDEAVKLLQLS 156

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

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

 Score = 189 (71.6 bits), Expect = 2.3e-17, Sum P(2) = 2.3e-17
 Identities = 40/77 (51%), Positives = 49/77 (63%)

Query:    13 NEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
             NE + +  +   FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L 
Sbjct:    39 NETQKVGAI--HFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALS 96

Query:    73 WYYDHKIVGLEKIEAKI 89
             W  D +    E+ EA++
Sbjct:    97 WLRDFEQKKREE-EARL 112

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

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

 Score = 189 (71.6 bits), Expect = 2.3e-17, Sum P(2) = 2.3e-17
 Identities = 40/77 (51%), Positives = 49/77 (63%)

Query:    13 NEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
             NE + +  +   FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L 
Sbjct:     3 NETQKVGAI--HFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALS 60

Query:    73 WYYDHKIVGLEKIEAKI 89
             W  D +    E+ EA++
Sbjct:    61 WLRDFEQKKREE-EARL 76

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

UNIPROTKB|E1BL06 E1BL06 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 183 (69.5 bits), Expect = 8.7e-17, Sum P(2) = 8.7e-17
 Identities = 35/52 (67%), Positives = 37/52 (71%)

Query:    25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD 76
             FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L W  D
Sbjct:    13 FPFPFTPYAIQKDFMAALYQVLEAGKIGIFESPTGTGKSLSLICGALSWLRD 64

GO:0030496 "midbody" evidence=IEA

GO:0007062 "sister chromatid cohesion" evidence=IEA

GO:0000922 "spindle pole" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 195 (73.7 bits), Expect = 1.8e-15, P = 1.8e-15
 Identities = 51/142 (35%), Positives = 75/142 (52%)

Query:    13 NEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
             NE + +  +   FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L 
Sbjct:     3 NETQKVGAI--HFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALS 60

Query:    73 WYYDHKIVGLEKIEAKIKDLEISK-NETVSEDWIEQQSFELKMRNQIDALKDALKSQ--- 128
             W  D +    E+ EA++ +      ++   E      S E        A + A  +Q   
Sbjct:    61 WLRDFEQKKREE-EARLLETGTGPLHDEKDESLCLSSSCEGAAGTPRPAGEPAWVTQFVQ 119

Query:   129 -KTYDELIENIRKQNEKRKKSL 149
              K   +L++ +++Q E+ +++L
Sbjct:   120 KKEERDLVDRLKRQEEEERENL 141

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

FB|FBgn0026876 CG11403 [Drosophila melanogaster (taxid:7227)]

 Score = 204 (76.9 bits), Expect = 3.1e-15, P = 3.1e-15
 Identities = 52/155 (33%), Positives = 84/155 (54%)

Query:     1 MASKTPNEDKEFNEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGT 60
             M+  TPN+  +     P A+   EF FP+  Y+IQ   M+ L+  L+  + GIFESPTGT
Sbjct:     1 MSQYTPNQRLD----TPGAQ---EFGFPYSPYEIQEQLMQELFQVLERGQVGIFESPTGT 53

Query:    61 GKSLSLICGILKWYYDHKIVGLEKIEAKIKDLE--ISKNETVSE---DWIEQQSFELKMR 115
             GKSL+L CG L W   H+ +   ++ A+I+ +E  ++K +  SE   +W+E Q      R
Sbjct:    54 GKSLTLTCGALTWLARHEELVRTEMLARIRGVEQELAKLKEESEQSSNWLESQGKSRAQR 113

Query:   116 NQIDALKDALKSQKTYDELIENIRKQNEKRKKSLR 150
              ++  L+         ++ ++ IRK  +K K+  R
Sbjct:   114 AELLRLQHLQALLDKQEQQLDQIRKGAKKHKRQGR 148

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

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

GO:0004386 "helicase activity" evidence=ISS

GO:0032508 "DNA duplex unwinding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" 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 = 57/162 (35%), Positives = 81/162 (50%)

Query:    13 NEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
             NE + +  +   FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L 
Sbjct:     3 NETQKVGAI--HFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALS 60

Query:    73 WYYDHKIVGLEKIEAKIKDLEISK-NETVSEDWIEQQSFELKMRNQIDALKDALKSQ--- 128
             W  D +    E+ EA++ +      ++   E      S E        A + A  +Q   
Sbjct:    61 WLRDFEQKKREE-EARLLETGTGPLHDEKDESLCLSSSCEGAAGTPRPAGEPAWVTQFVQ 119

Query:   129 -KTYDELIENI------RKQNEKRKKSLRNDQEVKVHALTYR 163
              K   +L++ +      RKQ E+R + L++  ++K  A   R
Sbjct:   120 KKEERDLVDRLKAEQARRKQREERLQQLQHRVQLKYAAKRLR 161

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 = 189 (71.6 bits), Expect = 6.9e-15, P = 6.9e-15
 Identities = 51/147 (34%), Positives = 77/147 (52%)

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

Query:    85 IEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKS-------QKTYD-ELIE 136
              EA++  LE         +  +     L  +  +   KD  +        QK  + +L++
Sbjct:    73 -EARL--LEAEATAAPLSNGKDPLLLPLASQGTLGPPKDPAEPDWVTQFVQKKEERDLVD 129

Query:   137 NIRKQNEKRKKSLRNDQEVKVHA-LTY 162
              ++++  +R+K     Q+++ +A L Y
Sbjct:   130 RLKEEQVRRRKREERLQQIRHNAQLKY 156

GO:0016817 "hydrolase activity, acting on acid anhydrides" 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 = 57/162 (35%), Positives = 81/162 (50%)

Query:    13 NEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK 72
             NE + +  +   FPFPF  Y IQ +FM  LY  L+  K GIFESPTGTGKSLSLICG L 
Sbjct:     3 NETQKVGAI--HFPFPFTPYSIQEDFMAELYRVLEAGKIGIFESPTGTGKSLSLICGALS 60

Query:    73 WYYDHKIVGLEKIEAKIKDLEISK-NETVSEDWIEQQSFELKMRNQIDALKDALKSQ--- 128
             W  D +    E+ EA++ +      ++   E      S E        A + A  +Q   
Sbjct:    61 WLRDFEQKKREE-EARLLETGTGPLHDEKDESLCLSSSCEGAAGTPRPAGEPAWVTQFVQ 119

Query:   129 -KTYDELIENI------RKQNEKRKKSLRNDQEVKVHALTYR 163
              K   +L++ +      RKQ E+R + L++  ++K  A   R
Sbjct:   120 KKEERDLVDRLKAEQARRKQREERLQQLQHRVQLKYAAKRLR 161

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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	194
smart00488	289	smart00488, DEXDc2, DEAD-like helicases superfamil	2e-21
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	5e-07
TIGR00604	705	TIGR00604, rad3, DNA repair helicase (rad3)	2e-06

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

 Score = 88.6 bits (220), Expect = 2e-21
 Identities = 52/174 (29%), Positives = 75/174 (43%), Gaps = 14/174 (8%)

Query: 24  EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLE 83
            F FP++ Y IQ  FM+ L   LD  K GI ESPTGTGK+LSL+C  L W          
Sbjct: 2   LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFP----- 56

Query: 84  KIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNE 143
             E   K   I  + TVSE  IE++  EL+   Q    +   +S+K    L E  R++ +
Sbjct: 57  --ERIQKIKLIYLSRTVSE--IEKRLEELRKLMQKVEYESDEESEKQAQLLHELGREKPK 112

Query: 144 KRKKSLRNDQEVKVHALT-----YRNRMDEKNSKEKRKEEERDGLENETQELDE 192
               SL + + + ++            +DE        +  +   EN   E   
Sbjct: 113 VLGLSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLTASKARKYRYENPKVERCP 166

Length = 289

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

 Score = 48.6 bits (116), Expect = 5e-07
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK 78
           FP  F+    Q    + +   L   +  + E+PTGTGK+L+ +   L +  +  
Sbjct: 10 AFP-GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG 63

Length = 654

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

 Score = 47.0 bits (112), Expect = 2e-06
 Identities = 19/48 (39%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW 73
          FP++  Y  Q ++M++L  +LD     I E P+GTGK++SL+  IL +
Sbjct: 6  FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAY 53

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	194
KOG1133|consensus	821		99.96
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.74
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.74
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.6
KOG1132|consensus	945		99.51
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.37
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.33
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.22
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.11
KOG1131|consensus	755		99.06
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.94
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.81
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	98.6
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	98.54
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.52
PTZ00424	401	helicase 45; Provisional	98.52
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	98.52
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	98.51
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	98.51
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.49
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.47
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	98.44
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	98.43
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	98.39
PTZ00110	545	helicase; Provisional	98.39
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	98.33
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.32
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	98.29
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	98.23
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	98.23
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.19
smart00487	201	DEXDc DEAD-like helicases superfamily.	98.13
KOG0348|consensus	708		98.11
KOG0345|consensus	567		98.1
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.07
PRK13767	876	ATP-dependent helicase; Provisional	98.06
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	98.06
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	98.04
PRK01172	674	ski2-like helicase; Provisional	97.97
COG1201	814	Lhr Lhr-like helicases [General function predictio	97.94
PRK02362	737	ski2-like helicase; Provisional	97.92
COG1205	851	Distinct helicase family with a unique C-terminal	97.92
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	97.9
PRK00254	720	ski2-like helicase; Provisional	97.89
KOG0331|consensus	519		97.86
KOG0344|consensus	593		97.75
KOG0330|consensus	476		97.69
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	97.68
PRK10689	1147	transcription-repair coupling factor; Provisional	97.62
KOG0335|consensus	482		97.56
KOG0350|consensus	620		97.53
PRK09694	878	helicase Cas3; Provisional	97.51
PRK09401	1176	reverse gyrase; Reviewed	97.45
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	97.37
KOG0346|consensus	569		97.37
PRK14701	1638	reverse gyrase; Provisional	97.35
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	97.3
PRK05580	679	primosome assembly protein PriA; Validated	97.28
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	97.25
KOG0334|consensus	997		97.22
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	97.19
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	97.17
KOG0338|consensus	691		97.15
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	97.13
KOG0342|consensus	543		97.02
PHA02558	501	uvsW UvsW helicase; Provisional	97.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	96.93
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.92
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.91
PHA02653	675	RNA helicase NPH-II; Provisional	96.9
PRK13766	773	Hef nuclease; Provisional	96.86
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	96.86
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	96.85
KOG0354|consensus	746		96.82
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	96.79
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.78
COG1204	766	Superfamily II helicase [General function predicti	96.78
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	96.77
PRK09200	790	preprotein translocase subunit SecA; Reviewed	96.76
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	96.71
KOG0333|consensus	673		96.71
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	96.63
KOG0336|consensus	629		96.61
KOG0340|consensus	442		96.53
KOG0343|consensus	758		96.45
PRK08181	269	transposase; Validated	96.42
PF13245	76	AAA_19: Part of AAA domain	96.38
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	96.36
PRK10536	262	hypothetical protein; Provisional	96.36
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	96.34
PRK12904	830	preprotein translocase subunit SecA; Reviewed	96.15
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	96.15
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.04
KOG0337|consensus	529		95.84
PRK13107	908	preprotein translocase subunit SecA; Reviewed	95.82
KOG0352|consensus	641		95.82
KOG0351|consensus	941		95.79
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	95.69
PRK06835	329	DNA replication protein DnaC; Validated	95.69
KOG0327|consensus	397		95.68
PHA02244	383	ATPase-like protein	95.63
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	95.44
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	95.43
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.39
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	95.38
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	95.37
PRK15483	986	type III restriction-modification system StyLTI en	95.37
KOG0326|consensus	459		95.28
COG4096	875	HsdR Type I site-specific restriction-modification	95.26
KOG0347|consensus	731		95.21
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	95.12
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.04
PRK06526	254	transposase; Provisional	95.01
KOG0952|consensus	1230		94.97
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.89
PRK13851	344	type IV secretion system protein VirB11; Provision	94.88
KOG0328|consensus	400		94.83
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	94.8
PRK12402	337	replication factor C small subunit 2; Reviewed	94.77
PRK09183	259	transposase/IS protein; Provisional	94.75
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	94.71
smart00382	148	AAA ATPases associated with a variety of cellular	94.65
COG0714	329	MoxR-like ATPases [General function prediction onl	94.56
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	94.44
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	94.42
KOG0353|consensus	695		94.35
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	94.1
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.91
PRK13531	498	regulatory ATPase RavA; Provisional	93.88
PRK08939	306	primosomal protein DnaI; Reviewed	93.82
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.81
COG1484	254	DnaC DNA replication protein [DNA replication, rec	93.62
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	93.61
TIGR00376	637	DNA helicase, putative. The gene product may repre	93.57
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	93.56
PRK12326	764	preprotein translocase subunit SecA; Reviewed	93.55
KOG1803|consensus	649		93.52
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	93.4
PLN03025	319	replication factor C subunit; Provisional	93.28
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	93.25
KOG0989|consensus	346		93.13
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	93.03
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	92.94
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	92.9
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	92.9
TIGR02533	486	type_II_gspE general secretory pathway protein E.	92.9
PRK10436	462	hypothetical protein; Provisional	92.86
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	92.83
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	92.79
COG4889	1518	Predicted helicase [General function prediction on	92.75
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	92.68
PRK00440	319	rfc replication factor C small subunit; Reviewed	92.6
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	92.55
PRK08116	268	hypothetical protein; Validated	92.54
KOG0339|consensus	731		92.49
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	92.49
PRK07952	244	DNA replication protein DnaC; Validated	92.44
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	92.23
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	92.22
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	92.22
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	92.19
) 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	92.17
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	92.11
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	91.99
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	91.92
PRK12377	248	putative replication protein; Provisional	91.81
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	91.78
KOG0341|consensus	610		91.69
PF13476	202	AAA_23: AAA domain; PDB: 3AV0_B 3AUY_B 3AUX_A 2O5V	91.67
TIGR00595	505	priA primosomal protein N'. All proteins in this f	91.61
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	91.51
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	91.38
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	91.34
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	91.33
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	91.26
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	91.22
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	91.2
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	91.18
KOG0947|consensus	1248		90.92
PRK13765	637	ATP-dependent protease Lon; Provisional	90.76
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	90.73
PF12846	304	AAA_10: AAA-like domain	90.63
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	90.57
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	90.46
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	90.36
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	90.21
PRK13764	602	ATPase; Provisional	90.2
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	90.13
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	90.1
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	90.1
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	90.03
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	89.87
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	89.86
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	89.79
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	89.65
PRK08769	319	DNA polymerase III subunit delta'; Validated	89.59
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	89.57
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	89.52
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	89.45
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	89.39
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	89.33
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	89.32
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	89.31
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	89.2
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	89.18
KOG0991|consensus	333		89.15
PRK00411	394	cdc6 cell division control protein 6; Reviewed	89.12
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	89.11
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	89.11
PF13555	62	AAA_29: P-loop containing region of AAA domain	89.1
KOG0349|consensus	725		89.08
PRK08903	227	DnaA regulatory inactivator Hda; Validated	89.07
PRK06921	266	hypothetical protein; Provisional	88.85
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	88.76
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	88.73
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	88.64
TIGR03238	504	dnd_assoc_3 dnd system-associated protein 3. cereu	88.6
CHL00122	870	secA preprotein translocase subunit SecA; Validate	88.57
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	88.56
KOG0922|consensus	674		88.45
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	88.35
cd01376	319	KISc_KID_like Kinesin motor domain, KIF22/Kid-like	88.28
KOG4284|consensus	980		88.21
PRK08727	233	hypothetical protein; Validated	88.14
PF00004	132	AAA: ATPase family associated with various cellula	88.11
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	88.04
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	87.98
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	87.96
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	87.92
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	87.87
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	87.85
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	87.83
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	87.71
PRK13342	413	recombination factor protein RarA; Reviewed	87.7
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	87.69
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	87.65
PHA00729	226	NTP-binding motif containing protein	87.62
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	87.56
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	87.54
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	87.49
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	87.46
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	87.39
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	87.37
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	87.34
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	87.29
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	87.24
PRK00300	205	gmk guanylate kinase; Provisional	87.22
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	87.18
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	87.13
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	87.12
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	87.12
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	87.06
PRK08084	235	DNA replication initiation factor; Provisional	87.02
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	87.01
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	86.97
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	86.96
TIGR02759	566	TraD_Ftype type IV conjugative transfer system cou	86.9
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	86.84
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	86.75
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	86.73
PRK13850	670	type IV secretion system protein VirD4; Provisiona	86.73
PRK10865	857	protein disaggregation chaperone; Provisional	86.46
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	86.41
PF05729	166	NACHT: NACHT domain	86.27
PRK13897	606	type IV secretion system component VirD4; Provisio	86.27
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	86.15
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	86.15
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	86.08
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	86.06
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	85.97
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	85.97
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	85.86
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	85.81
COG0606	490	Predicted ATPase with chaperone activity [Posttran	85.79
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	85.28
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	85.27
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	85.27
PRK13876	663	conjugal transfer coupling protein TraG; Provision	85.26
PRK05541	176	adenylylsulfate kinase; Provisional	85.13
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	85.11
KOG1808|consensus	1856		85.08
PRK04296	190	thymidine kinase; Provisional	85.07
cd01373	337	KISc_KLP2_like Kinesin motor domain, KLP2-like sub	85.01
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	85.0
PRK14729	300	miaA tRNA delta(2)-isopentenylpyrophosphate transf	84.89
CHL00181	287	cbbX CbbX; Provisional	84.83
PRK05298	652	excinuclease ABC subunit B; Provisional	84.79
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	84.72
PRK00698	205	tmk thymidylate kinase; Validated	84.62
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	84.61
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	84.38
PRK13880	636	conjugal transfer coupling protein TraG; Provision	84.31
CHL00095	821	clpC Clp protease ATP binding subunit	84.28
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	84.2
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	84.16
KOG0332|consensus	477		84.09
PRK04195	482	replication factor C large subunit; Provisional	84.06
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	84.06
PRK10869	553	recombination and repair protein; Provisional	83.98
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	83.95
KOG0744|consensus	423		83.92
cd03241	276	ABC_RecN RecN ATPase involved in DNA repair; ABC (	83.83
PRK09112	351	DNA polymerase III subunit delta'; Validated	83.79
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	83.77
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	83.74
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	83.69
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	83.68
cd01366	329	KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/	83.58
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	83.51
PF13173	128	AAA_14: AAA domain	83.51
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	83.48
PHA02544	316	44 clamp loader, small subunit; Provisional	83.46
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	83.45
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	83.43
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	83.37
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	83.25
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	83.21
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	83.21
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	83.17
COG1198	730	PriA Primosomal protein N' (replication factor Y)	83.15
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	83.11
cd01375	334	KISc_KIF9_like Kinesin motor domain, KIF9-like sub	83.11
cd03115	173	SRP The signal recognition particle (SRP) mediates	82.95
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	82.87
COG0419	908	SbcC ATPase involved in DNA repair [DNA replicatio	82.76
TIGR00041	195	DTMP_kinase thymidylate kinase. Function: phosphor	82.72
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	82.65
KOG0390|consensus	776		82.64
KOG0743|consensus	457		82.63
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	82.61
PTZ00112	1164	origin recognition complex 1 protein; Provisional	82.57
PRK14974	336	cell division protein FtsY; Provisional	82.53
KOG1802|consensus	935		82.48
PRK10875	615	recD exonuclease V subunit alpha; Provisional	82.3
PRK06871	325	DNA polymerase III subunit delta'; Validated	82.26
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	82.26
PRK13822	641	conjugal transfer coupling protein TraG; Provision	82.0
TIGR00634	563	recN DNA repair protein RecN. All proteins in this	81.94
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	81.93
cd01374	321	KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like	81.92
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	81.89
PLN03188	1320	kinesin-12 family protein; Provisional	81.78
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	81.76
PRK06090	319	DNA polymerase III subunit delta'; Validated	81.64
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	81.63
KOG0923|consensus	902		81.53
KOG0239|consensus	670		81.5
KOG0948|consensus	1041		81.43
cd01367	322	KISc_KIF2_like Kinesin motor domain, KIF2-like gro	81.42
PRK10416	318	signal recognition particle-docking protein FtsY;	81.38
PRK11608	326	pspF phage shock protein operon transcriptional ac	81.32
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	81.27
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	81.19
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	81.18
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	80.98
KOG0951|consensus	1674		80.96
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	80.88
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	80.88
PF00005	137	ABC_tran: ABC transporter This structure is on hol	80.82
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	80.74
cd01371	333	KISc_KIF3 Kinesin motor domain, kinesins II or KIF	80.72
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	80.69
cd01369	325	KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy	80.66
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	80.53
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	80.5
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	80.5
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	80.44
cd01370	338	KISc_KIP3_like Kinesin motor domain, KIP3-like sub	80.44
COG3973	747	Superfamily I DNA and RNA helicases [General funct	80.43
PRK07993	334	DNA polymerase III subunit delta'; Validated	80.38
TIGR02237	209	recomb_radB DNA repair and recombination protein R	80.35
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	80.31
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	80.24
KOG0745|consensus	564		80.23
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	80.15

>KOG1133|consensus

Probab=99.96  E-value=3.8e-29  Score=240.96  Aligned_cols=158  Identities=34%  Similarity=0.540  Sum_probs=128.3

Q ss_pred             CccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhHHHHHHHHHhhhh-hcCCCCC
Q psy14272         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEI-SKNETVS  101 (194)
Q Consensus        23 ~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~~~~~~~~~~~~~-~~~~d~e  101 (194)
                      ..|+|||+||+||.+||+.||++|+.|+++|||||||||||||+||++|+||++++.++..+....+..+.+ ..+.+++
T Consensus         8 ~~F~fPy~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~~eek~~t~~~~~l~~v~~~~~d~kde   87 (821)
T KOG1133|consen    8 IEFPFPYTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRDFEEKKRTEEARLLETVTGPLHDEKDE   87 (821)
T ss_pred             cccCCCCCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHHhHHhhhhHHHhhhccCCCcccccccc
Confidence            569999999999999999999999999999999999999999999999999999999888877666654421 2444677


Q ss_pred             ch----HHHHHHHHHHHHhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccchHHHhhhhhhhhhhhhhchhhhhH
Q psy14272        102 ED----WIEQQSFELKMRNQIDA-LKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRK  176 (194)
Q Consensus       102 Pd----Wv~e~~~~~~~~~~~~~-~~~~~~~~~~~E~rL~~ir~~~~~~k~~~r~~~~~~~~~~~~~~~~~e~~~~~~r~  176 (194)
                      ||    |+.++.++...+....+ ++......+.++.+++++...++..+.+.+++++.-..+--+.++|.+++    |.
T Consensus        88 ~d~~s~wl~~~~~~~~er~~~~r~l~~~qa~~~~re~r~q~~~~~~e~~k~ak~~~~e~~~reyl~~~e~~~pg----~~  163 (821)
T KOG1133|consen   88 SDSSSAWLTQFVQKKEERDLVDRNLKAEQARFKQREERLQQLQHRVQGKKGAKRLRQEEEEREYLLSREMLEPG----RL  163 (821)
T ss_pred             ccchhHHHHHHHHHHHhhccchHHHHHhhchHHHHHHHHHhhhhHHhhhhhhhccccccccchhcchhhccCcc----ch
Confidence            77    99999999999999888 77778888899999999999999999999999866332222344454444    44


Q ss_pred             HHhhcccc
Q psy14272        177 EEERDGLE  184 (194)
Q Consensus       177 ~~~~~~~~  184 (194)
                      |+-..|++
T Consensus       164 eq~e~~~~  171 (821)
T KOG1133|consen  164 EQLESGEE  171 (821)
T ss_pred             hhhhcccc
Confidence            44444443

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.74  E-value=2.7e-18  Score=150.67  Aligned_cols=56  Identities=50%  Similarity=0.867  Sum_probs=53.1

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .|+|||+|||+|.+||..|++++.+|+++|||||||||||+|||||++.|+..++.
T Consensus         2 ~~~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00488        2 LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            48999999999999999999999999999999999999999999999999987655

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.74  E-value=2.7e-18  Score=150.67  Aligned_cols=56  Identities=50%  Similarity=0.867  Sum_probs=53.1

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .|+|||+|||+|.+||..|++++.+|+++|||||||||||+|||||++.|+..++.
T Consensus         2 ~~~FPy~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~   57 (289)
T smart00489        2 LFYFPYEPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPE   57 (289)
T ss_pred             cccCCCCCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcc
Confidence            48999999999999999999999999999999999999999999999999987655

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.60  E-value=1e-15  Score=148.13  Aligned_cols=55  Identities=35%  Similarity=0.622  Sum_probs=52.2

Q ss_pred             ccCCCCCC-CHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         24 EFPFPFDA-YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        24 ~~~fPy~p-y~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .++|||+| ||.|.+||..|+++|..++++++|||||||||+|+|||+|.|+..++
T Consensus         3 ~v~FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~   58 (705)
T TIGR00604         3 LVYFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP   58 (705)
T ss_pred             ceecCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc
Confidence            47899996 99999999999999999999999999999999999999999998655

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=99.51  E-value=1.1e-14  Score=143.99  Aligned_cols=61  Identities=43%  Similarity=0.690  Sum_probs=57.8

Q ss_pred             CCccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhH
Q psy14272         22 PSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGL   82 (194)
Q Consensus        22 ~~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~   82 (194)
                      |..+.|||+||+.|+.||..|..||..+..+++|||||||||||+||++|+|.+.++.+..
T Consensus        13 Gv~V~fP~qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~   73 (945)
T KOG1132|consen   13 GVPVEFPFQPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKP   73 (945)
T ss_pred             CceeeccCCcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhcccc
Confidence            8889999999999999999999999999999999999999999999999999999885543

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

Probab=99.37  E-value=5.6e-13  Score=126.77  Aligned_cols=58  Identities=24%  Similarity=0.368  Sum_probs=52.9

Q ss_pred             cCCC-CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhH
Q psy14272         25 FPFP-FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGL   82 (194)
Q Consensus        25 ~~fP-y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~   82 (194)
                      ..|| |+||+.|.+||..|+.++.+++++++|||||||||++||||++.|....++++.
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~~~vi   67 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVI   67 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcCCcEE
Confidence            3455 779999999999999999999999999999999999999999999998876654

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.33  E-value=1.2e-12  Score=127.47  Aligned_cols=57  Identities=23%  Similarity=0.249  Sum_probs=51.8

Q ss_pred             CCC-CCCCHHHHHHHHHHHHHHhc-----CCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhH
Q psy14272         26 PFP-FDAYDIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLICGILKWYYDHKIVGL   82 (194)
Q Consensus        26 ~fP-y~py~iQ~e~M~~I~~~L~~-----gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~   82 (194)
                      .+| |++|+.|.+||..|+++|.+     ++++++||||||||||+||+|++.|+...+++++
T Consensus        20 ~~~~~e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k~vV   82 (697)
T PRK11747         20 QLPGFIPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKKKLV   82 (697)
T ss_pred             hCCCCCcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCCeEE
Confidence            345 99999999999999999987     5899999999999999999999999998877754

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

Probab=99.22  E-value=1.1e-11  Score=124.10  Aligned_cols=53  Identities=26%  Similarity=0.382  Sum_probs=49.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      |++||.|.+||..|+++|.+++++++|||||||||++||+|++.|+...++++
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            89999999999999999999999999999999999999999999988666654

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

Probab=99.11  E-value=6.1e-11  Score=117.34  Aligned_cols=49  Identities=24%  Similarity=0.333  Sum_probs=46.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ..|++||+|.+||..|+++|.+++++++|||||||||++||+|++.|+.
T Consensus       242 ~~~~~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~  290 (850)
T TIGR01407       242 LGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI  290 (850)
T ss_pred             cCCccCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc
Confidence            4589999999999999999999999999999999999999999999987

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.

>KOG1131|consensus

Probab=99.06  E-value=2e-10  Score=110.17  Aligned_cols=62  Identities=29%  Similarity=0.414  Sum_probs=58.0

Q ss_pred             CCCCCccCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         19 AEVPSEFPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        19 ~~~~~~~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      -+++..+.|||. .||.|.++|..|..+|+.++++++|+|+|||||.|+|.-+++|...++..
T Consensus         4 ~id~l~v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~   66 (755)
T KOG1131|consen    4 YIDDLLVYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDE   66 (755)
T ss_pred             eecCeeEecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcc
Confidence            467788999998 99999999999999999999999999999999999999999999998843

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

Probab=98.94  E-value=1.1e-09  Score=108.88  Aligned_cols=47  Identities=19%  Similarity=0.247  Sum_probs=44.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .|++|+.|.+||..|+++|.+++++|+|||||||||++||+|++.+.
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            39999999999999999999999999999999999999999988865

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

Probab=98.81  E-value=4.6e-09  Score=102.27  Aligned_cols=43  Identities=30%  Similarity=0.496  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         34 IQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|.+||..|+++|.+++++|+|||||||||++||+|++.|+..
T Consensus         1 ~Q~~~~~~i~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~   43 (636)
T TIGR03117         1 EQALFYLNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKE   43 (636)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHh
Confidence            3999999999999999999999999999999999999999874

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.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.60  E-value=6e-08  Score=88.04  Aligned_cols=47  Identities=17%  Similarity=0.186  Sum_probs=40.6

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+.|. |+|+|.+.+..+    -+|+++|+.||||||||++|++|++..+..
T Consensus        25 ~~g~~~pt~iQ~~aip~i----l~g~dvi~~ApTGsGKTla~llp~l~~l~~   72 (423)
T PRK04837         25 KKGFHNCTPIQALALPLT----LAGRDVAGQAQTGTGKTMAFLTATFHYLLS   72 (423)
T ss_pred             HCCCCCCCHHHHHHHHHH----hCCCcEEEECCCCchHHHHHHHHHHHHHHh
Confidence            46776 999999987765    478999999999999999999999987654

>cd00268 DEADc DEAD-box helicases

Probab=98.54  E-value=1.4e-07  Score=76.09  Aligned_cols=47  Identities=23%  Similarity=0.300  Sum_probs=40.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ++|. ||+.|.+.++.+.    +|+++++.+|||+|||++|+.|++..+...
T Consensus        17 ~~~~~~~~~Q~~~~~~~~----~~~~~li~~~TG~GKT~~~~~~~l~~~~~~   64 (203)
T cd00268          17 LGFEKPTPIQARAIPPLL----SGRDVIGQAQTGSGKTAAFLIPILEKLDPS   64 (203)
T ss_pred             cCCCCCCHHHHHHHHHHh----cCCcEEEECCCCCcHHHHHHHHHHHHHHhh
Confidence            5666 9999999888876    388999999999999999999998877665

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.

>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=98.52  E-value=1.2e-07  Score=73.69  Aligned_cols=47  Identities=21%  Similarity=0.381  Sum_probs=38.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC---CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g---k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      |++||.|.+.+..|.+.+...   ..++|.+|||||||+.++..+.....
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            668999999999999999875   89999999999999998865444433

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 ....

>PTZ00424 helicase 45; Provisional

Probab=98.52  E-value=1.2e-07  Score=84.24  Aligned_cols=48  Identities=21%  Similarity=0.328  Sum_probs=41.0

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|.|. |+|+|.+.+..++    +|..+|+.||||||||++|++|++.++..
T Consensus        44 ~~~~~~~~~~~Q~~ai~~i~----~~~d~ii~apTGsGKT~~~~l~~l~~~~~   92 (401)
T PTZ00424         44 YSYGFEKPSAIQQRGIKPIL----DGYDTIGQAQSGTGKTATFVIAALQLIDY   92 (401)
T ss_pred             HHcCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHhcC
Confidence            346776 9999999877764    68889999999999999999999988753

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=98.52  E-value=1.5e-07  Score=86.88  Aligned_cols=48  Identities=17%  Similarity=0.215  Sum_probs=41.0

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+.|. |+|+|.+.+..|.    +|+++|+.||||||||++|++|++..+...
T Consensus        18 ~~g~~~pt~iQ~~ai~~il----~g~dvlv~apTGsGKTla~~lpil~~l~~~   66 (456)
T PRK10590         18 EQGYREPTPIQQQAIPAVL----EGRDLMASAQTGTGKTAGFTLPLLQHLITR   66 (456)
T ss_pred             HCCCCCCCHHHHHHHHHHh----CCCCEEEECCCCCcHHHHHHHHHHHHhhhc
Confidence            35665 9999999887764    689999999999999999999999887653

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

Probab=98.51  E-value=1.3e-07  Score=88.93  Aligned_cols=46  Identities=17%  Similarity=0.265  Sum_probs=39.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+|. |+|+|.+.+..+.    .|+++|+.||||||||++|++|+|..+..
T Consensus       139 ~g~~~ptpiQ~~aip~il----~g~dviv~ApTGSGKTlayllPil~~l~~  185 (518)
T PLN00206        139 AGYEFPTPIQMQAIPAAL----SGRSLLVSADTGSGKTASFLVPIISRCCT  185 (518)
T ss_pred             cCCCCCCHHHHHHHHHHh----cCCCEEEEecCCCCccHHHHHHHHHHHHh
Confidence            4676 9999999877764    78999999999999999999999987653

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=98.51  E-value=1.7e-07  Score=85.16  Aligned_cols=47  Identities=21%  Similarity=0.296  Sum_probs=40.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|. |+++|.+.+..+.    +|+.+|+.||||+|||++|++|++.++.+.
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            5666 9999999777764    678999999999999999999999988654

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

Probab=98.49  E-value=2.4e-07  Score=71.78  Aligned_cols=42  Identities=24%  Similarity=0.381  Sum_probs=36.8

Q ss_pred             CHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|.|.+.+..++    +|+.+|+.||||+|||++|+.+++.++...
T Consensus         1 t~~Q~~~~~~i~----~~~~~li~aptGsGKT~~~~~~~l~~~~~~   42 (169)
T PF00270_consen    1 TPLQQEAIEAII----SGKNVLISAPTGSGKTLAYILPALNRLQEG   42 (169)
T ss_dssp             -HHHHHHHHHHH----TTSEEEEECSTTSSHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHH----cCCCEEEECCCCCccHHHHHHHHHhhhccC
Confidence            378999888875    688999999999999999999999988765

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 ....

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=98.47  E-value=1.8e-07  Score=86.69  Aligned_cols=44  Identities=23%  Similarity=0.207  Sum_probs=38.0

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      -.|+|. |||+|.+.+..+.    +|+.+++.+|||+|||++|++|++.
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l----~g~dvlv~apTGsGKTl~y~lp~l~   49 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVL----LGRDCFVVMPTGGGKSLCYQLPALC   49 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHH----cCCCEEEEcCCCCcHhHHHHHHHHH
Confidence            357887 9999999777763    6789999999999999999999875

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

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.44  E-value=3.1e-07  Score=84.90  Aligned_cols=47  Identities=21%  Similarity=0.267  Sum_probs=40.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|. ||++|.+.+..+    .+|+++|+.||||||||++|++|++.-+...
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            5666 999999987765    4789999999999999999999999876543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=98.43  E-value=3.2e-07  Score=84.22  Aligned_cols=47  Identities=21%  Similarity=0.258  Sum_probs=40.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ..|. |+|+|.+.+..+.    +|+++|+.||||||||++|++|++..+...
T Consensus        22 ~g~~~~t~iQ~~ai~~~l----~g~dvi~~a~TGsGKT~a~~lpil~~l~~~   69 (460)
T PRK11776         22 LGYTEMTPIQAQSLPAIL----AGKDVIAQAKTGSGKTAAFGLGLLQKLDVK   69 (460)
T ss_pred             CCCCCCCHHHHHHHHHHh----cCCCEEEECCCCCcHHHHHHHHHHHHhhhc
Confidence            5676 9999999887764    689999999999999999999999987543

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=98.39  E-value=4.1e-07  Score=87.03  Aligned_cols=47  Identities=19%  Similarity=0.207  Sum_probs=40.6

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+.|. |+|+|.+.+..++    +|+++|+.||||||||++|++|++..+..
T Consensus        26 ~~g~~~ptpiQ~~~ip~~l----~G~Dvi~~ApTGSGKTlafllpil~~l~~   73 (572)
T PRK04537         26 SAGFTRCTPIQALTLPVAL----PGGDVAGQAQTGTGKTLAFLVAVMNRLLS   73 (572)
T ss_pred             HCCCCCCCHHHHHHHHHHh----CCCCEEEEcCCCCcHHHHHHHHHHHHHHh
Confidence            35676 9999999887764    78999999999999999999999987653

>PTZ00110 helicase; Provisional

Probab=98.39  E-value=4.3e-07  Score=86.27  Aligned_cols=46  Identities=20%  Similarity=0.081  Sum_probs=39.5

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..|. |+|+|.+.+..+    ..|+.+|+.||||||||++|++|++..+..
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            4576 999999977665    478999999999999999999999887654

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

Probab=98.33  E-value=7.2e-07  Score=87.97  Aligned_cols=47  Identities=17%  Similarity=0.177  Sum_probs=40.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ..|+ ||++|.+.+..+    .+|+++|+.||||||||++|++|+|..+...
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 999999977765    5799999999999999999999999988653

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=98.32  E-value=6.7e-07  Score=84.99  Aligned_cols=43  Identities=26%  Similarity=0.333  Sum_probs=37.9

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|+|+ ++|+|.+.+..|.    +|+++++.+|||+|||++|++|++.
T Consensus         8 ~fg~~~fr~~Q~~~i~~il----~g~dvlv~~PTG~GKTl~y~lpal~   51 (591)
T TIGR01389         8 TFGYDDFRPGQEEIISHVL----DGRDVLVVMPTGGGKSLCYQVPALL   51 (591)
T ss_pred             hcCCCCCCHHHHHHHHHHH----cCCCEEEEcCCCccHhHHHHHHHHH
Confidence            48887 8999999887764    6889999999999999999999874

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=98.29  E-value=7.9e-07  Score=85.39  Aligned_cols=43  Identities=23%  Similarity=0.290  Sum_probs=37.7

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|+|+ |||+|.+.+..+.    +|+.+|+.+|||+|||++|++|++.
T Consensus        20 ~fG~~~~r~~Q~~ai~~il----~g~dvlv~apTGsGKTl~y~lpal~   63 (607)
T PRK11057         20 TFGYQQFRPGQQEIIDAVL----SGRDCLVVMPTGGGKSLCYQIPALV   63 (607)
T ss_pred             HcCCCCCCHHHHHHHHHHH----cCCCEEEEcCCCchHHHHHHHHHHH
Confidence            58887 9999999887764    7889999999999999999999874

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=98.23  E-value=1.8e-06  Score=84.22  Aligned_cols=52  Identities=15%  Similarity=0.245  Sum_probs=45.9

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      -.|||+|+++|...+..|...+..+  ...++.||||||||++|++|++..+..
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            3589999999999999999888765  468999999999999999999887754

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=98.23  E-value=1.7e-06  Score=84.06  Aligned_cols=46  Identities=20%  Similarity=0.231  Sum_probs=39.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+    ..++.+|+.||||||||++|++|++..+..
T Consensus        24 ~G~~~ptpiQ~~ai~~l----l~g~dvl~~ApTGsGKT~af~lpll~~l~~   70 (629)
T PRK11634         24 LGYEKPSPIQAECIPHL----LNGRDVLGMAQTGSGKTAAFSLPLLHNLDP   70 (629)
T ss_pred             CCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCCcHHHHHHHHHHHHhhh
Confidence            5676 999999977775    368899999999999999999999887654

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

Probab=98.19  E-value=2.3e-06  Score=81.02  Aligned_cols=46  Identities=20%  Similarity=0.261  Sum_probs=40.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      -.|. |.|||...+..+.    .|+.+|..|+||||||+||++|+|..+..
T Consensus        47 ~gf~~pt~IQ~~~IP~~l----~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~   93 (513)
T COG0513          47 LGFEEPTPIQLAAIPLIL----AGRDVLGQAQTGTGKTAAFLLPLLQKILK   93 (513)
T ss_pred             cCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHHhc
Confidence            3576 9999999888874    67999999999999999999999998774

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=98.13  E-value=3.5e-06  Score=64.58  Aligned_cols=47  Identities=21%  Similarity=0.173  Sum_probs=39.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .++.+++.|.+++..++    +. +.+++.+|||||||.+++.+++..+...
T Consensus         5 ~~~~~~~~Q~~~~~~~~----~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~   52 (201)
T smart00487        5 GFEPLRPYQKEAIEALL----SGLRDVILAAPTGSGKTLAALLPALEALKRG   52 (201)
T ss_pred             CCCCCCHHHHHHHHHHH----cCCCcEEEECCCCCchhHHHHHHHHHHhccc
Confidence            34569999999888875    44 8999999999999999999887777654

>KOG0348|consensus

Probab=98.11  E-value=1.9e-06  Score=83.29  Aligned_cols=51  Identities=16%  Similarity=0.199  Sum_probs=45.0

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhH
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGL   82 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~   82 (194)
                      .+. |..+|.+-+..|.    +|+.+++.|+||||||||||+|++.-|.....++.
T Consensus       156 ~i~~pTsVQkq~IP~lL----~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~  207 (708)
T KOG0348|consen  156 KISAPTSVQKQAIPVLL----EGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQ  207 (708)
T ss_pred             ccCccchHhhcchhhhh----cCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccc
Confidence            454 8999999888875    49999999999999999999999999998877764

>KOG0345|consensus

Probab=98.10  E-value=3.9e-06  Score=80.03  Aligned_cols=45  Identities=27%  Similarity=0.373  Sum_probs=39.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.|+ ..|+|..-+..+    -.++.+++||||||||||||++|++.-+.
T Consensus        24 ~GF~~mTpVQa~tIPll----l~~KDVvveavTGSGKTlAFllP~le~i~   69 (567)
T KOG0345|consen   24 SGFEKMTPVQAATIPLL----LKNKDVVVEAVTGSGKTLAFLLPMLEIIY   69 (567)
T ss_pred             cCCcccCHHHHhhhHHH----hcCCceEEEcCCCCCchhhHHHHHHHHHH
Confidence            4465 889999988876    47899999999999999999999999883

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

Probab=98.07  E-value=4.3e-06  Score=86.30  Aligned_cols=43  Identities=23%  Similarity=0.110  Sum_probs=37.2

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|+|. +||+|.+.+..+    ..|+.+|+-+|||+||||+|++|+|.
T Consensus       455 ~FG~~sFRp~Q~eaI~ai----L~GrDVLVimPTGSGKSLcYQLPAL~  498 (1195)
T PLN03137        455 VFGNHSFRPNQREIINAT----MSGYDVFVLMPTGGGKSLTYQLPALI  498 (1195)
T ss_pred             HcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCccHHHHHHHHHHH
Confidence            46676 999999977765    47899999999999999999999874

>PRK13767 ATP-dependent helicase; Provisional

Probab=98.06  E-value=5.1e-06  Score=83.27  Aligned_cols=44  Identities=25%  Similarity=0.350  Sum_probs=38.4

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        29 y~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      |. |+|+|.+.+..|    .+|+++|+.||||||||++|++|++..+..
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 999999987765    578999999999999999999999987654

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=98.06  E-value=6.9e-06  Score=79.30  Aligned_cols=51  Identities=20%  Similarity=0.316  Sum_probs=44.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+||+|+++|...+..|...+...  ...++.||||||||++|+.|++..+..
T Consensus       231 ~lpf~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~  283 (630)
T TIGR00643       231 SLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA  283 (630)
T ss_pred             hCCCCCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            589999999999999998877654  358999999999999999998876654

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=98.04  E-value=7e-06  Score=83.16  Aligned_cols=52  Identities=17%  Similarity=0.223  Sum_probs=45.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|||+|+|+|...+..|...+..+  ...++.||||+|||++++.|++..+...
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            589999999999999999888765  5789999999999999999988776544

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.

>PRK01172 ski2-like helicase; Provisional

Probab=97.97  E-value=1.1e-05  Score=77.85  Aligned_cols=47  Identities=26%  Similarity=0.348  Sum_probs=39.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+|++||+|.+.+..+    .+++++|+.||||+|||++++.+++..+...
T Consensus        19 ~~~~l~~~Q~~ai~~l----~~~~nvlv~apTGSGKTl~a~lail~~l~~~   65 (674)
T PRK01172         19 NDFELYDHQRMAIEQL----RKGENVIVSVPTAAGKTLIAYSAIYETFLAG   65 (674)
T ss_pred             CCCCCCHHHHHHHHHH----hcCCcEEEECCCCchHHHHHHHHHHHHHHhC
Confidence            4688999999987764    6788999999999999999999887765543

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

Probab=97.94  E-value=1.2e-05  Score=80.50  Aligned_cols=45  Identities=16%  Similarity=0.199  Sum_probs=41.4

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        29 y~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      |. |+|.|...+..|+    +|+++++-||||+|||+|.++|++.-+...
T Consensus        20 ~~~~t~~Q~~a~~~i~----~G~nvLiiAPTGsGKTeAAfLpil~~l~~~   65 (814)
T COG1201          20 FTSLTPPQRYAIPEIH----SGENVLIIAPTGSGKTEAAFLPVINELLSL   65 (814)
T ss_pred             cCCCCHHHHHHHHHHh----CCCceEEEcCCCCChHHHHHHHHHHHHHhc
Confidence            65 9999999998885    899999999999999999999999988776

>PRK02362 ski2-like helicase; Provisional

Probab=97.92  E-value=1.4e-05  Score=78.24  Aligned_cols=46  Identities=24%  Similarity=0.218  Sum_probs=38.5

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|. +||+|.+.+..   .+..|+++|+.||||+|||+++++|++..+..
T Consensus        20 g~~~l~p~Q~~ai~~---~~~~g~nvlv~APTGSGKTlia~lail~~l~~   66 (737)
T PRK02362         20 GIEELYPPQAEAVEA---GLLDGKNLLAAIPTASGKTLIAELAMLKAIAR   66 (737)
T ss_pred             CCCcCCHHHHHHHHH---HHhCCCcEEEECCCcchHHHHHHHHHHHHHhc
Confidence            454 99999997654   35678999999999999999999998887653

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

Probab=97.92  E-value=1.3e-05  Score=80.56  Aligned_cols=47  Identities=19%  Similarity=0.287  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .+|+.|.+.++.+    .+|+++|+-+|||||||+||++|++.-+......
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            3999999987776    5899999999999999999999999977765555

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=97.90  E-value=1.4e-05  Score=81.13  Aligned_cols=49  Identities=18%  Similarity=0.161  Sum_probs=40.8

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      -|..||..+|+|.+.|..+.    .+..+|.+|+||||||++|++|++.-+..
T Consensus        86 G~~~p~~~tp~qvQ~I~~i~----l~~gvIAeaqTGeGKTLAf~LP~l~~aL~  134 (970)
T PRK12899         86 GYHQQWDMVPYDVQILGAIA----MHKGFITEMQTGEGKTLTAVMPLYLNALT  134 (970)
T ss_pred             cccCCCCCChHHHHHhhhhh----cCCCeEEEeCCCCChHHHHHHHHHHHHhh
Confidence            37788888899999888764    45679999999999999999999976643

>PRK00254 ski2-like helicase; Provisional

Probab=97.89  E-value=1.4e-05  Score=78.01  Aligned_cols=47  Identities=19%  Similarity=0.200  Sum_probs=38.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..|. |||+|.+.+..   .+.+|+++|+.||||+|||+++.+|++..+..
T Consensus        19 ~g~~~l~~~Q~~ai~~---~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~   66 (720)
T PRK00254         19 RGIEELYPPQAEALKS---GVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR   66 (720)
T ss_pred             CCCCCCCHHHHHHHHH---HHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh
Confidence            4565 99999996654   35678999999999999999999998876543

>KOG0331|consensus

Probab=97.86  E-value=6.8e-06  Score=78.81  Aligned_cols=47  Identities=17%  Similarity=0.107  Sum_probs=41.2

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      -.|+ |.|||.+....+    ..|+.+|.-|-|||||||||++|++.++..+
T Consensus       109 ~g~~~PtpIQaq~wp~~----l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~  156 (519)
T KOG0331|consen  109 QGFEKPTPIQAQGWPIA----LSGRDLVGIARTGSGKTLAYLLPAIVHLNNE  156 (519)
T ss_pred             cCCCCCchhhhccccee----ccCCceEEEeccCCcchhhhhhHHHHHHHhc
Confidence            3465 999999987776    4799999999999999999999999999973

>KOG0344|consensus

Probab=97.75  E-value=2.2e-05  Score=75.98  Aligned_cols=50  Identities=26%  Similarity=0.301  Sum_probs=41.5

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .-+|. |.|+|.+.+..    +-.+.+++..+|||+||||||+||+|..|.++..
T Consensus       153 ~~~F~~Pt~iq~~aipv----fl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~  203 (593)
T KOG0344|consen  153 ELGFDEPTPIQKQAIPV----FLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQ  203 (593)
T ss_pred             hCCCCCCCcccchhhhh----hhcccceEEeccCCCcchhhhhhHHHHHHHHhhc
Confidence            34677 99999964443    3467899999999999999999999999998873

>KOG0330|consensus

Probab=97.69  E-value=3e-05  Score=72.83  Aligned_cols=49  Identities=20%  Similarity=0.170  Sum_probs=43.6

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .|. |.+||.+-|..+.    +|+++|.-|-||+|||++|++|+|.-|..+++.
T Consensus        80 ~~~~PT~IQ~~aiP~~L----~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~~  129 (476)
T KOG0330|consen   80 GWKKPTKIQSEAIPVAL----GGRDVIGLAETGSGKTGAFALPILQRLLQEPKL  129 (476)
T ss_pred             CcCCCchhhhhhcchhh----CCCcEEEEeccCCCchhhhHHHHHHHHHcCCCC
Confidence            365 9999999998874    789999999999999999999999988887665

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

Probab=97.68  E-value=3.9e-05  Score=77.32  Aligned_cols=41  Identities=17%  Similarity=0.296  Sum_probs=32.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCC-ceeeeCCCCCCchHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk-~~I~ESPTGTGKTLS~L~~al   71 (194)
                      +.|+|||+|.+.+..+.    .|+ ++++.+|||||||.++.++.+
T Consensus        12 ~G~~PtpiQ~~~i~~il----~G~~~v~~~apTGSGKTaa~aafll   53 (844)
T TIGR02621        12 HGYSPFPWQLSLAERFV----AGQPPESCSTPTGLGKTSIIAAWLL   53 (844)
T ss_pred             hCCCCCHHHHHHHHHHH----cCCCcceEecCCCCcccHHHHHhhc
Confidence            46779999999888763    565 688899999999997654444

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=97.62  E-value=9.4e-05  Score=76.59  Aligned_cols=51  Identities=14%  Similarity=0.107  Sum_probs=43.2

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      -.|||.|.++|.+.+..|..-+...  ...++.||||+|||+.++.+++..+.
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            3699999999999999998877654  67999999999999998887765554

>KOG0335|consensus

Probab=97.56  E-value=2.7e-05  Score=74.18  Aligned_cols=48  Identities=15%  Similarity=0.240  Sum_probs=40.8

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .|. |.|+|.--+..|    ..|..++..||||+|||.+||+|++.++.+.+.
T Consensus        93 ~~~~ptpvQk~sip~i----~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~  141 (482)
T KOG0335|consen   93 GYTKPTPVQKYSIPII----SGGRDLMACAQTGSGKTAAFLIPIISYLLDEGP  141 (482)
T ss_pred             cccCCCcceeecccee----ecCCceEEEccCCCcchHHHHHHHHHHHHhcCc
Confidence            355 888888866665    578899999999999999999999999988744

>KOG0350|consensus

Probab=97.53  E-value=6e-05  Score=72.63  Aligned_cols=49  Identities=18%  Similarity=0.362  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHHHHHHHhc-----CCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~-----gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .+|+|...+..|...+..     ...+.+-|||||||||||.+|+++.|-...-
T Consensus       160 ~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v  213 (620)
T KOG0350|consen  160 LFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPV  213 (620)
T ss_pred             ccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHHHccCCc
Confidence            568999999998888862     4678999999999999999999998877643

>PRK09694 helicase Cas3; Provisional

Probab=97.51  E-value=0.00011  Score=74.32  Aligned_cols=44  Identities=18%  Similarity=0.219  Sum_probs=34.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .|.|||.|..++...    ...+.+|+++|||+|||.+.|..+...+.
T Consensus       284 ~~~p~p~Q~~~~~~~----~~pgl~ileApTGsGKTEAAL~~A~~l~~  327 (878)
T PRK09694        284 GYQPRQLQTLVDALP----LQPGLTIIEAPTGSGKTEAALAYAWRLID  327 (878)
T ss_pred             CCCChHHHHHHHhhc----cCCCeEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            578999999864331    35678999999999999999888765443

>PRK09401 reverse gyrase; Reviewed

Probab=97.45  E-value=0.00017  Score=74.93  Aligned_cols=46  Identities=17%  Similarity=0.153  Sum_probs=36.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|.|+++|...+..+    ..|+.+++.||||||||+ ++++++.|+...
T Consensus        77 ~G~~pt~iQ~~~i~~i----l~g~dv~i~ApTGsGKT~-f~l~~~~~l~~~  122 (1176)
T PRK09401         77 TGSKPWSLQRTWAKRL----LLGESFAIIAPTGVGKTT-FGLVMSLYLAKK  122 (1176)
T ss_pred             cCCCCcHHHHHHHHHH----HCCCcEEEEcCCCCCHHH-HHHHHHHHHHhc
Confidence            5778999999977776    378999999999999996 555555666543

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

Probab=97.37  E-value=0.00031  Score=72.73  Aligned_cols=50  Identities=14%  Similarity=0.173  Sum_probs=39.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.+.+|+.|.+.+..+.+++.+| +.+++.+|||||||++.+..+..+++.
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            34569999999999999999765 568889999999999866554444443

>KOG0346|consensus

Probab=97.37  E-value=0.00015  Score=69.11  Aligned_cols=49  Identities=20%  Similarity=0.181  Sum_probs=40.3

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .|+ |.-||...+.-+    -+|+.+|..|-||||||++||+|.|.-|...+..
T Consensus        38 G~ekpTlIQs~aIpla----LEgKDvvarArTGSGKT~AYliPllqkll~~k~t   87 (569)
T KOG0346|consen   38 GWEKPTLIQSSAIPLA----LEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKT   87 (569)
T ss_pred             CcCCcchhhhcccchh----hcCcceeeeeccCCCchHHHHHHHHHHHHHhhhc
Confidence            455 788888866654    3588999999999999999999999988776655

>PRK14701 reverse gyrase; Provisional

Probab=97.35  E-value=0.00026  Score=75.67  Aligned_cols=44  Identities=27%  Similarity=0.222  Sum_probs=36.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .++|+|+++|.+.+..+.    +|+.+++-||||+|||+.++.+++..
T Consensus        75 ~~G~~pt~iQ~~~i~~il----~G~d~li~APTGsGKTl~~~~~al~~  118 (1638)
T PRK14701         75 ITGFEFWSIQKTWAKRIL----RGKSFSIVAPTGMGKSTFGAFIALFL  118 (1638)
T ss_pred             hhCCCCCHHHHHHHHHHH----cCCCEEEEEcCCCCHHHHHHHHHHHH
Confidence            377899999999888764    68899999999999999666665544

>TIGR01054 rgy reverse gyrase

Probab=97.30  E-value=0.00033  Score=72.81  Aligned_cols=46  Identities=17%  Similarity=0.204  Sum_probs=36.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ..+.|+++|...+..+    -.|+.+++.||||||||+ |++|++.++...
T Consensus        75 ~g~~p~~iQ~~~i~~i----l~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~  120 (1171)
T TIGR01054        75 VGSEPWSIQKMWAKRV----LRGDSFAIIAPTGVGKTT-FGLAMSLFLAKK  120 (1171)
T ss_pred             cCCCCcHHHHHHHHHH----hCCCeEEEECCCCCCHHH-HHHHHHHHHHhc
Confidence            4467999999877765    478899999999999997 666777766543

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=97.28  E-value=0.00038  Score=68.30  Aligned_cols=51  Identities=14%  Similarity=0.026  Sum_probs=40.8

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..-|+.+++.|.+.+..|...+ .+.+.++.+|||+|||.+|+.++...+..
T Consensus       139 ~~~~~~Lt~~Q~~ai~~i~~~~-~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~  189 (679)
T PRK05580        139 AFEPPTLNPEQAAAVEAIRAAA-GFSPFLLDGVTGSGKTEVYLQAIAEVLAQ  189 (679)
T ss_pred             ccCCCCCCHHHHHHHHHHHhcc-CCCcEEEECCCCChHHHHHHHHHHHHHHc
Confidence            3456779999999888886544 45789999999999999999887666554

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

Probab=97.25  E-value=0.00043  Score=64.49  Aligned_cols=45  Identities=22%  Similarity=0.352  Sum_probs=37.8

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHH
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      +.+.|.+|+.|.+.+.++...+..++.+|+-.|||+|||+..+-.
T Consensus        31 ~~~~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~   75 (442)
T COG1061          31 VAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEA   75 (442)
T ss_pred             cccCCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHH
Confidence            566678999999988888777766888999999999999876554

>KOG0334|consensus

Probab=97.22  E-value=0.00016  Score=73.75  Aligned_cols=49  Identities=18%  Similarity=0.329  Sum_probs=42.2

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .+.|. |+|||.+++.+|    ..|..+|..|-||+|||++|++|.+....+.+
T Consensus       382 kl~y~k~~~IQ~qAiP~I----msGrdvIgvakTgSGKT~af~LPmirhi~dQr  431 (997)
T KOG0334|consen  382 KLGYEKPTPIQAQAIPAI----MSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQR  431 (997)
T ss_pred             HhcCCCCcchhhhhcchh----ccCcceEEeeccCCccchhhhcchhhhhhcCC
Confidence            46676 999999999997    68999999999999999999999996555443

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=97.19  E-value=0.00044  Score=68.16  Aligned_cols=45  Identities=20%  Similarity=0.115  Sum_probs=37.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+...|||+|..-...++    .|+  |.++.||+|||+++++|++..+..
T Consensus        99 ~lg~~p~~VQ~~~~~~ll----~G~--Iae~~TGeGKTla~~lp~~~~al~  143 (656)
T PRK12898         99 VLGQRHFDVQLMGGLALL----SGR--LAEMQTGEGKTLTATLPAGTAALA  143 (656)
T ss_pred             HhCCCCChHHHHHHHHHh----CCC--eeeeeCCCCcHHHHHHHHHHHhhc
Confidence            467789999999666653    566  999999999999999999876553

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

Probab=97.17  E-value=0.00033  Score=68.30  Aligned_cols=45  Identities=27%  Similarity=0.224  Sum_probs=37.9

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      -.|.|. .||.|.+.+..    +-+|+++|+-.|||.||||+|-+|++-.
T Consensus        11 ~~fGy~~FR~gQ~evI~~----~l~g~d~lvvmPTGgGKSlCyQiPAll~   56 (590)
T COG0514          11 QVFGYASFRPGQQEIIDA----LLSGKDTLVVMPTGGGKSLCYQIPALLL   56 (590)
T ss_pred             HHhCccccCCCHHHHHHH----HHcCCcEEEEccCCCCcchHhhhHHHhc
Confidence            357887 89999975554    4578999999999999999999998765

>KOG0338|consensus

Probab=97.15  E-value=0.00023  Score=69.04  Aligned_cols=52  Identities=17%  Similarity=0.039  Sum_probs=43.7

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      ...|. |.|||...+.-.    .-|+.++..|.||||||.+|.+|+|.-|.-.++++
T Consensus       198 ~lGy~~PTpIQ~a~IPva----llgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~~  250 (691)
T KOG0338|consen  198 TLGYKKPTPIQVATIPVA----LLGKDICACAATGSGKTAAFALPILERLLYRPKKV  250 (691)
T ss_pred             hcCCCCCCchhhhcccHH----hhcchhhheecccCCchhhhHHHHHHHHhcCcccC
Confidence            46787 999999988753    24899999999999999999999999887666653

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=97.13  E-value=0.00045  Score=69.12  Aligned_cols=43  Identities=26%  Similarity=0.334  Sum_probs=29.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ...||++|  +|..+.  +..|  .|++++||+||||++++|++..+..
T Consensus        68 glrpydVQ--lig~l~--l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~  110 (762)
T TIGR03714        68 GMFPYDVQ--VLGAIV--LHQG--NIAEMKTGEGKTLTATMPLYLNALT  110 (762)
T ss_pred             CCCccHHH--HHHHHH--hcCC--ceeEecCCcchHHHHHHHHHHHhhc
Confidence            33455555  445542  3445  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.

>KOG0342|consensus

Probab=97.02  E-value=0.00026  Score=67.94  Aligned_cols=50  Identities=22%  Similarity=0.276  Sum_probs=41.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ..|+ ..++|...+..|    -.|+.++.-|-|||||||+||+|++.|+...+..
T Consensus       100 ~GF~~MT~VQ~~ti~pl----l~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~  150 (543)
T KOG0342|consen  100 MGFETMTPVQQKTIPPL----LEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFK  150 (543)
T ss_pred             cCccchhHHHHhhcCcc----CCCccceeeeccCCCceeeehhHHHHHHHhcccC
Confidence            4465 778998876665    3688999999999999999999999999876543

>PHA02558 uvsW UvsW helicase; Provisional

Probab=97.00  E-value=0.0011  Score=62.35  Aligned_cols=37  Identities=22%  Similarity=0.171  Sum_probs=28.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHH
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~   68 (194)
                      .+.||++|.+.+.   .++. +..+|+.+|||+|||+.++.
T Consensus       112 ~~~~r~~Q~~av~---~~l~-~~~~il~apTGsGKT~i~~~  148 (501)
T PHA02558        112 KIEPHWYQYDAVY---EGLK-NNRRLLNLPTSAGKSLIQYL  148 (501)
T ss_pred             cCCCCHHHHHHHH---HHHh-cCceEEEeCCCCCHHHHHHH
Confidence            4689999999554   4444 55689999999999997543

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=96.93  E-value=0.00088  Score=60.48  Aligned_cols=34  Identities=26%  Similarity=0.438  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHHHHHHHH
Q psy14272         35 QSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        35 Q~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      |.+..+.+    .++.  ++|+.||||+|||+++++|++.
T Consensus         2 Q~~~~~~~----~~~~~~~~~i~apTGsGKT~~~~~~~l~   37 (357)
T TIGR03158         2 QVATFEAL----QSKDADIIFNTAPTGAGKTLAWLTPLLH   37 (357)
T ss_pred             HHHHHHHH----HcCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            55544444    4453  5788999999999999998774

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.92  E-value=0.00091  Score=48.12  Aligned_cols=27  Identities=30%  Similarity=0.496  Sum_probs=22.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +++++.+|||+|||..++..+...+..
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~   27 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS   27 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc
Confidence            368999999999999988887665543

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

>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=96.91  E-value=0.0014  Score=56.11  Aligned_cols=42  Identities=24%  Similarity=0.381  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ..|..+|+++.    +..++++.+|.|||||+-.+..++..+.+..
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            78999999886    6789999999999999999999999887633

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

>PHA02653 RNA helicase NPH-II; Provisional

Probab=96.90  E-value=0.0011  Score=65.46  Aligned_cols=44  Identities=16%  Similarity=0.190  Sum_probs=33.0

Q ss_pred             CHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH---------HHHHHHHHHh
Q psy14272         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS---------LICGILKWYY   75 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS---------~L~~al~wl~   75 (194)
                      .+.|.+.=..+..++..++++|+.|+||||||.+         |+.|.+.++.
T Consensus       162 ~~~~~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~  214 (675)
T PHA02653        162 ASLQPDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLD  214 (675)
T ss_pred             CchhHHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhh
Confidence            3455555556666667899999999999999997         5666677664

>PRK13766 Hef nuclease; Provisional

Probab=96.86  E-value=0.0018  Score=63.43  Aligned_cols=44  Identities=20%  Similarity=0.134  Sum_probs=34.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+++||+.|.++...+   +..  .+|+-+|||+|||+.+++++...+.
T Consensus        12 ~~~~~r~yQ~~~~~~~---l~~--n~lv~~ptG~GKT~~a~~~i~~~l~   55 (773)
T PRK13766         12 NTIEARLYQQLLAATA---LKK--NTLVVLPTGLGKTAIALLVIAERLH   55 (773)
T ss_pred             CcCCccHHHHHHHHHH---hcC--CeEEEcCCCccHHHHHHHHHHHHHH
Confidence            4567999999976654   443  7899999999999998888766553

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=96.86  E-value=0.00084  Score=59.15  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=21.8

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ++|+.||||+|||++++.+++..+.
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~   25 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIK   25 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            4789999999999999999887654

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.

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=96.85  E-value=0.0013  Score=66.17  Aligned_cols=37  Identities=27%  Similarity=0.392  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      ..+..|.++|.++.++|+.||||||||.+|..++|..
T Consensus         8 ~~~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~   44 (812)
T PRK11664          8 AVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQH   44 (812)
T ss_pred             HHHHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHc
Confidence            3456788888899999999999999999999988863

>KOG0354|consensus

Probab=96.82  E-value=0.0014  Score=65.41  Aligned_cols=46  Identities=20%  Similarity=0.268  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      |..|+.|.++.+.   +|  |++.|+-+|||+|||+....-++.|++-.++
T Consensus        61 ~~lR~YQ~eivq~---AL--gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~  106 (746)
T KOG0354|consen   61 LELRNYQEELVQP---AL--GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK  106 (746)
T ss_pred             ccccHHHHHHhHH---hh--cCCeEEEeecCCCccchHHHHHHHHHhcCCc
Confidence            6699999996554   56  9999999999999999999999999988776

>TIGR00603 rad25 DNA repair helicase rad25

Probab=96.79  E-value=0.0026  Score=63.60  Aligned_cols=45  Identities=22%  Similarity=0.287  Sum_probs=34.3

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al   71 (194)
                      ...+.+.+||.|.+.+..   ++.+|  ..+|+..|||+|||+..|..+.
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            344557899999995554   45555  4799999999999999876643

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=96.78  E-value=0.0017  Score=51.94  Aligned_cols=38  Identities=21%  Similarity=0.420  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      +.|..   +|..++....+.++.||.|||||- +|+.++..+
T Consensus         4 ~~Q~~---Ai~~~~~~~~~~~i~GpPGTGKT~-~l~~~i~~~   41 (236)
T PF13086_consen    4 ESQRE---AIQSALSSNGITLIQGPPGTGKTT-TLASIIAQL   41 (236)
T ss_dssp             HHHHH---HHHHHCTSSE-EEEE-STTSSHHH-HHHHHHHHH
T ss_pred             HHHHH---HHHHHHcCCCCEEEECCCCCChHH-HHHHHHHHh
Confidence            46777   444455655569999999999994 455556655

>COG1204 Superfamily II helicase [General function prediction only]

Probab=96.78  E-value=0.0011  Score=66.40  Aligned_cols=45  Identities=22%  Similarity=0.336  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +-|+.|..   +|+..+..++++|+.+|||+|||+..+++++.-+.++
T Consensus        31 el~~~qq~---av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~   75 (766)
T COG1204          31 ELFNPQQE---AVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG   75 (766)
T ss_pred             HhhHHHHH---HhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc
Confidence            57888888   6666667789999999999999999999999888876

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=96.77  E-value=0.0013  Score=65.79  Aligned_cols=44  Identities=25%  Similarity=0.209  Sum_probs=33.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHH-HHHh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL-KWYY   75 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al-~wl~   75 (194)
                      .+.+.||++|.--.-.    |..|.  |.+++||+|||+++++|++ ..+.
T Consensus        52 ~lg~~p~~vQlig~~~----l~~G~--Iaem~TGeGKTLva~lpa~l~aL~   96 (745)
T TIGR00963        52 VLGMRPFDVQLIGGIA----LHKGK--IAEMKTGEGKTLTATLPAYLNALT   96 (745)
T ss_pred             HhCCCccchHHhhhhh----hcCCc--eeeecCCCccHHHHHHHHHHHHHh
Confidence            4667789999874443    34554  9999999999999999984 4554

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=96.76  E-value=0.0018  Score=65.19  Aligned_cols=43  Identities=26%  Similarity=0.234  Sum_probs=32.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .+...||++|.--.-.    +..|.  |.++.||+|||+++++|++...
T Consensus        74 ~~g~~p~~vQl~~~~~----l~~G~--Iaem~TGeGKTL~a~lp~~l~a  116 (790)
T PRK09200         74 VLGMRPYDVQLIGALV----LHEGN--IAEMQTGEGKTLTATMPLYLNA  116 (790)
T ss_pred             HhCCCCchHHHHhHHH----HcCCc--eeeecCCCcchHHHHHHHHHHH
Confidence            3566788998764333    34564  9999999999999999987443

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

Probab=96.71  E-value=0.0022  Score=62.89  Aligned_cols=44  Identities=18%  Similarity=0.276  Sum_probs=36.5

Q ss_pred             CCHHHHHHHHHHHHHHhc------CCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDN------SKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~------gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      |++.|...++.+...+.+      .+.+|+.+|||||||++.+..+...+
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~  288 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKAL  288 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHH
Confidence            788999999999999865      35799999999999998776654433

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

>KOG0333|consensus

Probab=96.71  E-value=0.001  Score=64.71  Aligned_cols=47  Identities=19%  Similarity=0.214  Sum_probs=40.1

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        29 y~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      |. |.|||...+..+    .+.+..|.-+-||+|||++|++|.|.|+...+.
T Consensus       265 y~eptpIqR~aipl~----lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~  312 (673)
T KOG0333|consen  265 YKEPTPIQRQAIPLG----LQNRDPIGVAETGSGKTAAFLIPLLIWISSLPP  312 (673)
T ss_pred             CCCCchHHHhhccch----hccCCeeeEEeccCCccccchhhHHHHHHcCCC
Confidence            65 999999977743    466788889999999999999999999988773

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=96.63  E-value=0.0024  Score=64.31  Aligned_cols=38  Identities=24%  Similarity=0.297  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .++..|.++|.++.++|+.||||||||.+|..+++...
T Consensus         5 ~~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~   42 (819)
T TIGR01970         5 AVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAP   42 (819)
T ss_pred             HHHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhh
Confidence            35668888889999999999999999999999988654

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.

>KOG0336|consensus

Probab=96.61  E-value=0.00039  Score=66.29  Aligned_cols=51  Identities=24%  Similarity=0.058  Sum_probs=41.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      -.|. |.|||-++-..+    -+|..+|.-|.|||||||+||.|.+-.+.......
T Consensus       238 ~GFqKPtPIqSQaWPI~----LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~  289 (629)
T KOG0336|consen  238 TGFQKPTPIQSQAWPIL----LQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRR  289 (629)
T ss_pred             ccCCCCCcchhccccee----ecCcceEEEEecCCCcCHHHhccceeeeeccchhh
Confidence            3565 888888876665    47999999999999999999999988877665543

>KOG0340|consensus

Probab=96.53  E-value=0.002  Score=60.29  Aligned_cols=48  Identities=19%  Similarity=0.167  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +.|.|+|..-+..|.    .|..+|-.|-||||||++|-+|+|.-+..++-.
T Consensus        28 ~~pTpiQ~~cIpkIL----eGrdcig~AkTGsGKT~AFaLPil~rLsedP~g   75 (442)
T KOG0340|consen   28 KKPTPIQQACIPKIL----EGRDCIGCAKTGSGKTAAFALPILNRLSEDPYG   75 (442)
T ss_pred             CCCCchHhhhhHHHh----cccccccccccCCCcchhhhHHHHHhhccCCCc
Confidence            459999999888874    799999999999999999999999977766544

>KOG0343|consensus

Probab=96.45  E-value=0.0011  Score=64.87  Aligned_cols=43  Identities=23%  Similarity=0.324  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +..||.+-|...   | .|+.+|--|-|||||||+||+|+|..|...
T Consensus        92 ~teiQ~~~Ip~a---L-~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~  134 (758)
T KOG0343|consen   92 MTEIQRDTIPMA---L-QGHDVLGAAKTGSGKTLAFLVPVLEALYRL  134 (758)
T ss_pred             HHHHHHhhcchh---c-cCcccccccccCCCceeeehHHHHHHHHHc
Confidence            678888855543   3 588999999999999999999999866543

>PRK08181 transposase; Validated

Probab=96.42  E-value=0.011  Score=52.30  Aligned_cols=32  Identities=22%  Similarity=0.083  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      +.|..-...+..++..+..++|-+|+|||||.
T Consensus        90 ~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTH  121 (269)
T PRK08181         90 KAQVMAIAAGDSWLAKGANLLLFGPPGGGKSH  121 (269)
T ss_pred             HHHHHHHHHHHHHHhcCceEEEEecCCCcHHH
Confidence            45555444444678888999999999999995

>PF13245 AAA_19: Part of AAA domain

Probab=96.38  E-value=0.0049  Score=44.58  Aligned_cols=34  Identities=26%  Similarity=0.399  Sum_probs=25.0

Q ss_pred             HHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        41 ~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .|..++..+...|+.+|.|||||..++--+..++
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHH
Confidence            3555677567788899999999977666655555

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=96.36  E-value=0.0072  Score=52.29  Aligned_cols=37  Identities=22%  Similarity=0.196  Sum_probs=32.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      |-+.|...++.+.+..++..+..+++++|+|||||..
T Consensus         1 ~~~t~~~~~l~~~~l~~l~~g~~vLL~G~~GtGKT~l   37 (262)
T TIGR02640         1 FIETDAVKRVTSRALRYLKSGYPVHLRGPAGTGKTTL   37 (262)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCeEEEEcCCCCCHHHH
Confidence            3456788899999999999999999999999999964

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).

>PRK10536 hypothetical protein; Provisional

Probab=96.36  E-value=0.0096  Score=53.05  Aligned_cols=44  Identities=14%  Similarity=0.203  Sum_probs=33.4

Q ss_pred             CCCC-HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         29 FDAY-DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        29 y~py-~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..|+ ..|..++..|    .+..++++.+|+|||||+-.++.++..+.+
T Consensus        57 i~p~n~~Q~~~l~al----~~~~lV~i~G~aGTGKT~La~a~a~~~l~~  101 (262)
T PRK10536         57 ILARNEAQAHYLKAI----ESKQLIFATGEAGCGKTWISAAKAAEALIH  101 (262)
T ss_pred             ccCCCHHHHHHHHHH----hcCCeEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            3455 6788877755    557799999999999998877777765543

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

Probab=96.34  E-value=0.0065  Score=62.77  Aligned_cols=51  Identities=22%  Similarity=0.326  Sum_probs=39.7

Q ss_pred             CCccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         22 PSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        22 ~~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +....|||++.+.|.+-+.    +|+.|..+++.||||+|||+..-.++-.-+++
T Consensus       111 ~~~~~~~F~LD~fQ~~a~~----~Ler~esVlV~ApTssGKTvVaeyAi~~al~~  161 (1041)
T COG4581         111 PPAREYPFELDPFQQEAIA----ILERGESVLVCAPTSSGKTVVAEYAIALALRD  161 (1041)
T ss_pred             cHHHhCCCCcCHHHHHHHH----HHhCCCcEEEEccCCCCcchHHHHHHHHHHHc
Confidence            3345599999999998544    56899999999999999999887774443433

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=96.15  E-value=0.0046  Score=62.58  Aligned_cols=47  Identities=21%  Similarity=0.231  Sum_probs=34.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHH-HHHhhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL-KWYYDHK   78 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al-~wl~~~~   78 (194)
                      .....||++|.-  -.|  +|..|  -|.|++||+||||++.+|++ .++...+
T Consensus        77 ~lg~~~~dvQli--g~l--~L~~G--~Iaem~TGeGKTLva~lpa~l~aL~G~~  124 (830)
T PRK12904         77 VLGMRHFDVQLI--GGM--VLHEG--KIAEMKTGEGKTLVATLPAYLNALTGKG  124 (830)
T ss_pred             HhCCCCCccHHH--hhH--HhcCC--chhhhhcCCCcHHHHHHHHHHHHHcCCC
Confidence            356778898865  333  44566  48899999999999999985 6665433

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=96.15  E-value=0.004  Score=63.47  Aligned_cols=45  Identities=22%  Similarity=0.245  Sum_probs=32.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .....||++|+-  -.|  +|.+|  -|.+++||+||||++++|++..+..
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            355668888864  333  24556  4789999999999999999865543

>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=96.04  E-value=0.012  Score=42.73  Aligned_cols=30  Identities=30%  Similarity=0.380  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHhc--CCceeeeCCCCCCchH
Q psy14272         35 QSNFMKNLYYTLDN--SKFGIFESPTGTGKSL   64 (194)
Q Consensus        35 Q~e~M~~I~~~L~~--gk~~I~ESPTGTGKTL   64 (194)
                      +...+..|...+..  +.++++-+|+|+|||.
T Consensus         3 ~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~   34 (151)
T cd00009           3 QEEAIEALREALELPPPKNLLLYGPPGTGKTT   34 (151)
T ss_pred             hHHHHHHHHHHHhCCCCCeEEEECCCCCCHHH
Confidence            45566777777776  7889999999999995

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.

>KOG0337|consensus

Probab=95.84  E-value=0.0039  Score=59.46  Aligned_cols=47  Identities=17%  Similarity=0.227  Sum_probs=41.5

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .|. |.|||..-|..|    -++..++--|-||+|||.||++|+++-|..+-
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            365 999999988876    47888999999999999999999999998876

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=95.82  E-value=0.0073  Score=61.65  Aligned_cols=45  Identities=27%  Similarity=0.316  Sum_probs=33.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+...||++|+-  -.|  +|.+|  -|.|++||+||||++++|++..+..
T Consensus        78 ~lgm~~ydVQli--Ggl--~L~~G--~IaEm~TGEGKTL~a~lp~~l~al~  122 (908)
T PRK13107         78 VFEMRHFDVQLL--GGM--VLDSN--RIAEMRTGEGKTLTATLPAYLNALT  122 (908)
T ss_pred             HhCCCcCchHHh--cch--HhcCC--ccccccCCCCchHHHHHHHHHHHhc
Confidence            466779999873  333  23455  5789999999999999998765543

>KOG0352|consensus

Probab=95.82  E-value=0.0085  Score=57.63  Aligned_cols=44  Identities=23%  Similarity=0.209  Sum_probs=33.8

Q ss_pred             CCCCC--CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFD--AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~--py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|.|.  -.+-|.+.+.   .++..++.+.+.+|||+||||+|-+|+|-
T Consensus        14 ~FGh~kFKs~LQE~A~~---c~VK~k~DVyVsMPTGaGKSLCyQLPaL~   59 (641)
T KOG0352|consen   14 LFGHKKFKSRLQEQAIN---CIVKRKCDVYVSMPTGAGKSLCYQLPALV   59 (641)
T ss_pred             HhCchhhcChHHHHHHH---HHHhccCcEEEeccCCCchhhhhhchHHH
Confidence            45555  3478888444   44677889999999999999999888764

>KOG0351|consensus

Probab=95.79  E-value=0.0033  Score=64.32  Aligned_cols=46  Identities=24%  Similarity=0.062  Sum_probs=37.6

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..|.+. .||.|.+.+.    ++..|+..++..|||.||||+|-+|++-+-
T Consensus       258 ~~Fg~~~FR~~Q~eaI~----~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~~  304 (941)
T KOG0351|consen  258 EVFGHKGFRPNQLEAIN----ATLSGKDCFVLMPTGGGKSLCYQLPALLLG  304 (941)
T ss_pred             HHhccccCChhHHHHHH----HHHcCCceEEEeecCCceeeEeeccccccC
Confidence            347776 8899999555    446899999999999999999999976543

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=95.69  E-value=0.011  Score=50.54  Aligned_cols=40  Identities=18%  Similarity=0.209  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+...+..++..++.+||-+|||||||-. +...+.++...
T Consensus       115 ~~~~~l~~~v~~~~~ili~G~tGSGKTT~-l~all~~i~~~  154 (270)
T PF00437_consen  115 EIAEFLRSAVRGRGNILISGPTGSGKTTL-LNALLEEIPPE  154 (270)
T ss_dssp             HHHHHHHHCHHTTEEEEEEESTTSSHHHH-HHHHHHHCHTT
T ss_pred             HHHHHHhhccccceEEEEECCCccccchH-HHHHhhhcccc
Confidence            33344555567789999999999999954 57777777766

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 ....

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.69  E-value=0.02  Score=52.01  Aligned_cols=48  Identities=21%  Similarity=0.183  Sum_probs=28.7

Q ss_pred             CCHHHHHHHHHHHHHHh----cCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         31 AYDIQSNFMKNLYYTLD----NSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~----~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      |+.....++..+...++    .+..++|-||||||||.-. +++...+...+.
T Consensus       161 ~~~~~~~~~~~~~~f~~~f~~~~~~Lll~G~~GtGKThLa-~aIa~~l~~~g~  212 (329)
T PRK06835        161 PRKNMEKILEKCKNFIENFDKNNENLLFYGNTGTGKTFLS-NCIAKELLDRGK  212 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHH-HHHHHHHHHCCC
Confidence            44444444444443444    4578999999999999843 333444444333

>KOG0327|consensus

Probab=95.68  E-value=0.0053  Score=57.43  Aligned_cols=47  Identities=21%  Similarity=0.355  Sum_probs=39.0

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.|.|+ |-.||...+..+   + .|.+++..+++|||||.+|+++++.-+.
T Consensus        42 y~yGFekPSaIQqraI~p~---i-~G~dv~~qaqsgTgKt~af~i~iLq~iD   89 (397)
T KOG0327|consen   42 YAYGFEKPSAIQQRAILPC---I-KGHDVIAQAQSGTGKTAAFLISILQQID   89 (397)
T ss_pred             HhhccCCchHHHhcccccc---c-cCCceeEeeeccccchhhhHHHHHhhcC
Confidence            458898 999999854443   3 5889999999999999999999988753

>PHA02244 ATPase-like protein

Probab=95.63  E-value=0.029  Score=52.45  Aligned_cols=40  Identities=8%  Similarity=0.012  Sum_probs=30.1

Q ss_pred             ccCCCCC--CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         24 EFPFPFD--AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        24 ~~~fPy~--py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      .|.|||.  .+..+..++ .+..++..+..+++.+|||||||.
T Consensus        93 ~~d~~~ig~sp~~~~~~~-ri~r~l~~~~PVLL~GppGtGKTt  134 (383)
T PHA02244         93 GIDTTKIASNPTFHYETA-DIAKIVNANIPVFLKGGAGSGKNH  134 (383)
T ss_pred             hCCCcccCCCHHHHHHHH-HHHHHHhcCCCEEEECCCCCCHHH
Confidence            4566664  444444544 667899999999999999999995

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=95.44  E-value=0.015  Score=52.96  Aligned_cols=42  Identities=31%  Similarity=0.351  Sum_probs=33.5

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHH-hcC-CceeeeCCCCCCchHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTL-DNS-KFGIFESPTGTGKSLS   65 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L-~~g-k~~I~ESPTGTGKTLS   65 (194)
                      .++|||.-.-+|.+.+..+.-++ ..| .+++|++|.|||||..
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            36788887788999999877544 455 7899999999999943

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=95.43  E-value=0.021  Score=51.81  Aligned_cols=40  Identities=20%  Similarity=0.085  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         36 SNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        36 ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..+...+..|+..++.++|-+|||||||- +|-+.+.++-.
T Consensus       147 ~~~~~~L~~~v~~~~nili~G~tgSGKTT-ll~aL~~~ip~  186 (332)
T PRK13900        147 KKIKEFLEHAVISKKNIIISGGTSTGKTT-FTNAALREIPA  186 (332)
T ss_pred             HHHHHHHHHHHHcCCcEEEECCCCCCHHH-HHHHHHhhCCC
Confidence            35566777788889999999999999995 44555555544

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.39  E-value=0.025  Score=51.14  Aligned_cols=34  Identities=18%  Similarity=0.284  Sum_probs=26.0

Q ss_pred             HHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        40 ~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..+..++..++.++|-+|||+||| +++-..+.++
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            345556778899999999999999 6666655554

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

Probab=95.38  E-value=0.021  Score=55.09  Aligned_cols=47  Identities=19%  Similarity=0.220  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHHHHhc-CCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhH
Q psy14272         32 YDIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYYDHKIVGL   82 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~-gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~   82 (194)
                      .+.|...+..+   +.. .+.++|-+|||||||-+ |.++|.++.....++.
T Consensus       243 ~~~~~~~~~~~---~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~~~nI~  290 (500)
T COG2804         243 SPFQLARLLRL---LNRPQGLILVTGPTGSGKTTT-LYAALSELNTPERNII  290 (500)
T ss_pred             CHHHHHHHHHH---HhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCCCceEE
Confidence            45565544443   333 37889999999999977 7778999988877654

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=95.37  E-value=0.024  Score=56.25  Aligned_cols=47  Identities=21%  Similarity=0.318  Sum_probs=37.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +|+.|...++.+...-..+..++++||||.|||.+.+.+++.-+...
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~  242 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK  242 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc
Confidence            58888887777655444444999999999999999999988877763

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

Probab=95.37  E-value=0.031  Score=57.66  Aligned_cols=29  Identities=17%  Similarity=0.033  Sum_probs=24.4

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .+-|+++||||||++||..++.....++-
T Consensus        61 n~~~~M~TGtGKT~~~~~~i~~l~~~~~~   89 (986)
T PRK15483         61 NIDIKMETGTGKTYVYTRLMYELHQKYGL   89 (986)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHHcCC
Confidence            68899999999999999998777666543

>KOG0326|consensus

Probab=95.28  E-value=0.0016  Score=60.48  Aligned_cols=51  Identities=20%  Similarity=0.152  Sum_probs=42.5

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .-.|+ |-|+|.+-+....    .|+.++.-|-.|||||-||++|+|.-+...+..
T Consensus       102 e~G~ekPSPiQeesIPiaL----tGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~~  153 (459)
T KOG0326|consen  102 EKGFEKPSPIQEESIPIAL----TGRDILARAKNGTGKTAAYCIPVLEKIDPKKNV  153 (459)
T ss_pred             HhccCCCCCccccccceee----cchhhhhhccCCCCCccceechhhhhcCccccc
Confidence            34677 8999999776653    689999999999999999999999988766554

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

Probab=95.26  E-value=0.024  Score=57.59  Aligned_cols=47  Identities=17%  Similarity=0.142  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .||+.|...++.|.+++.+| .-+++-+.||||||.+.+.-+-..++.
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTAiaii~rL~r~  212 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTAIAIIDRLIKS  212 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeHHHHHHHHHhc
Confidence            39999999999999999987 349999999999999877654443333

>KOG0347|consensus

Probab=95.21  E-value=0.0056  Score=60.11  Aligned_cols=43  Identities=23%  Similarity=0.273  Sum_probs=34.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ..|. |.+||.-.+..+   +.....++--|-|||||||+|-+|++.
T Consensus       199 ~gFs~Pt~IQsl~lp~a---i~gk~DIlGaAeTGSGKTLAFGIPiv~  242 (731)
T KOG0347|consen  199 LGFSRPTEIQSLVLPAA---IRGKVDILGAAETGSGKTLAFGIPIVE  242 (731)
T ss_pred             cCCCCCccchhhcccHh---hccchhcccccccCCCceeeecchhhh
Confidence            4576 999999866665   333367888999999999999999988

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=95.12  E-value=0.035  Score=49.51  Aligned_cols=38  Identities=21%  Similarity=0.081  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +...+..++..++.++|-+|||+|||- ++-+.+..+..
T Consensus       121 ~~~~L~~~v~~~~~ilI~G~tGSGKTT-ll~al~~~i~~  158 (299)
T TIGR02782       121 QRDVLREAVLARKNILVVGGTGSGKTT-LANALLAEIAK  158 (299)
T ss_pred             HHHHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHHhhc
Confidence            344566677888999999999999994 34555555543

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.

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.04  E-value=0.038  Score=50.27  Aligned_cols=34  Identities=18%  Similarity=0.220  Sum_probs=25.6

Q ss_pred             HHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        40 ~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..|..++..++.+||-+|||||||- +|-+.+..+
T Consensus       135 ~~L~~~v~~~~nilI~G~tGSGKTT-ll~aL~~~i  168 (323)
T PRK13833        135 SVIRSAIDSRLNIVISGGTGSGKTT-LANAVIAEI  168 (323)
T ss_pred             HHHHHHHHcCCeEEEECCCCCCHHH-HHHHHHHHH
Confidence            4566778888999999999999994 345555554

>PRK06526 transposase; Provisional

Probab=95.01  E-value=0.051  Score=47.46  Aligned_cols=37  Identities=19%  Similarity=0.108  Sum_probs=25.0

Q ss_pred             HHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        44 ~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      +++..+..++|-+|+|||||... +++..++...+..+
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa-~al~~~a~~~g~~v  129 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLA-IGLGIRACQAGHRV  129 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHH-HHHHHHHHHCCCch
Confidence            45677889999999999999643 33334444444443

>KOG0952|consensus

Probab=94.97  E-value=0.025  Score=58.77  Aligned_cols=49  Identities=27%  Similarity=0.322  Sum_probs=39.3

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      -.|+|. .-.+|-.....+|   ..+.+.|+.||||+|||..+++.+|.-+..
T Consensus       104 ~~f~f~~fN~iQS~vFp~aY---~SneNMLIcAPTGsGKT~la~L~ILr~ik~  153 (1230)
T KOG0952|consen  104 GFFSFEEFNRIQSEVFPVAY---KSNENMLICAPTGSGKTVLAELCILRTIKE  153 (1230)
T ss_pred             hcccHHHHHHHHHHhhhhhh---cCCCCEEEECCCCCCchHHHHHHHHHHHHh
Confidence            357776 4478888666655   667889999999999999999888888775

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

Probab=94.89  E-value=0.035  Score=45.77  Aligned_cols=37  Identities=24%  Similarity=0.281  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHH--HHHhcCCceeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLY--YTLDNSKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~--~~L~~gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      .++...+..+.  .+++++..++|-+|+|||||.-..+-
T Consensus        29 ~~~~~~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai   67 (178)
T PF01695_consen   29 GIDKAQIAQLAALEFIENGENLILYGPPGTGKTHLAVAI   67 (178)
T ss_dssp             -----HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHH
T ss_pred             hHHHHHHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHH
Confidence            44444454443  44567788999999999999754433

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.

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.88  E-value=0.03  Score=51.22  Aligned_cols=38  Identities=16%  Similarity=0.133  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ++...+..|+..++.++|-+|||||||- ++-+++.++.
T Consensus       150 ~~~~~l~~~v~~~~nilI~G~tGSGKTT-ll~aLl~~i~  187 (344)
T PRK13851        150 DLEAFLHACVVGRLTMLLCGPTGSGKTT-MSKTLISAIP  187 (344)
T ss_pred             HHHHHHHHHHHcCCeEEEECCCCccHHH-HHHHHHcccC
Confidence            3556677778889999999999999994 3444444443

>KOG0328|consensus

Probab=94.83  E-value=0.0052  Score=56.44  Aligned_cols=51  Identities=18%  Similarity=0.286  Sum_probs=42.6

Q ss_pred             cCCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         25 FPFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        25 ~~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      +.+.|+ |-.||...+..|.    .|..+|..|..|||||.+|-|++|.-+.-..+
T Consensus        43 Y~yGfekPS~IQqrAi~~Il----kGrdViaQaqSGTGKTa~~si~vlq~~d~~~r   94 (400)
T KOG0328|consen   43 YAYGFEKPSAIQQRAIPQIL----KGRDVIAQAQSGTGKTATFSISVLQSLDISVR   94 (400)
T ss_pred             HHhccCCchHHHhhhhhhhh----cccceEEEecCCCCceEEEEeeeeeecccccc
Confidence            357888 9999999777764    78999999999999999999998886654443

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=94.80  E-value=0.036  Score=56.11  Aligned_cols=45  Identities=22%  Similarity=0.265  Sum_probs=33.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+.+.||++|.-=  .|  +|..|.  |.|..||.||||...+|++.....
T Consensus        76 ~~g~~~~dvQlig--~l--~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~  120 (796)
T PRK12906         76 VLGLRPFDVQIIG--GI--VLHEGN--IAEMKTGEGKTLTATLPVYLNALT  120 (796)
T ss_pred             HhCCCCchhHHHH--HH--HHhcCC--cccccCCCCCcHHHHHHHHHHHHc
Confidence            4667799998753  33  355665  899999999999998886654443

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.77  E-value=0.04  Score=47.76  Aligned_cols=34  Identities=21%  Similarity=0.386  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      +|......+..++..+.  +++|.+|+|||||....
T Consensus        19 g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~   54 (337)
T PRK12402         19 GQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVR   54 (337)
T ss_pred             CCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHH
Confidence            56677778888888876  89999999999996543

>PRK09183 transposase/IS protein; Provisional

Probab=94.75  E-value=0.056  Score=47.08  Aligned_cols=40  Identities=20%  Similarity=0.371  Sum_probs=25.4

Q ss_pred             cCCCCCCC--HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         25 FPFPFDAY--DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        25 ~~fPy~py--~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      |.|.|.|.  ..|..-+..+ .++..+.+++|-+|+|||||.-
T Consensus        77 fd~~~~~~~~~~~i~~L~~~-~~i~~~~~v~l~Gp~GtGKThL  118 (259)
T PRK09183         77 YDFTFATGAPQKQLQSLRSL-SFIERNENIVLLGPSGVGKTHL  118 (259)
T ss_pred             cccccCCCCCHHHHHHHhcC-CchhcCCeEEEEeCCCCCHHHH
Confidence            44555443  3333322222 2378889999999999999953

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

Probab=94.71  E-value=0.058  Score=44.79  Aligned_cols=44  Identities=16%  Similarity=0.301  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         33 DIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +.|.+++..+   +.++ .+.++.+|.|||||.+ |..+...+...+.+
T Consensus         4 ~~Q~~a~~~~---l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~g~~   48 (196)
T PF13604_consen    4 EEQREAVRAI---LTSGDRVSVLQGPAGTGKTTL-LKALAEALEAAGKR   48 (196)
T ss_dssp             HHHHHHHHHH---HHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHTT--
T ss_pred             HHHHHHHHHH---HhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhCCCe
Confidence            6799977776   3444 6899999999999975 45555555554443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=94.65  E-value=0.03  Score=39.91  Aligned_cols=21  Identities=19%  Similarity=0.251  Sum_probs=16.5

Q ss_pred             CCceeeeCCCCCCchHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      +.+++|-+|+|||||..+..-
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l   22 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARAL   22 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHH
Confidence            467899999999999754433

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.

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

Probab=94.56  E-value=0.029  Score=49.81  Aligned_cols=43  Identities=19%  Similarity=0.227  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+-++.+.+..+..++..|+++++++|+|+|||.  |.-.++...
T Consensus        25 ~~~g~~~~~~~~l~a~~~~~~vll~G~PG~gKT~--la~~lA~~l   67 (329)
T COG0714          25 VVVGDEEVIELALLALLAGGHVLLEGPPGVGKTL--LARALARAL   67 (329)
T ss_pred             eeeccHHHHHHHHHHHHcCCCEEEECCCCccHHH--HHHHHHHHh
Confidence            3445889999999999999999999999999996  444444333

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=94.44  E-value=0.02  Score=61.18  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=20.1

Q ss_pred             eeCCCCCCchHHHHHHHHHHHhh
Q psy14272         54 FESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        54 ~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.||||||||++|++|+|..+..
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~   23 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFR   23 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHh
Confidence            46899999999999999987754

>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=94.42  E-value=0.048  Score=45.88  Aligned_cols=39  Identities=21%  Similarity=0.332  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|..++..      ..+.+++.|+.|||||.+++.-++..+...
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            567765544      367899999999999998877755545443

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 ....

>KOG0353|consensus

Probab=94.35  E-value=0.03  Score=53.47  Aligned_cols=38  Identities=24%  Similarity=0.154  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .||.|+..++.+    ..|+.+++-.|||-||||+|-+|+|.
T Consensus        95 frplq~~ain~~----ma~ed~~lil~tgggkslcyqlpal~  132 (695)
T KOG0353|consen   95 FRPLQLAAINAT----MAGEDAFLILPTGGGKSLCYQLPALC  132 (695)
T ss_pred             cChhHHHHhhhh----hccCceEEEEeCCCccchhhhhhHHh
Confidence            678888766554    57888999999999999999888775

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

Probab=94.10  E-value=0.06  Score=49.71  Aligned_cols=54  Identities=17%  Similarity=0.247  Sum_probs=37.0

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhc-CCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~-gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      .|.+ |.-.|+.+=..+.+.++. .+.+++-+|||||||-+ |.+++.|+..+....
T Consensus       101 Ip~~i~~~e~LglP~i~~~~~~~~~GLILVTGpTGSGKSTT-lAamId~iN~~~~~H  156 (353)
T COG2805         101 IPSKIPTLEELGLPPIVRELAESPRGLILVTGPTGSGKSTT-LAAMIDYINKHKAKH  156 (353)
T ss_pred             cCccCCCHHHcCCCHHHHHHHhCCCceEEEeCCCCCcHHHH-HHHHHHHHhccCCcc
Confidence            5655 555566554455554443 36788999999999976 677788988776553

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

Probab=93.91  E-value=0.078  Score=46.36  Aligned_cols=35  Identities=20%  Similarity=0.286  Sum_probs=24.2

Q ss_pred             HHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         42 LYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        42 I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +..++. .++.++|-+|||+|||-. |.+++.++...
T Consensus        72 l~~~~~~~~GlilisG~tGSGKTT~-l~all~~i~~~  107 (264)
T cd01129          72 FRKLLEKPHGIILVTGPTGSGKTTT-LYSALSELNTP  107 (264)
T ss_pred             HHHHHhcCCCEEEEECCCCCcHHHH-HHHHHhhhCCC
Confidence            344454 346899999999999954 45566666543

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=93.88  E-value=0.047  Score=52.66  Aligned_cols=34  Identities=18%  Similarity=0.108  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      -+|.+.++.+..++..+.+++|++|+|||||+..
T Consensus        23 ~gre~vI~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         23 YERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             cCcHHHHHHHHHHHccCCCEEEECCCChhHHHHH
Confidence            4677888889999999999999999999999743

>PRK08939 primosomal protein DnaI; Reviewed

Probab=93.82  E-value=0.14  Score=45.95  Aligned_cols=44  Identities=16%  Similarity=0.033  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHh------cCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         34 IQSNFMKNLYYTLD------NSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        34 iQ~e~M~~I~~~L~------~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .+..++..+...+.      .++.++|-||+|||||.- ++++...+...+
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThL-a~Aia~~l~~~g  184 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYL-LAAIANELAKKG  184 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHH-HHHHHHHHHHcC
Confidence            56666666666665      345788999999999963 333334444333

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

Probab=93.81  E-value=0.077  Score=43.31  Aligned_cols=30  Identities=23%  Similarity=0.377  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +.|.+   .+..++..+..++|-+|||+|||-.
T Consensus        12 ~~~~~---~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130          12 PLQAA---YLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             HHHHH---HHHHHHhCCCEEEEECCCCCCHHHH
Confidence            44555   4445678899999999999999953

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.

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

Probab=93.62  E-value=0.17  Score=44.19  Aligned_cols=30  Identities=20%  Similarity=0.257  Sum_probs=22.8

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHHHH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L   67 (194)
                      -...+..++.+++.++|-+|+|||||.-+.
T Consensus        94 ~~~~~~~~~~~~~nl~l~G~~G~GKThLa~  123 (254)
T COG1484          94 DLASLVEFFERGENLVLLGPPGVGKTHLAI  123 (254)
T ss_pred             HHHHHHHHhccCCcEEEECCCCCcHHHHHH
Confidence            333445677788999999999999997433

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

Probab=93.61  E-value=0.077  Score=41.48  Aligned_cols=35  Identities=11%  Similarity=0.216  Sum_probs=17.6

Q ss_pred             CCHHHHHHHHHHHHHH--hcCCceeeeCCCCCCchHH
Q psy14272         31 AYDIQSNFMKNLYYTL--DNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L--~~gk~~I~ESPTGTGKTLS   65 (194)
                      =|..|.+.+..+..+.  ..+.++++.||.|+|||.-
T Consensus         4 gR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~l   40 (185)
T PF13191_consen    4 GREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSL   40 (185)
T ss_dssp             T-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHH
Confidence            3556666444443322  2347899999999999953

>TIGR00376 DNA helicase, putative

Probab=93.57  E-value=0.14  Score=50.36  Aligned_cols=42  Identities=21%  Similarity=0.328  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .-+.|..   +|..++....+.++.+|+|||||-.+..-+..++.
T Consensus       158 ln~~Q~~---Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~  199 (637)
T TIGR00376       158 LNESQKE---AVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVK  199 (637)
T ss_pred             CCHHHHH---HHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            4578888   55556776688999999999999765554444443

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.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=93.56  E-value=0.086  Score=48.36  Aligned_cols=33  Identities=18%  Similarity=0.290  Sum_probs=23.8

Q ss_pred             HHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         42 LYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        42 I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.+.+. .++.++|-+|||||||-. |.+++.++.
T Consensus       126 ~~~~~~~~~glilI~GpTGSGKTTt-L~aLl~~i~  159 (358)
T TIGR02524       126 IIDAIAPQEGIVFITGATGSGKSTL-LAAIIRELA  159 (358)
T ss_pred             HHHHHhccCCEEEEECCCCCCHHHH-HHHHHHHHh
Confidence            344443 678999999999999965 455566664

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.

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=93.55  E-value=0.1  Score=52.65  Aligned_cols=45  Identities=20%  Similarity=0.264  Sum_probs=35.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+.+.||++|.-=|-.+.    .|  -|.|..||.||||...+|++..+..
T Consensus        74 ~lg~r~ydvQlig~l~Ll----~G--~VaEM~TGEGKTLvA~l~a~l~AL~  118 (764)
T PRK12326         74 TLGLRPFDVQLLGALRLL----AG--DVIEMATGEGKTLAGAIAAAGYALQ  118 (764)
T ss_pred             HcCCCcchHHHHHHHHHh----CC--CcccccCCCCHHHHHHHHHHHHHHc
Confidence            466789999998776653    55  4779999999999999987765543

>KOG1803|consensus

Probab=93.52  E-value=0.096  Score=51.81  Aligned_cols=53  Identities=23%  Similarity=0.252  Sum_probs=37.2

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .-+||..--+.|.+   ++.-++......++.+|.|||||.++.--+.+.+. .+++
T Consensus       179 ~~~~~~~ln~SQk~---Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk-~~k~  231 (649)
T KOG1803|consen  179 ITFFNKNLNSSQKA---AVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVK-QKKR  231 (649)
T ss_pred             cccCCccccHHHHH---HHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHH-cCCe
Confidence            34677777788988   44445566688999999999999986655444444 3344

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=93.40  E-value=0.079  Score=54.38  Aligned_cols=43  Identities=26%  Similarity=0.280  Sum_probs=30.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ....||++|+-  -.|  +|.+|  -|.|+.||.||||+..+|++..+.
T Consensus        79 lGm~~ydVQli--Gg~--~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al  121 (913)
T PRK13103         79 MGMRHFDVQLI--GGM--TLHEG--KIAEMRTGEGKTLVGTLAVYLNAL  121 (913)
T ss_pred             hCCCcchhHHH--hhh--HhccC--ccccccCCCCChHHHHHHHHHHHH
Confidence            35668898874  333  24455  578999999999999988765433

>PLN03025 replication factor C subunit; Provisional

Probab=93.28  E-value=0.11  Score=45.99  Aligned_cols=35  Identities=23%  Similarity=0.321  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~   68 (194)
                      +|.+.+..|...+..+  .+++|.||.|||||-...+
T Consensus        17 g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~   53 (319)
T PLN03025         17 GNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILA   53 (319)
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHH
Confidence            5667777777777765  5689999999999955443

>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=93.25  E-value=0.13  Score=46.27  Aligned_cols=38  Identities=21%  Similarity=0.280  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|.-++.+++.++.+|+.+|||||||- +|.+++..+-.
T Consensus       132 ~~ayL~~~ie~~~siii~G~t~sGKTt-~lnall~~Ip~  169 (312)
T COG0630         132 QAAYLWLAIEARKSIIICGGTASGKTT-LLNALLDFIPP  169 (312)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHH-HHHHHHHhCCc
Confidence            344588899999999999999999994 45555555443

>KOG0989|consensus

Probab=93.13  E-value=0.13  Score=47.50  Aligned_cols=41  Identities=22%  Similarity=0.192  Sum_probs=33.0

Q ss_pred             CHHHHHHHHHHHHHHhc--CCceeeeCCCCCCchHHHHHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      --+|....+.+..++..  .-+.+|-+|.|||||-+.++.+-+
T Consensus        38 ~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~   80 (346)
T KOG0989|consen   38 LAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARA   80 (346)
T ss_pred             hcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHH
Confidence            35788888888888876  368999999999999887766433

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=93.03  E-value=0.16  Score=53.92  Aligned_cols=31  Identities=16%  Similarity=0.244  Sum_probs=24.7

Q ss_pred             HHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        41 ~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .|..+|.++.++|+.|+||||||.  .+|.+.+
T Consensus        81 ~Il~ai~~~~VviI~GeTGSGKTT--qlPq~ll  111 (1294)
T PRK11131         81 DILEAIRDHQVVIVAGETGSGKTT--QLPKICL  111 (1294)
T ss_pred             HHHHHHHhCCeEEEECCCCCCHHH--HHHHHHH
Confidence            566667888999999999999998  4674443

>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=92.94  E-value=0.15  Score=44.95  Aligned_cols=35  Identities=23%  Similarity=0.215  Sum_probs=25.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      |...-..+.--+--.+.++..+++-||||||||..
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            66554555445555678899999999999999974

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=92.90  E-value=0.17  Score=46.20  Aligned_cols=40  Identities=28%  Similarity=0.284  Sum_probs=33.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhc--CCceeeeCCCCCCchHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS~   66 (194)
                      |||.---+|..+..++.-++-+  ...+++.+|+|+|||..+
T Consensus         1 ~pf~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~   42 (337)
T TIGR02030         1 FPFTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAV   42 (337)
T ss_pred             CCccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHH
Confidence            7898778999999998777655  467899999999999643

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.

>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=92.90  E-value=0.084  Score=46.25  Aligned_cols=55  Identities=15%  Similarity=0.138  Sum_probs=44.5

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      |...+-.|+.|.++...+.+. ..|+..|.+.-.|-||| |.|+|++.++.+.+.++
T Consensus        18 ~e~~iliR~~Q~~ia~~mi~~-~~~~n~v~QlnMGeGKT-sVI~Pmla~~LAdg~~L   72 (229)
T PF12340_consen   18 IESNILIRPVQVEIAREMISP-PSGKNSVMQLNMGEGKT-SVIVPMLALALADGSRL   72 (229)
T ss_pred             HHcCceeeHHHHHHHHHHhCC-CCCCCeEeeecccCCcc-chHHHHHHHHHcCCCcE
Confidence            334455999999999888753 46788999999999999 46899999988887663

There are two conserved sequence motifs: LLE and NMG.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=92.90  E-value=0.11  Score=49.50  Aligned_cols=38  Identities=18%  Similarity=0.260  Sum_probs=25.0

Q ss_pred             HHHHHHhc-CCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         41 NLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        41 ~I~~~L~~-gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .+..++.. ++.++|-+|||||||-++ .++|..+.....
T Consensus       233 ~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l~~~~~  271 (486)
T TIGR02533       233 RFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRLNTPER  271 (486)
T ss_pred             HHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhccCCCCC
Confidence            33344443 457899999999999764 555776654433

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PRK10436 hypothetical protein; Provisional

Probab=92.86  E-value=0.13  Score=48.83  Aligned_cols=33  Identities=24%  Similarity=0.339  Sum_probs=25.5

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      .++.++|-+|||||||-++ .++|.++.....++
T Consensus       217 ~~GliLvtGpTGSGKTTtL-~a~l~~~~~~~~~i  249 (462)
T PRK10436        217 PQGLILVTGPTGSGKTVTL-YSALQTLNTAQINI  249 (462)
T ss_pred             cCCeEEEECCCCCChHHHH-HHHHHhhCCCCCEE
Confidence            4678999999999999764 66788876555444

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

Probab=92.83  E-value=0.18  Score=46.41  Aligned_cols=40  Identities=20%  Similarity=0.197  Sum_probs=27.8

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC---CceeeeCCCCCCchHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g---k~~I~ESPTGTGKTLS~L~   68 (194)
                      +.-|..|.+-+..++..+-.|   .++++-+|||||||.+.-.
T Consensus        19 l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~   61 (366)
T COG1474          19 LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKF   61 (366)
T ss_pred             ccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHH
Confidence            447888887555554444333   4589999999999987543

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=92.79  E-value=0.18  Score=53.63  Aligned_cols=32  Identities=16%  Similarity=0.233  Sum_probs=26.0

Q ss_pred             HHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         40 KNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        40 ~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      ..|..+|.++.++|+.||||+|||-  .+|.+.+
T Consensus        73 ~~Il~~l~~~~vvii~g~TGSGKTT--qlPq~ll  104 (1283)
T TIGR01967        73 EDIAEAIAENQVVIIAGETGSGKTT--QLPKICL  104 (1283)
T ss_pred             HHHHHHHHhCceEEEeCCCCCCcHH--HHHHHHH
Confidence            5677778889999999999999997  4575544

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.

>COG4889 Predicted helicase [General function prediction only]

Probab=92.75  E-value=0.11  Score=54.11  Aligned_cols=45  Identities=16%  Similarity=0.167  Sum_probs=36.5

Q ss_pred             CccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHH
Q psy14272         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        23 ~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L   67 (194)
                      ....-|++|||.|.+.+++..+.+..+.-+=+-+..|||||++.|
T Consensus       154 l~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL  198 (1518)
T COG4889         154 LPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSL  198 (1518)
T ss_pred             cccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHH
Confidence            334558899999999999999888776666667789999998754

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=92.68  E-value=0.14  Score=47.47  Aligned_cols=42  Identities=24%  Similarity=0.324  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         34 IQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        34 iQ~e~M~~I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|.-+...+.+.+. .++.+++-+|||||||-. |.+++.++..
T Consensus       133 ~~lgl~~~~~~~l~~~~GlilI~G~TGSGKTT~-l~al~~~i~~  175 (372)
T TIGR02525       133 KQMGIEPDLFNSLLPAAGLGLICGETGSGKSTL-AASIYQHCGE  175 (372)
T ss_pred             HHcCCCHHHHHHHHhcCCEEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            34444444444443 456789999999999965 4556677653

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).

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=92.60  E-value=0.17  Score=43.41  Aligned_cols=36  Identities=22%  Similarity=0.344  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~   68 (194)
                      -+|.+.+..+..++..+  .+++|.||+|||||...-+
T Consensus        20 ~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~   57 (319)
T PRK00440         20 VGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALA   57 (319)
T ss_pred             cCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHH
Confidence            36778888898888876  3589999999999976533

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=92.55  E-value=0.096  Score=48.23  Aligned_cols=43  Identities=26%  Similarity=0.231  Sum_probs=35.5

Q ss_pred             CccCCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         23 SEFPFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        23 ~~~~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      ....|||.---+|.++..++..++.+.  ..++|.+|+|||||..
T Consensus        10 ~~~~~pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~   54 (350)
T CHL00081         10 ERPVFPFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTT   54 (350)
T ss_pred             cCCCCCHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHH
Confidence            356899997789999999999888663  3478999999999953

>PRK08116 hypothetical protein; Validated

Probab=92.54  E-value=0.3  Score=42.76  Aligned_cols=46  Identities=13%  Similarity=-0.034  Sum_probs=27.1

Q ss_pred             CCHHHHHHHHHHHHHHhc-------CCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~-------gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.+.+...+..+...+.+       +..++|-||+|||||.- ++++...+...
T Consensus        89 ~~~~~~~a~~~a~~y~~~~~~~~~~~~gl~l~G~~GtGKThL-a~aia~~l~~~  141 (268)
T PRK08116         89 FDKGSEKAYKIARKYVKKFEEMKKENVGLLLWGSVGTGKTYL-AACIANELIEK  141 (268)
T ss_pred             CChHHHHHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHH-HHHHHHHHHHc
Confidence            446666555554433331       23488999999999963 33344455443

>KOG0339|consensus

Probab=92.49  E-value=0.043  Score=53.81  Aligned_cols=48  Identities=19%  Similarity=0.227  Sum_probs=37.8

Q ss_pred             CC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         29 FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        29 y~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      |. |||||-+.+...    -.|..+|--|-||+|||-+|+.|.+..+.+.+.-
T Consensus       243 y~kptpiq~qalpta----lsgrdvigIAktgSgktaAfi~pm~~himdq~eL  291 (731)
T KOG0339|consen  243 YEKPTPIQCQALPTA----LSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPEL  291 (731)
T ss_pred             cccCCcccccccccc----cccccchheeeccCcchhHHHHHHHHHhcchhhh
Confidence            44 788887755543    3577888899999999999999999988876543

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=92.49  E-value=0.2  Score=40.95  Aligned_cols=33  Identities=18%  Similarity=0.212  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHhc--CCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS   65 (194)
                      +.+...+..+..++..  +..++|.||+|||||..
T Consensus        20 ~~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~l   54 (226)
T TIGR03420        20 GGNAELLAALRQLAAGKGDRFLYLWGESGSGKSHL   54 (226)
T ss_pred             CCcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHH
Confidence            3567777787776543  46799999999999954

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=92.44  E-value=0.37  Score=42.07  Aligned_cols=44  Identities=20%  Similarity=0.144  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHHhc---C-CceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         33 DIQSNFMKNLYYTLDN---S-KFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~---g-k~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|...+..+...+.+   + ..++|-+|+|||||.- ++++..++...
T Consensus        79 ~~q~~al~~a~~~~~~~~~~~~~~~l~G~~GtGKThL-a~aia~~l~~~  126 (244)
T PRK07952         79 EGQMNALSKARQYVEEFDGNIASFIFSGKPGTGKNHL-AAAICNELLLR  126 (244)
T ss_pred             chHHHHHHHHHHHHHhhccCCceEEEECCCCCCHHHH-HHHHHHHHHhc
Confidence            4676666666555542   2 4689999999999964 44445555443

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

Probab=92.23  E-value=0.14  Score=50.52  Aligned_cols=43  Identities=23%  Similarity=0.387  Sum_probs=37.8

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~   66 (194)
                      ..+-||.|-.-|-+.+..|.+.|.+| +.-++-+.||||||++.
T Consensus         6 ~l~s~f~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~   49 (663)
T COG0556           6 KLHSPFKPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTM   49 (663)
T ss_pred             EeccCCCCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHH
Confidence            45678999999999999999999987 67888999999999873

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

Probab=92.22  E-value=0.15  Score=49.58  Aligned_cols=46  Identities=20%  Similarity=0.062  Sum_probs=36.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      ++||..|..+...   +|..  +.++-.|||-|||+..+.-+..+++.++.
T Consensus        14 ie~R~YQ~~i~a~---al~~--NtLvvlPTGLGKT~IA~~V~~~~l~~~~~   59 (542)
T COG1111          14 IEPRLYQLNIAAK---ALFK--NTLVVLPTGLGKTFIAAMVIANRLRWFGG   59 (542)
T ss_pred             ccHHHHHHHHHHH---Hhhc--CeEEEecCCccHHHHHHHHHHHHHHhcCC
Confidence            5699999986554   4553  68888899999999888887888888777

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=92.22  E-value=0.18  Score=48.80  Aligned_cols=44  Identities=18%  Similarity=0.311  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         33 DIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +.|.+.   +..++. ..+.++|-+|||||||-+ |.+++.++.....+
T Consensus       302 ~~~~~~---l~~~~~~~~Glilv~G~tGSGKTTt-l~a~l~~~~~~~~~  346 (564)
T TIGR02538       302 PDQKAL---FLEAIHKPQGMVLVTGPTGSGKTVS-LYTALNILNTEEVN  346 (564)
T ss_pred             HHHHHH---HHHHHHhcCCeEEEECCCCCCHHHH-HHHHHHhhCCCCce
Confidence            444443   333344 457889999999999976 46778877543333

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.

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

Probab=92.19  E-value=0.12  Score=52.79  Aligned_cols=27  Identities=19%  Similarity=0.374  Sum_probs=22.8

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      ...|.+++.+..++||.+|||+|||-.
T Consensus        55 ~~~i~~ai~~~~vvii~getGsGKTTq   81 (845)
T COG1643          55 RDEILKAIEQNQVVIIVGETGSGKTTQ   81 (845)
T ss_pred             HHHHHHHHHhCCEEEEeCCCCCChHHH
Confidence            346667778999999999999999964

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

Probab=92.17  E-value=0.21  Score=40.27  Aligned_cols=31  Identities=29%  Similarity=0.294  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHhcC---Ccee--eeCCCCCCchHH
Q psy14272         35 QSNFMKNLYYTLDNS---KFGI--FESPTGTGKSLS   65 (194)
Q Consensus        35 Q~e~M~~I~~~L~~g---k~~I--~ESPTGTGKTLS   65 (194)
                      +..++++|...+.+.   |.+|  |-+|||||||+.
T Consensus        34 ~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v   69 (127)
T PF06309_consen   34 VEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFV   69 (127)
T ss_pred             HHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHH
Confidence            334556666666543   4444  899999999964

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

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.11  E-value=0.19  Score=46.08  Aligned_cols=41  Identities=20%  Similarity=0.266  Sum_probs=32.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      |.-.-+|...+..+..++.+|.+   .||.+|.|+|||....+-
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~   58 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVF   58 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHH
Confidence            44344799999999999998743   789999999999665443

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

Probab=91.99  E-value=0.083  Score=39.29  Aligned_cols=18  Identities=22%  Similarity=0.534  Sum_probs=12.0

Q ss_pred             cCCceeeeCCCCCCchHH
Q psy14272         48 NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS   65 (194)
                      +++.+++.||+|+|||..
T Consensus         3 ~~~~~~i~G~~G~GKT~~   20 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTL   20 (131)
T ss_dssp             ----EEEEE-TTSSHHHH
T ss_pred             CCcccEEEcCCCCCHHHH
Confidence            467899999999999965

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

Probab=91.92  E-value=0.28  Score=41.19  Aligned_cols=36  Identities=22%  Similarity=0.299  Sum_probs=26.9

Q ss_pred             CCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~   66 (194)
                      +-+.+...+..+...+..+ ..+++-+|+|+|||..+
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            3456667777777777665 47899999999999643

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.

>PRK12377 putative replication protein; Provisional

Probab=91.81  E-value=0.55  Score=41.09  Aligned_cols=46  Identities=17%  Similarity=0.052  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHH---hc-CCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         33 DIQSNFMKNLYYTL---DN-SKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L---~~-gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      +.|...+..+...+   .. ...++|-+|+|||||.- ++++...+...+.
T Consensus        81 ~~~~~a~~~a~~~a~~~~~~~~~l~l~G~~GtGKThL-a~AIa~~l~~~g~  130 (248)
T PRK12377         81 DGQRYALSQAKSIADELMTGCTNFVFSGKPGTGKNHL-AAAIGNRLLAKGR  130 (248)
T ss_pred             hhHHHHHHHHHHHHHHHHhcCCeEEEECCCCCCHHHH-HHHHHHHHHHcCC
Confidence            56765555444333   22 35789999999999963 3333445544433

>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=91.78  E-value=0.27  Score=43.69  Aligned_cols=44  Identities=23%  Similarity=0.194  Sum_probs=29.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+.+.||++|.--.-.    |..|.  |.|..||=||||+..+|++....
T Consensus        73 ~~g~~p~~vQll~~l~----L~~G~--laEm~TGEGKTli~~l~a~~~AL  116 (266)
T PF07517_consen   73 TLGLRPYDVQLLGALA----LHKGR--LAEMKTGEGKTLIAALPAALNAL  116 (266)
T ss_dssp             HTS----HHHHHHHHH----HHTTS--EEEESTTSHHHHHHHHHHHHHHT
T ss_pred             HcCCcccHHHHhhhhh----cccce--eEEecCCCCcHHHHHHHHHHHHH
Confidence            4678899999874433    34554  89999999999998888665444

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 ....

>KOG0341|consensus

Probab=91.69  E-value=0.026  Score=53.93  Aligned_cols=47  Identities=17%  Similarity=0.204  Sum_probs=37.8

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .|.|||.+=+..|    -.|...|--|-|||||||.|.+|++-+.......
T Consensus       192 ~PTpIQvQGlPvv----LsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~  238 (610)
T KOG0341|consen  192 HPTPIQVQGLPVV----LSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMM  238 (610)
T ss_pred             CCCceeecCcceE----eecCceeeEEeecCCceEEEeHHHHHHHHHHHhc
Confidence            3888998866665    3688889999999999999999988877655433

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

Probab=91.67  E-value=0.13  Score=40.41  Aligned_cols=27  Identities=22%  Similarity=0.463  Sum_probs=20.2

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .++.||-||+|+|||-  |+-+|.|+...
T Consensus        19 ~g~~vi~G~Ng~GKSt--il~ai~~~L~~   45 (202)
T PF13476_consen   19 PGLNVIYGPNGSGKST--ILEAIRYALGG   45 (202)
T ss_dssp             SEEEEEEESTTSSHHH--HHHHHHHHHHS
T ss_pred             CCcEEEECCCCCCHHH--HHHHHHHHHcC
Confidence            3588999999999995  44556776643

>TIGR00595 priA primosomal protein N'

Probab=91.61  E-value=0.12  Score=49.40  Aligned_cols=23  Identities=26%  Similarity=0.264  Sum_probs=17.4

Q ss_pred             eeeCCCCCCchHHHHHHHHHHHh
Q psy14272         53 IFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        53 I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ++.+|||+|||..|+-.+...+.
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~   23 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLA   23 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHH
Confidence            46799999999999876444443

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).

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

Probab=91.51  E-value=0.23  Score=47.61  Aligned_cols=29  Identities=24%  Similarity=0.379  Sum_probs=23.6

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      ....+..+|..++++||.+|+|||||...
T Consensus       183 ~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        183 TIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             HHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            34566777888999999999999999543

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

Probab=91.38  E-value=0.07  Score=49.15  Aligned_cols=22  Identities=32%  Similarity=0.475  Sum_probs=19.9

Q ss_pred             CceeeeCCCCCCchHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al   71 (194)
                      .++++-||||+|||.++++|.|
T Consensus        45 ~h~lvig~tgSGKt~~~viP~l   66 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNL   66 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHH
Confidence            4799999999999999999965

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

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=91.34  E-value=0.24  Score=45.07  Aligned_cols=37  Identities=16%  Similarity=0.148  Sum_probs=25.2

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ...+..++..++.++|-+|||+|||-. |...+..+..
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            344455567789999999999999853 3444444443

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=91.33  E-value=0.2  Score=45.24  Aligned_cols=29  Identities=24%  Similarity=0.481  Sum_probs=21.3

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..++.++|-+|||+|||-.+ ..++.++..
T Consensus       120 ~~~g~ili~G~tGSGKTT~l-~al~~~i~~  148 (343)
T TIGR01420       120 RPRGLILVTGPTGSGKSTTL-ASMIDYINK  148 (343)
T ss_pred             hcCcEEEEECCCCCCHHHHH-HHHHHhhCc
Confidence            34688999999999999654 444555543

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.26  E-value=0.19  Score=46.74  Aligned_cols=30  Identities=17%  Similarity=0.155  Sum_probs=21.3

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..+.+++|-+|||+|||..+.--+..+...
T Consensus       135 ~~g~ii~lvGptGvGKTTtiakLA~~~~~~  164 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTAKLAARCVMR  164 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            457899999999999997654443333333

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=91.22  E-value=0.29  Score=47.14  Aligned_cols=37  Identities=27%  Similarity=0.205  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      -+|..++..+..++..++   ..||.||.|||||....+-
T Consensus        24 iGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~Aril   63 (507)
T PRK06645         24 QGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARII   63 (507)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHH
Confidence            489999999999888875   5899999999999665444

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.20  E-value=0.29  Score=44.35  Aligned_cols=36  Identities=14%  Similarity=0.113  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~   68 (194)
                      -+|......+..++..++  + .+|.||.|+|||....+
T Consensus        19 iGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~   57 (363)
T PRK14961         19 IGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARL   57 (363)
T ss_pred             cChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHH
Confidence            389999999999998874  3 58999999999965433

>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=91.18  E-value=0.21  Score=43.14  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      -+|...-+++.-+...+.++++.+|.|||||+.
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            357777788887888889999999999999964

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.

>KOG0947|consensus

Probab=90.92  E-value=0.34  Score=50.54  Aligned_cols=56  Identities=16%  Similarity=0.251  Sum_probs=42.4

Q ss_pred             CCCCccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         20 EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        20 ~~~~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ++..-+.|||++-.-|++   +|| +|+.|..+++-|+|.+|||+..=.+ +.....|..+
T Consensus       287 Vpe~a~~~pFelD~FQk~---Ai~-~lerg~SVFVAAHTSAGKTvVAEYA-ialaq~h~TR  342 (1248)
T KOG0947|consen  287 VPEMALIYPFELDTFQKE---AIY-HLERGDSVFVAAHTSAGKTVVAEYA-IALAQKHMTR  342 (1248)
T ss_pred             chhHHhhCCCCccHHHHH---HHH-HHHcCCeEEEEecCCCCcchHHHHH-HHHHHhhccc
Confidence            344457899999999998   443 6789999999999999999876555 4444555444

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=90.76  E-value=0.61  Score=46.20  Aligned_cols=37  Identities=19%  Similarity=0.190  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      ++-...|.+.+..|..++..+.+++|.+|+|||||..
T Consensus        30 ~~~vigq~~a~~~L~~~~~~~~~~l~~G~~G~GKttl   66 (637)
T PRK13765         30 IDQVIGQEHAVEVIKKAAKQRRHVMMIGSPGTGKSML   66 (637)
T ss_pred             HHHcCChHHHHHHHHHHHHhCCeEEEECCCCCcHHHH
Confidence            4455689999999999999999999999999999954

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=90.73  E-value=0.19  Score=41.71  Aligned_cols=36  Identities=11%  Similarity=-0.027  Sum_probs=25.4

Q ss_pred             HHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      -|..|...++-||+|+|||.-.+--++.++..++..
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~   44 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKP   44 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCc
Confidence            455678999999999999965554455566553433

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.

>PF12846 AAA_10: AAA-like domain

Probab=90.63  E-value=0.27  Score=41.03  Aligned_cols=28  Identities=21%  Similarity=0.171  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .++++-++||+|||..+.+- +..+...+
T Consensus         2 ~h~~i~G~tGsGKT~~~~~l-~~~~~~~g   29 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLKNL-LEQLIRRG   29 (304)
T ss_pred             CeEEEECCCCCcHHHHHHHH-HHHHHHcC
Confidence            57899999999999877744 44444333

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.57  E-value=0.33  Score=46.18  Aligned_cols=36  Identities=28%  Similarity=0.304  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLI   67 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L   67 (194)
                      .-+|...+..+..++.++.+   .||.||.|||||....
T Consensus        16 ivGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         16 VVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVAR   54 (472)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHH
Confidence            34678888888899988854   6999999999995443

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=90.46  E-value=0.56  Score=41.27  Aligned_cols=26  Identities=23%  Similarity=0.367  Sum_probs=18.0

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.+++|-+|||+|||-+.. -...|+.
T Consensus       194 ~~vi~~vGptGvGKTTt~~-kLa~~~~  219 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLA-KLAARFV  219 (282)
T ss_pred             CeEEEEECCCCCCHHHHHH-HHHHHHH
Confidence            4578899999999996543 3334443

>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=90.36  E-value=0.29  Score=38.68  Aligned_cols=25  Identities=16%  Similarity=0.089  Sum_probs=17.4

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.++.+|+|||||.-.+--+...+.
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~   25 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLA   25 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            3688999999999754444444443

A related protein is found in archaea.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=90.21  E-value=0.33  Score=43.07  Aligned_cols=35  Identities=20%  Similarity=0.198  Sum_probs=24.8

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ...+.-++..+..++|-+|||+|||-. |...+.++
T Consensus       134 ~~~l~~~v~~~~~ili~G~tGsGKTTl-l~al~~~~  168 (308)
T TIGR02788       134 KEFLRLAIASRKNIIISGGTGSGKTTF-LKSLVDEI  168 (308)
T ss_pred             HHHHHHHhhCCCEEEEECCCCCCHHHH-HHHHHccC
Confidence            344556678899999999999999953 33334444

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.

>PRK13764 ATPase; Provisional

Probab=90.20  E-value=0.31  Score=48.06  Aligned_cols=33  Identities=18%  Similarity=0.332  Sum_probs=24.1

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ..++.+++-+|||||||- ++.+++.++...+..
T Consensus       255 ~~~~~ILIsG~TGSGKTT-ll~AL~~~i~~~~ri  287 (602)
T PRK13764        255 ERAEGILIAGAPGAGKST-FAQALAEFYADMGKI  287 (602)
T ss_pred             hcCCEEEEECCCCCCHHH-HHHHHHHHHhhCCCE
Confidence            446779999999999995 456666777654433

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

Probab=90.13  E-value=0.067  Score=48.33  Aligned_cols=22  Identities=23%  Similarity=0.323  Sum_probs=18.6

Q ss_pred             ceeeeCCCCCCchHHHHHHHHH
Q psy14272         51 FGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ++++-||||+|||.++++|.+-
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll   22 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLL   22 (384)
T ss_pred             CeeEecCCCCCCccEEEccchh
Confidence            4688999999999999888543

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.

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.10  E-value=0.32  Score=47.83  Aligned_cols=37  Identities=27%  Similarity=0.252  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      -+|......|..++..+++   .||.||.|+|||....+-
T Consensus        19 iGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~l   58 (620)
T PRK14948         19 VGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARIL   58 (620)
T ss_pred             cChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHH
Confidence            4788888899999988754   599999999999765443

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

Probab=90.10  E-value=0.5  Score=49.50  Aligned_cols=45  Identities=24%  Similarity=0.246  Sum_probs=34.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|.|+..|.--.+.|.    .|+..-+-||||+|||---++.++ |+..
T Consensus        79 ~G~~~ws~QR~WakR~~----rg~SFaiiAPTGvGKTTfg~~~sl-~~a~  123 (1187)
T COG1110          79 TGFRPWSAQRVWAKRLV----RGKSFAIIAPTGVGKTTFGLLMSL-YLAK  123 (1187)
T ss_pred             hCCCchHHHHHHHHHHH----cCCceEEEcCCCCchhHHHHHHHH-HHHh
Confidence            56789999999888874    688888889999999965444444 4443

>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=90.03  E-value=0.24  Score=41.50  Aligned_cols=19  Identities=32%  Similarity=0.455  Sum_probs=15.2

Q ss_pred             CceeeeCCCCCCchHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~   68 (194)
                      ++++|-+|||+|||-++.=
T Consensus         2 ~vi~lvGptGvGKTTt~aK   20 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAK   20 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHH
T ss_pred             EEEEEECCCCCchHhHHHH
Confidence            4688999999999976443

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 ....

>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=89.87  E-value=0.35  Score=39.51  Aligned_cols=29  Identities=24%  Similarity=0.243  Sum_probs=20.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ...++++-++||+|||..+-+-++..+..
T Consensus        37 ~~~h~li~G~tgsGKS~~l~~ll~~l~~~   65 (205)
T PF01580_consen   37 KNPHLLIAGATGSGKSTLLRTLLLSLALT   65 (205)
T ss_dssp             GS-SEEEE--TTSSHHHHHHHHHHHHHTT
T ss_pred             CCceEEEEcCCCCCccHHHHHHHHHHHHH
Confidence            44589999999999999877665555553

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.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=89.86  E-value=0.27  Score=43.47  Aligned_cols=41  Identities=15%  Similarity=0.101  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         36 SNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        36 ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ..+++.|......+.++.|-+|+|+|||- ++.....++...
T Consensus        21 ~~~~~~~~~~~~~~~~i~i~G~~G~GKtt-l~~~l~~~~~~~   61 (300)
T TIGR00750        21 KQLLDRIMPYTGNAHRVGITGTPGAGKST-LLEALGMELRRR   61 (300)
T ss_pred             HHHHHhCCcccCCceEEEEECCCCCCHHH-HHHHHHHHHHHC
Confidence            34666666655667888889999999994 334434444443

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.

>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=89.79  E-value=0.18  Score=38.42  Aligned_cols=23  Identities=26%  Similarity=0.329  Sum_probs=16.3

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+|+.+|+|+|||.  |+-.+.++.
T Consensus         1 ~vlL~G~~G~GKt~--l~~~la~~~   23 (139)
T PF07728_consen    1 PVLLVGPPGTGKTT--LARELAALL   23 (139)
T ss_dssp             EEEEEESSSSSHHH--HHHHHHHHH
T ss_pred             CEEEECCCCCCHHH--HHHHHHHHh
Confidence            37899999999995  344444444

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.65  E-value=0.44  Score=45.94  Aligned_cols=37  Identities=27%  Similarity=0.192  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      -+|...+..|..++..+++   .||.||.|||||-...+-
T Consensus        21 VGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriL   60 (484)
T PRK14956         21 IHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARIL   60 (484)
T ss_pred             hChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            4789999999999998865   599999999999654443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=89.59  E-value=0.7  Score=41.97  Aligned_cols=39  Identities=18%  Similarity=0.106  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      .||-|....+.+..++.+|+   -.+|.+|.|+||+....+-
T Consensus         5 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~l   46 (319)
T PRK08769          5 FSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALAL   46 (319)
T ss_pred             ccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHH
Confidence            78999999999999999885   3789999999998755544

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

Probab=89.57  E-value=0.57  Score=42.53  Aligned_cols=47  Identities=17%  Similarity=0.275  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHh--cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         33 DIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~--~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +.|...++.|.+++.  .+..+.+.+|-|||||+.+=+ +..+++..+..
T Consensus         4 ~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~~-i~~~~~~~~~~   52 (364)
T PF05970_consen    4 EEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIKA-IIDYLRSRGKK   52 (364)
T ss_pred             HHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHHH-HHHHhccccce
Confidence            579999999988884  457788999999999975433 34566554443

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

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.52  E-value=0.38  Score=46.59  Aligned_cols=38  Identities=18%  Similarity=0.266  Sum_probs=30.4

Q ss_pred             CHHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      .-+|...+..|..++.++++   .||.||.|+|||....+-
T Consensus        18 iiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~l   58 (585)
T PRK14950         18 LVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARIL   58 (585)
T ss_pred             hcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHH
Confidence            34788889999999988754   499999999999765444

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

Probab=89.45  E-value=0.47  Score=45.35  Aligned_cols=32  Identities=28%  Similarity=0.274  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHhc----------------CCceeeeCCCCCCchH
Q psy14272         33 DIQSNFMKNLYYTLDN----------------SKFGIFESPTGTGKSL   64 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~----------------gk~~I~ESPTGTGKTL   64 (194)
                      -+|.+..+.|..++.+                .++++|.+|||+|||.
T Consensus        18 iGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~   65 (443)
T PRK05201         18 IGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTE   65 (443)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHH
Confidence            5677777777777744                3689999999999993

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

Probab=89.39  E-value=0.5  Score=44.73  Aligned_cols=26  Identities=23%  Similarity=0.335  Sum_probs=19.6

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      +++++|-+|||.|||-++-=-|..|.
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~  228 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYV  228 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHH
Confidence            78999999999999876543333444

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=89.33  E-value=0.59  Score=40.34  Aligned_cols=33  Identities=18%  Similarity=0.239  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHhc-----C--CceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDN-----S--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~-----g--k~~I~ESPTGTGKTLS~   66 (194)
                      +|......|..++..     +  .+++|.+|.|||||...
T Consensus         8 G~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635         8 GQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            455555566555541     2  46899999999999543

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.

>TIGR03263 guanyl_kin guanylate kinase

Probab=89.32  E-value=0.2  Score=39.71  Aligned_cols=16  Identities=31%  Similarity=0.561  Sum_probs=14.3

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      |++++|.+|+|+|||-
T Consensus         1 g~ii~l~G~~GsGKsT   16 (180)
T TIGR03263         1 GLLIVISGPSGVGKST   16 (180)
T ss_pred             CcEEEEECCCCCCHHH
Confidence            5789999999999985

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.

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

Probab=89.31  E-value=0.33  Score=38.71  Aligned_cols=29  Identities=14%  Similarity=0.204  Sum_probs=23.1

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ..|..++|-||+|+|||...+--++.++.
T Consensus        30 ~~g~l~~i~g~~g~GKT~~~~~l~~~~~~   58 (193)
T PF13481_consen   30 PRGELTLIAGPPGSGKTTLALQLAAALAT   58 (193)
T ss_dssp             -TTSEEEEEECSTSSHHHHHHHHHHHHHT
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            35789999999999999877666666664

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=89.20  E-value=0.6  Score=41.18  Aligned_cols=36  Identities=31%  Similarity=0.187  Sum_probs=22.7

Q ss_pred             CCHHHHHHH-HHHHHHHhcC--CceeeeCCCCCCchHHH
Q psy14272         31 AYDIQSNFM-KNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        31 py~iQ~e~M-~~I~~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      -|..|.+-+ ..|..++..+  ..++|-||+|||||...
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            456666433 3333334332  57999999999999653

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.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=89.18  E-value=0.73  Score=44.16  Aligned_cols=33  Identities=24%  Similarity=0.188  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      .+...+..+...++++.++|+-+|+|||||--+
T Consensus       194 ~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla  226 (449)
T TIGR02688       194 QKLLLLARLLPLVEPNYNLIELGPKGTGKSYIY  226 (449)
T ss_pred             HHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHH
Confidence            444445555567889999999999999999433

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.

>KOG0991|consensus

Probab=89.15  E-value=2  Score=39.15  Aligned_cols=44  Identities=23%  Similarity=0.268  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         37 NFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        37 e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +-|..+.-...+|  .++||-+|.|||||-|.+|-+=..|-+.-+.
T Consensus        34 ~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke   79 (333)
T KOG0991|consen   34 DTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYKE   79 (333)
T ss_pred             HHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhhh
Confidence            3444444344455  6799999999999999999887766544333

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=89.12  E-value=0.45  Score=42.52  Aligned_cols=38  Identities=24%  Similarity=0.187  Sum_probs=24.4

Q ss_pred             CCHHHH-HHHHHHHHHHhcC--CceeeeCCCCCCchHHHHH
Q psy14272         31 AYDIQS-NFMKNLYYTLDNS--KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        31 py~iQ~-e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~   68 (194)
                      -|..+. ++...+..++..+  ..++|-||+|||||..+-.
T Consensus        34 ~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~   74 (394)
T PRK00411         34 HREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKK   74 (394)
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHH
Confidence            345453 3444444555432  5689999999999986443

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=89.11  E-value=0.32  Score=45.57  Aligned_cols=25  Identities=24%  Similarity=0.332  Sum_probs=18.4

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      +++++|-+|||+|||-+.+.-+..+
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~  245 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARY  245 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            5688899999999997655443333

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=89.11  E-value=0.53  Score=44.97  Aligned_cols=40  Identities=33%  Similarity=0.252  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHhcC----------------CceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNS----------------KFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g----------------k~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      -+|.+..+.+.-++.++                +.+++.+|||+|||.  |+-+|+-.
T Consensus        15 iGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~--lAraLA~~   70 (441)
T TIGR00390        15 IGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTE--IARRLAKL   70 (441)
T ss_pred             cCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHH--HHHHHHHH
Confidence            46777777776666542                689999999999995  45544433

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.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=89.10  E-value=0.46  Score=33.66  Aligned_cols=29  Identities=17%  Similarity=0.314  Sum_probs=22.4

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      |.+.+|-+|+|+|||-  |+-|+.|+.-...
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            4589999999999994  6667777765544

>KOG0349|consensus

Probab=89.08  E-value=0.073  Score=51.60  Aligned_cols=45  Identities=18%  Similarity=0.268  Sum_probs=37.6

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+. |.++|.+.+..|    -.|..++.-|.||||||=+|.+|+|+....
T Consensus        21 dw~lptdvqaeaipli----lgggdvlmaaetgsgktgaf~lpilqiv~e   66 (725)
T KOG0349|consen   21 DWTLPTDVQAEAIPLI----LGGGDVLMAAETGSGKTGAFCLPILQIVWE   66 (725)
T ss_pred             ccccccccccccccEE----ecCCcEEEEeccCCCCccceehhhHHHHHH
Confidence            344 889999988876    367889999999999999999999886553

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=89.07  E-value=0.6  Score=38.74  Aligned_cols=28  Identities=18%  Similarity=0.252  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHh---cCCceeeeCCCCCCchH
Q psy14272         37 NFMKNLYYTLD---NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        37 e~M~~I~~~L~---~gk~~I~ESPTGTGKTL   64 (194)
                      .++..+..+..   .+..++|-+|+|||||-
T Consensus        27 ~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~   57 (227)
T PRK08903         27 ELVARLRELAAGPVADRFFYLWGEAGSGRSH   57 (227)
T ss_pred             HHHHHHHHHHhccCCCCeEEEECCCCCCHHH
Confidence            34555555544   34679999999999994

>PRK06921 hypothetical protein; Provisional

Probab=88.85  E-value=1.3  Score=38.78  Aligned_cols=28  Identities=14%  Similarity=0.074  Sum_probs=19.3

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+..++|-+|||+|||.-+ +++...+..
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~  143 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMR  143 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhh
Confidence            3567999999999999643 333444443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.76  E-value=0.53  Score=45.19  Aligned_cols=37  Identities=24%  Similarity=0.354  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHHHhcCCce---eeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFG---IFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~---I~ESPTGTGKTLS~L~~   69 (194)
                      -+|......|..++..+++.   +|.+|.|||||....+-
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            46888888888888887543   99999999999765443

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.73  E-value=0.52  Score=46.51  Aligned_cols=37  Identities=19%  Similarity=0.225  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      -+|......+..++.+|++   .||.||.|+|||....+-
T Consensus        19 vGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~l   58 (620)
T PRK14954         19 TAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVF   58 (620)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHH
Confidence            3789999999999988743   789999999999655443

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

Probab=88.64  E-value=0.57  Score=38.34  Aligned_cols=28  Identities=21%  Similarity=0.224  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      ++++.+..+......+++.+++||||++
T Consensus        10 ~~~~~~~~~a~~~~pVlI~GE~GtGK~~   37 (168)
T PF00158_consen   10 RLREQAKRAASSDLPVLITGETGTGKEL   37 (168)
T ss_dssp             HHHHHHHHHTTSTS-EEEECSTTSSHHH
T ss_pred             HHHHHHHHHhCCCCCEEEEcCCCCcHHH
Confidence            4445555555566889999999999995

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 ....

>TIGR03238 dnd_assoc_3 dnd system-associated protein 3

Probab=88.60  E-value=0.28  Score=47.51  Aligned_cols=36  Identities=25%  Similarity=0.313  Sum_probs=29.6

Q ss_pred             CCCCHHHHHHHHHHHH---HHhcCCceeeeCCCCCCchH
Q psy14272         29 FDAYDIQSNFMKNLYY---TLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~---~L~~gk~~I~ESPTGTGKTL   64 (194)
                      |--++||.+|+..|..   .+..|.++.+.||.|+|||-
T Consensus         9 hi~r~Ie~~l~~vL~~Vsl~i~~GEiv~L~G~SGsGKST   47 (504)
T TIGR03238         9 YVKRKIQTDLERILVKFNKELPSSSLLFLCGSSGDGKSE   47 (504)
T ss_pred             eechHHHHHHHHHHhCCceeecCCCEEEEECCCCCCHHH
Confidence            3468999999888765   24678999999999999994

cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=88.57  E-value=0.49  Score=48.58  Aligned_cols=41  Identities=27%  Similarity=0.309  Sum_probs=29.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ...+.||++|.-=  .|  +|..|  -|.|+.||-||||+..+|++.
T Consensus        72 ~lG~r~ydvQlig--~l--~L~~G--~IaEm~TGEGKTL~a~l~ayl  112 (870)
T CHL00122         72 TLGLRHFDVQLIG--GL--VLNDG--KIAEMKTGEGKTLVATLPAYL  112 (870)
T ss_pred             HhCCCCCchHhhh--hH--hhcCC--ccccccCCCCchHHHHHHHHH
Confidence            3566788988653  22  23344  788999999999999988743

>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=88.56  E-value=0.39  Score=39.47  Aligned_cols=15  Identities=27%  Similarity=0.472  Sum_probs=13.0

Q ss_pred             CceeeeCCCCCCchH
Q psy14272         50 KFGIFESPTGTGKSL   64 (194)
Q Consensus        50 k~~I~ESPTGTGKTL   64 (194)
                      .+++|-+|||+|||.
T Consensus         4 ~~~ll~GpsGvGKT~   18 (171)
T PF07724_consen    4 SNFLLAGPSGVGKTE   18 (171)
T ss_dssp             EEEEEESSTTSSHHH
T ss_pred             EEEEEECCCCCCHHH
Confidence            468899999999994

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 ....

>KOG0922|consensus

Probab=88.45  E-value=0.41  Score=47.74  Aligned_cols=29  Identities=24%  Similarity=0.509  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      ++.+.|..++++.+++|+-+.||+|||--
T Consensus        54 ~~r~~il~~ve~nqvlIviGeTGsGKSTQ   82 (674)
T KOG0922|consen   54 KYRDQILYAVEDNQVLIVIGETGSGKSTQ   82 (674)
T ss_pred             HHHHHHHHHHHHCCEEEEEcCCCCCcccc
Confidence            56788889999999999999999999953

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.35  E-value=0.51  Score=46.23  Aligned_cols=38  Identities=26%  Similarity=0.266  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~~a   70 (194)
                      -+|......|..++..++  + .||.+|.|||||.+..+-+
T Consensus        16 vGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lA   56 (584)
T PRK14952         16 VGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILA   56 (584)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            378888999999998874  3 5899999999997665543

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

Probab=88.28  E-value=0.25  Score=43.95  Aligned_cols=43  Identities=16%  Similarity=0.234  Sum_probs=28.3

Q ss_pred             ccCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      .|.|.  |.+-..|.++...+    ...+-+|.  .++.-++||||||.++
T Consensus        48 ~f~FD~vf~~~~~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKTyTm   98 (319)
T cd01376          48 KYQFDAFYGTECTQEDIFSREVKPIVPHLLSGQNATVFAYGSTGAGKTHTM   98 (319)
T ss_pred             EEecCeEECCCCCHHHHHHHHHHHHHHHHhCCCceEEEEECCCCCCCcEEE
Confidence            45554  55777888877762    22333453  3566799999999976

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

>KOG4284|consensus

Probab=88.21  E-value=0.1  Score=52.53  Aligned_cols=46  Identities=20%  Similarity=0.259  Sum_probs=36.6

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|. |.+||...+..+.    .+-.+|+.|-.||||||.|-+.++.-|..+
T Consensus        44 ~f~~ptkiQaaAIP~~~----~kmDliVQaKSGTGKTlVfsv~av~sl~~~   90 (980)
T KOG4284|consen   44 AFALPTKIQAAAIPAIF----SKMDLIVQAKSGTGKTLVFSVLAVESLDSR   90 (980)
T ss_pred             cccCCCchhhhhhhhhh----cccceEEEecCCCCceEEEEeeeehhcCcc
Confidence            455 8888888777764    566799999999999999988888766543

>PRK08727 hypothetical protein; Validated

Probab=88.14  E-value=1.2  Score=37.88  Aligned_cols=26  Identities=19%  Similarity=0.229  Sum_probs=17.3

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..++|-+|+|||||-- ++++...+..
T Consensus        42 ~~l~l~G~~G~GKThL-~~a~~~~~~~   67 (233)
T PRK08727         42 DWLYLSGPAGTGKTHL-ALALCAAAEQ   67 (233)
T ss_pred             CeEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            4589999999999952 3343333333

>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=88.11  E-value=0.45  Score=34.96  Aligned_cols=14  Identities=36%  Similarity=0.615  Sum_probs=12.0

Q ss_pred             eeeeCCCCCCchHH
Q psy14272         52 GIFESPTGTGKSLS   65 (194)
Q Consensus        52 ~I~ESPTGTGKTLS   65 (194)
                      +++.+|.|||||..
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            57899999999963

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 ....

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=88.04  E-value=1.1  Score=41.21  Aligned_cols=28  Identities=21%  Similarity=0.204  Sum_probs=23.0

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      ....|..+|..++.+++++|+|||||..
T Consensus        53 ~~~~vl~~l~~~~~ilL~G~pGtGKTtl   80 (327)
T TIGR01650        53 TTKAICAGFAYDRRVMVQGYHGTGKSTH   80 (327)
T ss_pred             HHHHHHHHHhcCCcEEEEeCCCChHHHH
Confidence            3446777788889999999999999963

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.

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

Probab=87.98  E-value=0.43  Score=44.73  Aligned_cols=16  Identities=38%  Similarity=0.551  Sum_probs=13.9

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      .+++|.+|||||||+.
T Consensus       109 ~~iLl~Gp~GtGKT~l  124 (412)
T PRK05342        109 SNILLIGPTGSGKTLL  124 (412)
T ss_pred             ceEEEEcCCCCCHHHH
Confidence            5699999999999953

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=87.96  E-value=0.38  Score=48.61  Aligned_cols=34  Identities=24%  Similarity=0.197  Sum_probs=27.2

Q ss_pred             CHHHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTLS   65 (194)
                      .-+|-..|..|..+|...           .+.+|.+|||||||..
T Consensus       567 v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~l  611 (852)
T TIGR03346       567 VVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTEL  611 (852)
T ss_pred             cCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHH
Confidence            357888999999888642           3578999999999954

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.

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

Probab=87.92  E-value=0.42  Score=40.59  Aligned_cols=33  Identities=24%  Similarity=0.184  Sum_probs=23.0

Q ss_pred             HHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        44 ~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..+..|.+++|-||||+|||.-.+--+..++..
T Consensus        25 gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~   57 (271)
T cd01122          25 KGLRKGELIILTAGTGVGKTTFLREYALDLITQ   57 (271)
T ss_pred             EEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh
Confidence            345567899999999999996444334444444

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

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

Probab=87.87  E-value=0.32  Score=45.26  Aligned_cols=40  Identities=15%  Similarity=0.124  Sum_probs=26.3

Q ss_pred             HHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhhH
Q psy14272         41 NLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIVGL   82 (194)
Q Consensus        41 ~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~   82 (194)
                      .|..++.....+++-+.||||||- +|-+.+.+..... +++
T Consensus       165 ~L~~av~~r~NILisGGTGSGKTT-lLNal~~~i~~~e-RvI  204 (355)
T COG4962         165 FLRRAVGIRCNILISGGTGSGKTT-LLNALSGFIDSDE-RVI  204 (355)
T ss_pred             HHHHHHhhceeEEEeCCCCCCHHH-HHHHHHhcCCCcc-cEE
Confidence            445555666889999999999994 3444444444444 544

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

Probab=87.85  E-value=0.27  Score=46.01  Aligned_cols=25  Identities=28%  Similarity=0.397  Sum_probs=18.4

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ..++++-+||||||||  |.-.|+-+.
T Consensus        97 KSNILLiGPTGsGKTl--LAqTLAk~L  121 (408)
T COG1219          97 KSNILLIGPTGSGKTL--LAQTLAKIL  121 (408)
T ss_pred             eccEEEECCCCCcHHH--HHHHHHHHh
Confidence            3578999999999995  555555444

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=87.83  E-value=0.56  Score=35.13  Aligned_cols=19  Identities=26%  Similarity=0.314  Sum_probs=14.4

Q ss_pred             ceeeeCCCCCCchHHHHHH
Q psy14272         51 FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~   69 (194)
                      +++|-+|+|+|||.-+..-
T Consensus         1 ~~~i~G~~G~GKT~l~~~i   19 (165)
T cd01120           1 LILVFGPTGSGKTTLALQL   19 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHH
Confidence            4678999999999754333

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=87.71  E-value=0.46  Score=39.35  Aligned_cols=26  Identities=27%  Similarity=0.571  Sum_probs=18.9

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.++|-+|||+|||-.+ ..++.++..
T Consensus         2 GlilI~GptGSGKTTll-~~ll~~~~~   27 (198)
T cd01131           2 GLVLVTGPTGSGKSTTL-AAMIDYINK   27 (198)
T ss_pred             cEEEEECCCCCCHHHHH-HHHHHHhhh
Confidence            46889999999999764 444555553

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=87.70  E-value=0.48  Score=43.62  Aligned_cols=35  Identities=23%  Similarity=0.223  Sum_probs=26.7

Q ss_pred             CHHHHHHHHH---HHHHHhcC--CceeeeCCCCCCchHHH
Q psy14272         32 YDIQSNFMKN---LYYTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        32 y~iQ~e~M~~---I~~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      +-+|..++..   +..++.++  ..+||-+|+|||||...
T Consensus        14 ~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA   53 (413)
T PRK13342         14 VVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLA   53 (413)
T ss_pred             hcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHH
Confidence            4567777655   88888776  36899999999999543

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

Probab=87.69  E-value=0.75  Score=46.06  Aligned_cols=54  Identities=17%  Similarity=0.285  Sum_probs=46.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      ..||++...|...++.|..-|.+.  ..=++.+--|||||+..+++++.-..+..+
T Consensus       258 ~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G~Q  313 (677)
T COG1200         258 ALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQ  313 (677)
T ss_pred             hCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcCCe
Confidence            589999999999999999888876  456899999999999999998887665433

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=87.65  E-value=0.64  Score=41.19  Aligned_cols=37  Identities=19%  Similarity=0.230  Sum_probs=25.9

Q ss_pred             CCHHHHHHHHHHHHHHhc----C---CceeeeCCCCCCchHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDN----S---KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~----g---k~~I~ESPTGTGKTLS~L   67 (194)
                      -+-+|.+.+..+...+..    +   .+++|.+|+|||||....
T Consensus        26 ~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~   69 (328)
T PRK00080         26 EFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLAN   69 (328)
T ss_pred             HhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHH
Confidence            344677777666655542    2   479999999999996543

>PHA00729 NTP-binding motif containing protein

Probab=87.62  E-value=0.69  Score=40.37  Aligned_cols=25  Identities=20%  Similarity=0.340  Sum_probs=17.7

Q ss_pred             HHHHHHHhcC--CceeeeCCCCCCchH
Q psy14272         40 KNLYYTLDNS--KFGIFESPTGTGKSL   64 (194)
Q Consensus        40 ~~I~~~L~~g--k~~I~ESPTGTGKTL   64 (194)
                      ..+...|..+  ..++|-+|+|||||.
T Consensus         6 k~~~~~l~~~~f~nIlItG~pGvGKT~   32 (226)
T PHA00729          6 KKIVSAYNNNGFVSAVIFGKQGSGKTT   32 (226)
T ss_pred             HHHHHHHhcCCeEEEEEECCCCCCHHH
Confidence            3444555444  468899999999994

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=87.56  E-value=0.65  Score=48.03  Aligned_cols=44  Identities=23%  Similarity=0.219  Sum_probs=31.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .....||++|.-  -.|  +|..|  -|.|+.||-||||+..+|++..+.
T Consensus        81 ~lG~r~ydVQli--Ggl--~Lh~G--~IAEM~TGEGKTL~atlpaylnAL  124 (939)
T PRK12902         81 VLGMRHFDVQLI--GGM--VLHEG--QIAEMKTGEGKTLVATLPSYLNAL  124 (939)
T ss_pred             HhCCCcchhHHH--hhh--hhcCC--ceeeecCCCChhHHHHHHHHHHhh
Confidence            356678888864  333  23455  578999999999999988765443

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=87.54  E-value=0.58  Score=45.86  Aligned_cols=39  Identities=26%  Similarity=0.272  Sum_probs=32.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      |||..--+|..++..+.-++-+.  ..++|.+|+|||||..
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            78887778999888888777653  4599999999999864

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.

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

Probab=87.49  E-value=0.83  Score=35.30  Aligned_cols=27  Identities=30%  Similarity=0.324  Sum_probs=19.5

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      +...|.........+++.++.||||++
T Consensus        10 l~~~l~~~a~~~~pvli~GE~GtGK~~   36 (138)
T PF14532_consen   10 LRRQLERLAKSSSPVLITGEPGTGKSL   36 (138)
T ss_dssp             HHHHHHHHHCSSS-EEEECCTTSSHHH
T ss_pred             HHHHHHHHhCCCCcEEEEcCCCCCHHH
Confidence            344444445567889999999999996

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=87.46  E-value=0.78  Score=45.45  Aligned_cols=42  Identities=24%  Similarity=0.364  Sum_probs=36.1

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHH
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~   66 (194)
                      ..-||.|.-.|-..+..+.+.+.+| +..++-+.||||||+..
T Consensus         4 ~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~   46 (655)
T TIGR00631         4 LHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTM   46 (655)
T ss_pred             eccCCCCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHH
Confidence            4568999999999999999999876 35678999999999864

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

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=87.39  E-value=0.5  Score=37.50  Aligned_cols=28  Identities=21%  Similarity=0.309  Sum_probs=23.8

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      ++.+.|...|..|.++++.++-|+|||-
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            5667888889999999999999999993

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.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.37  E-value=0.65  Score=44.60  Aligned_cols=37  Identities=22%  Similarity=0.196  Sum_probs=29.8

Q ss_pred             CHHHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~   68 (194)
                      .-+|...+..+..++..++  + .+|.||.|+|||-...+
T Consensus        18 ivGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~   57 (509)
T PRK14958         18 VIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRI   57 (509)
T ss_pred             hcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHH
Confidence            3489999999999998873  3 58999999999965433

>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=87.34  E-value=0.57  Score=41.34  Aligned_cols=39  Identities=26%  Similarity=0.383  Sum_probs=26.0

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHh---c-C---CceeeeCCCCCCch
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLD---N-S---KFGIFESPTGTGKS   63 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~---~-g---k~~I~ESPTGTGKT   63 (194)
                      .+--|+-|-+|..+...+.-.+.   . +   .++||-+|.|+|||
T Consensus        19 RP~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKT   64 (233)
T PF05496_consen   19 RPKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKT   64 (233)
T ss_dssp             S-SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHH
T ss_pred             CCCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchh
Confidence            34457788899998887544333   2 2   47999999999997

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.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.29  E-value=0.76  Score=44.77  Aligned_cols=40  Identities=23%  Similarity=0.262  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~   68 (194)
                      |.-.-+|......+..++..+++   .||.||.|+|||....+
T Consensus        15 f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~   57 (546)
T PRK14957         15 FAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRL   57 (546)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHH
Confidence            33334888888889999988754   68999999999964433

>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=87.24  E-value=0.28  Score=36.19  Aligned_cols=14  Identities=43%  Similarity=0.660  Sum_probs=12.1

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      +++|.+|+|||||-
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            47889999999993

...

>PRK00300 gmk guanylate kinase; Provisional

Probab=87.22  E-value=0.3  Score=39.64  Aligned_cols=17  Identities=29%  Similarity=0.565  Sum_probs=15.2

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|.+++|.+|+|+|||-
T Consensus         4 ~g~~i~i~G~sGsGKst   20 (205)
T PRK00300          4 RGLLIVLSGPSGAGKST   20 (205)
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57899999999999993

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

Probab=87.18  E-value=0.98  Score=38.62  Aligned_cols=39  Identities=21%  Similarity=0.261  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHhc--CCc-eeeeCCCCCCchHHHHHHHHH
Q psy14272         34 IQSNFMKNLYYTLDN--SKF-GIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~--gk~-~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|.............  ..+ .+|.+|.|+|||.+.++-+=.
T Consensus         6 ~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~   47 (325)
T COG0470           6 WQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKE   47 (325)
T ss_pred             chhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHH
Confidence            333333333333433  356 999999999999887776533

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=87.13  E-value=0.48  Score=41.73  Aligned_cols=17  Identities=29%  Similarity=0.313  Sum_probs=14.2

Q ss_pred             CceeeeCCCCCCchHHH
Q psy14272         50 KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~   66 (194)
                      .+++|.+|+|||||...
T Consensus        59 ~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        59 LHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            36899999999999643

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.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=87.12  E-value=0.59  Score=37.53  Aligned_cols=28  Identities=25%  Similarity=0.353  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      ++...|..+|..+.++++.++-|+|||-
T Consensus        10 ~l~~~l~~~l~~~~~i~l~G~lGaGKTt   37 (133)
T TIGR00150        10 KFGKAFAKPLDFGTVVLLKGDLGAGKTT   37 (133)
T ss_pred             HHHHHHHHhCCCCCEEEEEcCCCCCHHH
Confidence            4566777778888999999999999984

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.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=87.12  E-value=0.85  Score=44.73  Aligned_cols=37  Identities=16%  Similarity=0.134  Sum_probs=32.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +..--+|.+.+..+..++..+.+++|-+|+|||||..
T Consensus        17 ~~~viG~~~a~~~l~~a~~~~~~~ll~G~pG~GKT~l   53 (608)
T TIGR00764        17 IDQVIGQEEAVEIIKKAAKQKRNVLLIGEPGVGKSML   53 (608)
T ss_pred             HhhccCHHHHHHHHHHHHHcCCCEEEECCCCCCHHHH
Confidence            4455689999999999999999999999999999953

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

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=87.06  E-value=0.8  Score=40.16  Aligned_cols=35  Identities=26%  Similarity=0.358  Sum_probs=28.4

Q ss_pred             CHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSL   66 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~   66 (194)
                      .-+|.+.+..+..++.+|+   ..+|.||.|+|||-..
T Consensus        16 iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a   53 (355)
T TIGR02397        16 VIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIA   53 (355)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHH
Confidence            3578888889999998874   4689999999999554

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=87.02  E-value=0.92  Score=38.61  Aligned_cols=31  Identities=23%  Similarity=0.270  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHhc--CCceeeeCCCCCCchH
Q psy14272         34 IQSNFMKNLYYTLDN--SKFGIFESPTGTGKSL   64 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTL   64 (194)
                      .....+..+..+...  +..++|-+|+|+|||-
T Consensus        28 ~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKTh   60 (235)
T PRK08084         28 DNDSLLAALQNALRQEHSGYIYLWSREGAGRSH   60 (235)
T ss_pred             ccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHH
Confidence            445556666665543  3578999999999995

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=87.01  E-value=1.2  Score=39.82  Aligned_cols=44  Identities=14%  Similarity=0.203  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .=.++++.+.++-...  .-.|+-++.|||||.+ |+-++.|+...+
T Consensus         6 ~t~el~~~l~~~~~~~~~~r~vL~G~~GsGKS~~-L~q~~~~A~~~~   51 (309)
T PF10236_consen    6 PTLELINKLKEADKSSKNNRYVLTGERGSGKSVL-LAQAVHYARENG   51 (309)
T ss_pred             HHHHHHHHHHHhcccCCceEEEEECCCCCCHHHH-HHHHHHHHHhCC
Confidence            3345566666653333  4589999999999987 556678887664

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).

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

Probab=86.97  E-value=0.69  Score=43.57  Aligned_cols=21  Identities=33%  Similarity=0.537  Sum_probs=16.2

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .+++|.+|||||||.  |+-+|+
T Consensus       117 ~~iLL~GP~GsGKT~--lAraLA  137 (413)
T TIGR00382       117 SNILLIGPTGSGKTL--LAQTLA  137 (413)
T ss_pred             ceEEEECCCCcCHHH--HHHHHH
Confidence            469999999999996  344444

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.

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

Probab=86.96  E-value=0.52  Score=46.79  Aligned_cols=31  Identities=29%  Similarity=0.385  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchH
Q psy14272         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSL   64 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTL   64 (194)
                      +|.+.+..|..++...           .+.+|.+|||||||.
T Consensus       458 GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~  499 (731)
T TIGR02639       458 GQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTE  499 (731)
T ss_pred             CcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHH
Confidence            4666777777777531           246899999999994

>TIGR02759 TraD_Ftype type IV conjugative transfer system coupling protein TraD

Probab=86.90  E-value=0.47  Score=46.17  Aligned_cols=31  Identities=26%  Similarity=0.461  Sum_probs=23.9

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ..++++-||||||||. +|-..|.|++..+.+
T Consensus       176 ~~h~li~G~tGsGKs~-~i~~ll~~~~~~g~~  206 (566)
T TIGR02759       176 TQHILIHGTTGSGKSV-AIRKLLRWIRQRGDR  206 (566)
T ss_pred             ccceEEEcCCCCCHHH-HHHHHHHHHHhcCCe
Confidence            4689999999999996 456678887655544

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).

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=86.84  E-value=0.76  Score=45.12  Aligned_cols=37  Identities=14%  Similarity=0.134  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      -+|..+++.|..++..|+   ..||.+|.|+|||....+-
T Consensus        27 iGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~l   66 (598)
T PRK09111         27 IGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARIL   66 (598)
T ss_pred             cCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHH
Confidence            379999999999999884   4899999999999765544

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=86.75  E-value=0.65  Score=44.61  Aligned_cols=34  Identities=26%  Similarity=0.229  Sum_probs=27.7

Q ss_pred             CHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      --+|...|..+..++...  .+++|.+|+|||||..
T Consensus        67 iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~l  102 (531)
T TIGR02902        67 IIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAA  102 (531)
T ss_pred             eeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHH
Confidence            457888898988777543  6899999999999864

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.

>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=86.73  E-value=1.1  Score=36.11  Aligned_cols=36  Identities=19%  Similarity=0.298  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      +|.+....+...+.+++   ..||.+|.|+||+...+.-
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~   39 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAF   39 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHH
Confidence            47788888888998873   3699999999987655444

...

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=86.73  E-value=0.25  Score=49.12  Aligned_cols=23  Identities=22%  Similarity=0.431  Sum_probs=20.3

Q ss_pred             CCceeeeCCCCCCchHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      ..++++-||||+|||.++++|.|
T Consensus       139 ~~hvlviApTgSGKgvg~VIPnL  161 (670)
T PRK13850        139 QPHSLVVAPTRAGKGVGVVIPTL  161 (670)
T ss_pred             CceEEEEecCCCCceeeehHhHH
Confidence            36899999999999999999954

>PRK10865 protein disaggregation chaperone; Provisional

Probab=86.46  E-value=0.59  Score=47.50  Aligned_cols=35  Identities=23%  Similarity=0.186  Sum_probs=27.5

Q ss_pred             CHHHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTLS~   66 (194)
                      .-+|...|..|..+|...           .+++|.+|||||||...
T Consensus       570 viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA  615 (857)
T PRK10865        570 VIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELC  615 (857)
T ss_pred             EeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHH
Confidence            358888888888888632           35789999999999754

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=86.41  E-value=0.53  Score=40.41  Aligned_cols=17  Identities=35%  Similarity=0.452  Sum_probs=14.1

Q ss_pred             CceeeeCCCCCCchHHH
Q psy14272         50 KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~   66 (194)
                      .++||.+|+|||||...
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            46899999999999543

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.

>PF05729 NACHT: NACHT domain

Probab=86.27  E-value=0.86  Score=34.56  Aligned_cols=15  Identities=27%  Similarity=0.264  Sum_probs=13.2

Q ss_pred             ceeeeCCCCCCchHH
Q psy14272         51 FGIFESPTGTGKSLS   65 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS   65 (194)
                      ++++.|+.|+|||..
T Consensus         2 ~l~I~G~~G~GKStl   16 (166)
T PF05729_consen    2 VLWISGEPGSGKSTL   16 (166)
T ss_pred             EEEEECCCCCChHHH
Confidence            578999999999974

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=86.27  E-value=0.23  Score=48.89  Aligned_cols=23  Identities=26%  Similarity=0.522  Sum_probs=20.5

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .++++-||||+|||.++++|.|-
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL  181 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLL  181 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHH
Confidence            57899999999999999999654

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=86.15  E-value=0.58  Score=43.19  Aligned_cols=29  Identities=24%  Similarity=0.260  Sum_probs=21.6

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ..++++-+|||+|||.. |-.++.|+...+
T Consensus        42 ~~h~~i~g~tGsGKt~~-i~~l~~~~~~~~   70 (410)
T cd01127          42 EAHTMIIGTTGTGKTTQ-IRELLASIRARG   70 (410)
T ss_pred             hccEEEEcCCCCCHHHH-HHHHHHHHHhcC
Confidence            36899999999999975 555566665544

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.

>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=86.15  E-value=1.6  Score=36.55  Aligned_cols=38  Identities=18%  Similarity=0.218  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHH---------hcCCceeeeCCCCCCchHHHHHHHH
Q psy14272         34 IQSNFMKNLYYTL---------DNSKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        34 iQ~e~M~~I~~~L---------~~gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      .|.+.+..++.-.         ....-+|+-...|+|||+..|..+.
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            3777677666665         4446688888999999998776644

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.

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=86.08  E-value=1.2  Score=44.56  Aligned_cols=44  Identities=14%  Similarity=0.203  Sum_probs=30.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +..-+.|.+.+..|   +..+++.++.+|.|||||.. |.+++..+..
T Consensus       351 ~~Ls~~Q~~Av~~i---~~s~~~~il~G~aGTGKTtl-l~~i~~~~~~  394 (744)
T TIGR02768       351 YRLSEEQYEAVRHV---TGSGDIAVVVGRAGTGKSTM-LKAAREAWEA  394 (744)
T ss_pred             CCCCHHHHHHHHHH---hcCCCEEEEEecCCCCHHHH-HHHHHHHHHh
Confidence            44568999966665   44467999999999999964 4444444443

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.

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=86.06  E-value=0.72  Score=37.23  Aligned_cols=29  Identities=21%  Similarity=0.180  Sum_probs=19.6

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ++.|-+|+|+|||- ++..++.++...+.+
T Consensus         1 vi~i~G~~gsGKTt-l~~~l~~~l~~~G~~   29 (155)
T TIGR00176         1 VLQIVGPKNSGKTT-LIERLVKALKARGYR   29 (155)
T ss_pred             CEEEECCCCCCHHH-HHHHHHHHHHhcCCe
Confidence            35678999999995 455556666655433

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=85.97  E-value=0.87  Score=43.81  Aligned_cols=35  Identities=20%  Similarity=0.297  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~   68 (194)
                      +|...++.+..++..++  + .||.||.|+|||....+
T Consensus        20 Gq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~   57 (527)
T PRK14969         20 GQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARI   57 (527)
T ss_pred             CcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHH
Confidence            78888889999998874  3 48999999999965433

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=85.97  E-value=1.5  Score=40.91  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=17.2

Q ss_pred             CCceeeeCCCCCCchHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGI   70 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~a   70 (194)
                      ..+++|-+|||+|||-+..--+
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA  195 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLA  195 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHH
Confidence            3678999999999997754443

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=85.86  E-value=1  Score=47.10  Aligned_cols=49  Identities=24%  Similarity=0.273  Sum_probs=35.9

Q ss_pred             CCCCccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         20 EVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        20 ~~~~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..|..+.+...||++|+-  -.|  +|.+|  -|.|+.||=||||+..+|+...+
T Consensus       128 ~~g~~~~wdm~~ydVQLi--Ggi--vLh~G--~IAEM~TGEGKTLvatlp~yLnA  176 (1025)
T PRK12900        128 VMGREMTWDMVPYDVQLI--GGI--VLHSG--KISEMATGEGKTLVSTLPTFLNA  176 (1025)
T ss_pred             ccccccccCccccchHHh--hhH--HhhcC--CccccCCCCCcchHhHHHHHHHH
Confidence            346677778889999864  333  24466  46899999999999998865443

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

Probab=85.81  E-value=0.88  Score=37.72  Aligned_cols=29  Identities=14%  Similarity=0.230  Sum_probs=19.7

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|.++++.+|+|||||+=.+--+...+..
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~   46 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKN   46 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhh
Confidence            35889999999999996433333344444

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 ....

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

Probab=85.79  E-value=0.74  Score=44.53  Aligned_cols=33  Identities=21%  Similarity=0.244  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      .+|...=+++.-+...|.+++|.+|.|||||+.
T Consensus       182 ~GQ~~AKrAleiAAAGgHnLl~~GpPGtGKTml  214 (490)
T COG0606         182 KGQEQAKRALEIAAAGGHNLLLVGPPGTGKTML  214 (490)
T ss_pred             cCcHHHHHHHHHHHhcCCcEEEecCCCCchHHh
Confidence            467777778887778889999999999999974

>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=85.28  E-value=2.1  Score=36.28  Aligned_cols=25  Identities=24%  Similarity=0.230  Sum_probs=19.2

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+++-||+|+|||- +|.++...+..
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            58999999999998 56666555544

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=85.27  E-value=1.2  Score=42.12  Aligned_cols=41  Identities=22%  Similarity=0.116  Sum_probs=31.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      |.-.-+|...+..+..++..++   ..||.||.|+|||....+-
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~l   59 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIF   59 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHH
Confidence            3334478889999999998874   3789999999999665444

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

Probab=85.27  E-value=0.69  Score=46.65  Aligned_cols=32  Identities=25%  Similarity=0.281  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHhc--------C---CceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDN--------S---KFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~--------g---k~~I~ESPTGTGKTLS   65 (194)
                      +|-+.+..|..+|..        +   ..++|.+|||+|||..
T Consensus       462 GQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~l  504 (758)
T PRK11034        462 GQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEV  504 (758)
T ss_pred             CcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHH
Confidence            577778888877762        1   3579999999999954

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=85.26  E-value=0.3  Score=48.50  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=21.1

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ..++++-||||+|||.++++|.|.
T Consensus       144 ~~hvLviApTrSGKgvg~VIPnLL  167 (663)
T PRK13876        144 PEHVLCFAPTRSGKGVGLVVPTLL  167 (663)
T ss_pred             CceEEEEecCCCCcceeEehhhHH
Confidence            378999999999999999999644

>PRK05541 adenylylsulfate kinase; Provisional

Probab=85.13  E-value=0.34  Score=38.65  Aligned_cols=19  Identities=21%  Similarity=0.191  Sum_probs=16.2

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..+.+++|.++.|+|||-
T Consensus         4 ~~~~~~I~i~G~~GsGKst   22 (176)
T PRK05541          4 KPNGYVIWITGLAGSGKTT   22 (176)
T ss_pred             CCCCCEEEEEcCCCCCHHH
Confidence            3467899999999999984

>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=85.11  E-value=0.43  Score=34.89  Aligned_cols=13  Identities=23%  Similarity=0.212  Sum_probs=11.2

Q ss_pred             eeeeCCCCCCchH
Q psy14272         52 GIFESPTGTGKSL   64 (194)
Q Consensus        52 ~I~ESPTGTGKTL   64 (194)
                      ++|.+++|||||-
T Consensus         1 I~i~G~~GsGKtT   13 (129)
T PF13238_consen    1 IGISGIPGSGKTT   13 (129)
T ss_dssp             EEEEESTTSSHHH
T ss_pred             CEEECCCCCCHHH
Confidence            4788999999994

...

>KOG1808|consensus

Probab=85.08  E-value=2  Score=47.42  Aligned_cols=48  Identities=15%  Similarity=0.147  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      |.+.+-+...+..+..++..| ..++|.+|||+|||- +++- ++|..-++
T Consensus       419 ~i~T~~vq~~la~~~~a~~~~~~pillqG~tssGKts-ii~~-la~~~g~~  467 (1856)
T KOG1808|consen  419 YIITPRVQKNLADLARAISSGKFPILLQGPTSSGKTS-IIKE-LARATGKN  467 (1856)
T ss_pred             eeccHHHHHHHHHHHHHHhcCCCCeEEecCcCcCchh-HHHH-HHHHhccC
Confidence            667777777777777777777 689999999999993 3443 56655444

>PRK04296 thymidine kinase; Provisional

Probab=85.07  E-value=0.77  Score=37.85  Aligned_cols=31  Identities=16%  Similarity=0.218  Sum_probs=21.0

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      |.+.++-+|.|+|||..++--+..+.. ++.+
T Consensus         2 g~i~litG~~GsGKTT~~l~~~~~~~~-~g~~   32 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQRAYNYEE-RGMK   32 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHHHHHHHHH-cCCe
Confidence            567899999999999665544444433 3444

>cd01373 KISc_KLP2_like Kinesin motor domain, KLP2-like subgroup

Probab=85.01  E-value=0.54  Score=42.31  Aligned_cols=45  Identities=18%  Similarity=0.203  Sum_probs=29.8

Q ss_pred             CccCCC--CCCCHHHHHHHHHHH----HHHhcC--CceeeeCCCCCCchHHHH
Q psy14272         23 SEFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        23 ~~~~fP--y~py~iQ~e~M~~I~----~~L~~g--k~~I~ESPTGTGKTLS~L   67 (194)
                      ..|.|.  |.|-..|.++...+.    ..+-+|  ..++.-+.||||||.+++
T Consensus        41 ~~f~FD~vf~~~~~q~~vy~~~~~p~v~~~~~G~n~ti~aYGqTGSGKTyTm~   93 (337)
T cd01373          41 RMFTFDHVADSNTNQEDVFQSVGKPLVEDCLSGYNGSIFAYGQTGSGKTYTMM   93 (337)
T ss_pred             cEEeCCeEeCCCCCHHHHHHHHHHHHHHHHhCCCceeEEEeCCCCCCceEEec
Confidence            345555  567778888776553    233345  346668899999998764

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

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=85.00  E-value=1.1  Score=44.67  Aligned_cols=35  Identities=23%  Similarity=0.275  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLI   67 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L   67 (194)
                      =+|...+..|..++..+++   .||.||.|+|||....
T Consensus        19 vGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr   56 (647)
T PRK07994         19 VGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIAR   56 (647)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHH
Confidence            3789999999999998865   6999999999997433

>PRK14729 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Provisional

Probab=84.89  E-value=0.53  Score=42.53  Aligned_cols=17  Identities=35%  Similarity=0.409  Sum_probs=14.6

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .++++++-+|||||||-
T Consensus         3 ~~~ii~I~GpTasGKS~   19 (300)
T PRK14729          3 ENKIVFIFGPTAVGKSN   19 (300)
T ss_pred             CCcEEEEECCCccCHHH
Confidence            35689999999999995

>CHL00181 cbbX CbbX; Provisional

Probab=84.83  E-value=0.65  Score=41.15  Aligned_cols=19  Identities=26%  Similarity=0.303  Sum_probs=15.0

Q ss_pred             CceeeeCCCCCCchHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~   68 (194)
                      -+++|.+|+|||||...-+
T Consensus        60 ~~ill~G~pGtGKT~lAr~   78 (287)
T CHL00181         60 LHMSFTGSPGTGKTTVALK   78 (287)
T ss_pred             ceEEEECCCCCCHHHHHHH
Confidence            4589999999999965433

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=84.79  E-value=1.6  Score=42.96  Aligned_cols=43  Identities=19%  Similarity=0.331  Sum_probs=36.3

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHH
Q psy14272         25 FPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        25 ~~fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L   67 (194)
                      ..-||.|.+.|...+..+...+.++ +..++.+.||+|||+.+.
T Consensus         7 ~~~~~~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia   50 (652)
T PRK05298          7 LVSPYKPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA   50 (652)
T ss_pred             cccCCCCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH
Confidence            4568999999999999999999766 356789999999998643

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=84.72  E-value=0.88  Score=43.81  Aligned_cols=30  Identities=20%  Similarity=0.192  Sum_probs=21.4

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|.++.|-+|||+|||-+...-+..+...+
T Consensus       255 ~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~  284 (484)
T PRK06995        255 RGGVFALMGPTGVGKTTTTAKLAARCVMRH  284 (484)
T ss_pred             CCcEEEEECCCCccHHHHHHHHHHHHHHhc
Confidence            357899999999999977655544443343

>PRK00698 tmk thymidylate kinase; Validated

Probab=84.62  E-value=0.51  Score=37.90  Aligned_cols=22  Identities=32%  Similarity=0.373  Sum_probs=17.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      .|..++||+|.|+|||-  ++-.|
T Consensus         2 ~~~~I~ieG~~gsGKsT--~~~~L   23 (205)
T PRK00698          2 RGMFITIEGIDGAGKST--QIELL   23 (205)
T ss_pred             CceEEEEECCCCCCHHH--HHHHH
Confidence            36789999999999994  45444

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=84.61  E-value=1.3  Score=46.66  Aligned_cols=52  Identities=23%  Similarity=0.233  Sum_probs=36.9

Q ss_pred             CCCCCCCccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         17 PLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        17 ~~~~~~~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..+..|..+.+...||++|+-  -.|  +|.+|  -|.|+.||=||||+..+|+.-.+
T Consensus       156 ~w~~~g~~~~W~m~~yDVQli--Ggi--vLh~G--~IAEM~TGEGKTLvAtlp~yLnA  207 (1112)
T PRK12901        156 HWDAGGNEITWDMVHYDVQLI--GGV--VLHQG--KIAEMATGEGKTLVATLPVYLNA  207 (1112)
T ss_pred             ccccccccccCCCcccchHHh--hhh--hhcCC--ceeeecCCCCchhHHHHHHHHHH
Confidence            334456667777889999864  333  23455  57899999999999988865433

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.38  E-value=1.2  Score=42.94  Aligned_cols=36  Identities=17%  Similarity=0.093  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      +|..+.+.+..++..++   ..||.+|.|+|||-...+-
T Consensus        17 GQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~Aril   55 (491)
T PRK14964         17 GQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARII   55 (491)
T ss_pred             CcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHH
Confidence            68888888888998874   4899999999999654433

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=84.31  E-value=0.23  Score=48.93  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.5

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .++++-||||||||.++++|.|.
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL  198 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLL  198 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchh
Confidence            68999999999999999999653

>CHL00095 clpC Clp protease ATP binding subunit

Probab=84.28  E-value=0.97  Score=45.54  Aligned_cols=32  Identities=22%  Similarity=0.237  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchH
Q psy14272         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSL   64 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTL   64 (194)
                      -+|-+.+..|..+|...           ...+|-+|||+|||.
T Consensus       512 ~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~  554 (821)
T CHL00095        512 IGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTE  554 (821)
T ss_pred             cChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHH
Confidence            47889999998888632           136899999999994

>smart00763 AAA_PrkA PrkA AAA domain

Probab=84.20  E-value=1.3  Score=41.33  Aligned_cols=34  Identities=18%  Similarity=0.235  Sum_probs=24.1

Q ss_pred             CCHHHHHHHHHHHHHHh----cCCceeeeCCCCCCchH
Q psy14272         31 AYDIQSNFMKNLYYTLD----NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~----~gk~~I~ESPTGTGKTL   64 (194)
                      -.....+++..+..+..    ..++++|.+|+|+|||.
T Consensus        56 ~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKSt   93 (361)
T smart00763       56 MEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSS   93 (361)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHH
Confidence            44556666666655554    24788999999999995

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.16  E-value=1.4  Score=42.17  Aligned_cols=36  Identities=25%  Similarity=0.226  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~   68 (194)
                      -+|...+..+..++..+.+   .+|.||.|+|||....+
T Consensus        19 iGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~   57 (486)
T PRK14953         19 IGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARI   57 (486)
T ss_pred             cChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHH
Confidence            4899999999999988743   47999999999865444

>KOG0332|consensus

Probab=84.09  E-value=0.71  Score=44.01  Aligned_cols=46  Identities=24%  Similarity=0.305  Sum_probs=34.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhc-CCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~-gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ..|. |-.||.-.+.-+.   .+ -++.|..|..|||||.+|.+.+|+-..
T Consensus       108 M~F~kPskIQe~aLPlll---~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd  155 (477)
T KOG0332|consen  108 MKFQKPSKIQETALPLLL---AEPPQNLIAQSQSGTGKTAAFVLTMLSRVD  155 (477)
T ss_pred             hccCCcchHHHhhcchhh---cCCchhhhhhhcCCCchhHHHHHHHHHhcC
Confidence            4455 7788887666552   22 378999999999999999888877543

>PRK04195 replication factor C large subunit; Provisional

Probab=84.06  E-value=1.1  Score=42.05  Aligned_cols=32  Identities=19%  Similarity=0.226  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHh---c---CCceeeeCCCCCCchHHH
Q psy14272         35 QSNFMKNLYYTLD---N---SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        35 Q~e~M~~I~~~L~---~---gk~~I~ESPTGTGKTLS~   66 (194)
                      |.+....|..++.   .   .+.++|-||+|||||...
T Consensus        19 ~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         19 NEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            4444455555554   3   467999999999999543

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=84.06  E-value=0.98  Score=37.44  Aligned_cols=29  Identities=21%  Similarity=0.186  Sum_probs=19.9

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      +..|..+++.+|+|+|||.-.+.-+...+
T Consensus        17 i~~G~~~~i~G~~G~GKT~l~~~~~~~~~   45 (229)
T TIGR03881        17 IPRGFFVAVTGEPGTGKTIFCLHFAYKGL   45 (229)
T ss_pred             CcCCeEEEEECCCCCChHHHHHHHHHHHH
Confidence            34568899999999999864443333333

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.

>PRK10869 recombination and repair protein; Provisional

Probab=83.98  E-value=0.95  Score=43.82  Aligned_cols=24  Identities=25%  Similarity=0.375  Sum_probs=19.0

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +..||-+|||+|||.  |+-+|.|+.
T Consensus        23 glnvitGetGaGKS~--ildAi~~ll   46 (553)
T PRK10869         23 GMTVITGETGAGKSI--AIDALGLCL   46 (553)
T ss_pred             CcEEEECCCCCChHH--HHHHHHHHh
Confidence            678999999999984  556677664

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=83.95  E-value=1.9  Score=42.48  Aligned_cols=22  Identities=27%  Similarity=0.505  Sum_probs=17.9

Q ss_pred             HHhcCCceeeeCCCCCCchHHH
Q psy14272         45 TLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      ++..|++++|-+|||+|||-.+
T Consensus       346 ~l~~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        346 PLERGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             cccCCCEEEEECCCCCCHHHHH
Confidence            3456788999999999999654

>KOG0744|consensus

Probab=83.92  E-value=0.75  Score=43.28  Aligned_cols=22  Identities=32%  Similarity=0.738  Sum_probs=18.2

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ++.+++.+|.|||||-  ||-+|+
T Consensus       177 NRliLlhGPPGTGKTS--LCKaLa  198 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTS--LCKALA  198 (423)
T ss_pred             eeEEEEeCCCCCChhH--HHHHHH
Confidence            4678999999999994  777765

>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=83.83  E-value=1  Score=39.03  Aligned_cols=28  Identities=21%  Similarity=0.415  Sum_probs=21.1

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ....+|-+|||+|||.  |+-++.|+....
T Consensus        21 ~~~~~i~G~nGsGKS~--il~ai~~~~~~~   48 (276)
T cd03241          21 EGLTVLTGETGAGKSI--LLDALSLLLGGR   48 (276)
T ss_pred             CCeEEEEcCCCCCHHH--HHHHHHHHhcCC
Confidence            3578899999999985  566778775443

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=83.79  E-value=1.5  Score=40.09  Aligned_cols=51  Identities=20%  Similarity=0.152  Sum_probs=35.7

Q ss_pred             cCCCCC--CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         25 FPFPFD--AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        25 ~~fPy~--py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .++|-.  .--+|.+....+..++..|+   ..+|.+|.|+|||.....- ..++..
T Consensus        16 ~~~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~l-A~~Llc   71 (351)
T PRK09112         16 VPSPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHL-ANHILS   71 (351)
T ss_pred             CCCCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHH-HHHHcC
Confidence            356643  23578888889999999886   4899999999998544332 344433

>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=83.77  E-value=0.52  Score=35.59  Aligned_cols=14  Identities=43%  Similarity=0.653  Sum_probs=12.2

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      ++|+-+|+|||||-
T Consensus         1 lii~~G~pgsGKSt   14 (143)
T PF13671_consen    1 LIILCGPPGSGKST   14 (143)
T ss_dssp             EEEEEESTTSSHHH
T ss_pred             CEEEECCCCCCHHH
Confidence            47899999999993

...

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=83.74  E-value=1.2  Score=44.81  Aligned_cols=38  Identities=21%  Similarity=0.176  Sum_probs=30.7

Q ss_pred             CHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      .-+|...+..|..+|..++   .+||.+|.|+|||....+-
T Consensus        18 IIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriL   58 (709)
T PRK08691         18 LVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARIL   58 (709)
T ss_pred             HcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHH
Confidence            3479999999999999875   3699999999999655433

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=83.69  E-value=0.65  Score=42.75  Aligned_cols=16  Identities=44%  Similarity=0.704  Sum_probs=14.6

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      ++++|-+|+|||||+.
T Consensus       152 knVLFyGppGTGKTm~  167 (368)
T COG1223         152 KNVLFYGPPGTGKTMM  167 (368)
T ss_pred             ceeEEECCCCccHHHH
Confidence            7899999999999964

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=83.68  E-value=0.42  Score=47.22  Aligned_cols=22  Identities=23%  Similarity=0.184  Sum_probs=20.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al   71 (194)
                      .++++-||||+|||.++++|.+
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnL  233 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTA  233 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhh
Confidence            6899999999999999999953

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.

>cd01366 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins

Probab=83.58  E-value=0.64  Score=41.30  Aligned_cols=43  Identities=21%  Similarity=0.359  Sum_probs=26.3

Q ss_pred             ccCCC--CCCCHHHHHHHHHHHHHHh---cC--CceeeeCCCCCCchHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNLYYTLD---NS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I~~~L~---~g--k~~I~ESPTGTGKTLS~   66 (194)
                      .|.|.  |.+...|.++-..|...+.   +|  ..++.-++||||||.++
T Consensus        46 ~f~fD~vf~~~~~q~~v~~~v~p~v~~~~~G~~~~i~ayG~tgSGKT~tl   95 (329)
T cd01366          46 SFSFDRVFDPDASQEDVFEEVSPLVQSALDGYNVCIFAYGQTGSGKTYTM   95 (329)
T ss_pred             EEecCEEECCCCCHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCCcEEe
Confidence            34444  4455556655555433332   34  34667899999999987

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

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=83.51  E-value=1.6  Score=38.87  Aligned_cols=52  Identities=21%  Similarity=0.196  Sum_probs=35.9

Q ss_pred             CCHHHHHHHHHHHHHHhcC---CceeeeCCCCCCchHHHHHHHHHHHhhhhhhhHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGILKWYYDHKIVGLE   83 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~g---k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~~~   83 (194)
                      -|..|++.+..-...+-.|   .++++-++-|||||- ++=+++....+.+-++++
T Consensus        31 Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSS-lVkall~~y~~~GLRlIe   85 (249)
T PF05673_consen   31 GIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSS-LVKALLNEYADQGLRLIE   85 (249)
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHH-HHHHHHHHHhhcCceEEE
Confidence            5677887666655666555   579999999999984 445556666665555443

>PF13173 AAA_14: AAA domain

Probab=83.51  E-value=0.91  Score=34.64  Aligned_cols=19  Identities=42%  Similarity=0.623  Sum_probs=16.1

Q ss_pred             cCCceeeeCCCCCCchHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~   66 (194)
                      +++++++.||.|+|||..+
T Consensus         1 n~~~~~l~G~R~vGKTtll   19 (128)
T PF13173_consen    1 NRKIIILTGPRGVGKTTLL   19 (128)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4688999999999999643

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=83.48  E-value=1.1  Score=45.53  Aligned_cols=37  Identities=16%  Similarity=0.206  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchHHHHHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      +|-+.+..|.+++...           .+.+|-+|||+|||  +|+-+|.
T Consensus       570 GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT--~lA~~La  617 (852)
T TIGR03345       570 GQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKT--ETALALA  617 (852)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHH--HHHHHHH

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=83.46  E-value=1.6  Score=37.89  Aligned_cols=32  Identities=13%  Similarity=0.230  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS   65 (194)
                      +|.+....+..++..|.   .++|.||+|+|||..
T Consensus        25 ~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~l   59 (316)
T PHA02544         25 LPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTV   59 (316)
T ss_pred             CcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHH
Confidence            56666667777777773   445589999999964

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=83.45  E-value=1.3  Score=45.07  Aligned_cols=38  Identities=26%  Similarity=0.268  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICGI   70 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~~a   70 (194)
                      -+|...+..|..+|..++  + .||.+|.|+|||.+..+-+
T Consensus        18 iGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lA   58 (824)
T PRK07764         18 IGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILA   58 (824)
T ss_pred             cCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHH
Confidence            368888889999998873  3 6899999999997765553

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=83.43  E-value=1.3  Score=43.79  Aligned_cols=38  Identities=29%  Similarity=0.144  Sum_probs=29.9

Q ss_pred             CHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      .-+|...+..+..++..++   ..||.||.|+|||....+-
T Consensus        18 IIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~l   58 (605)
T PRK05896         18 IIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIF   58 (605)
T ss_pred             hcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHH
Confidence            3478888899999997763   3689999999999765544

>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=83.37  E-value=1.1  Score=37.15  Aligned_cols=24  Identities=29%  Similarity=0.437  Sum_probs=19.1

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCch
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKS   63 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKT   63 (194)
                      +..|...|.. +..+|-+|+|+|||
T Consensus        26 ~~~l~~~l~~-k~~vl~G~SGvGKS   49 (161)
T PF03193_consen   26 IEELKELLKG-KTSVLLGQSGVGKS   49 (161)
T ss_dssp             HHHHHHHHTT-SEEEEECSTTSSHH
T ss_pred             HHHHHHHhcC-CEEEEECCCCCCHH
Confidence            3455555665 99999999999998

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.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=83.25  E-value=0.87  Score=46.35  Aligned_cols=31  Identities=23%  Similarity=0.269  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchH
Q psy14272         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSL   64 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTL   64 (194)
                      +|-+.+.+|.+++...           .+.+|-+|||+|||-
T Consensus       495 GQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTE  536 (786)
T COG0542         495 GQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTE  536 (786)
T ss_pred             ChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHH
Confidence            6888888888888541           468899999999995

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.21  E-value=1.4  Score=44.47  Aligned_cols=37  Identities=19%  Similarity=0.171  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      -+|....+.|..++.+++   ..||.||.|+|||-...+-
T Consensus        18 IGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriL   57 (702)
T PRK14960         18 VGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARIL   57 (702)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            378888889999998884   3599999999999665443

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.21  E-value=1.3  Score=45.92  Aligned_cols=36  Identities=22%  Similarity=0.215  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~~   69 (194)
                      +|......|..++..++  + .||.||.|||||....+-
T Consensus        20 GQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiL   58 (944)
T PRK14949         20 GQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLF   58 (944)
T ss_pred             CcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHH
Confidence            78888888999998873  3 489999999999665443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.17  E-value=1.3  Score=39.58  Aligned_cols=38  Identities=29%  Similarity=0.423  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~   66 (194)
                      |+..-+|...+..+...+.+|.   ..+|.||.|+|||...
T Consensus        16 ~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a   56 (367)
T PRK14970         16 FDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCA   56 (367)
T ss_pred             HHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHH
Confidence            4444588888899999998874   5889999999999543

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

Probab=83.15  E-value=2  Score=43.43  Aligned_cols=49  Identities=18%  Similarity=0.135  Sum_probs=38.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      --+.|......|...+..-+..++.+.||+|||-.||-.+-..|...+.
T Consensus       199 Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~Gkq  247 (730)
T COG1198         199 LNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQGKQ  247 (730)
T ss_pred             cCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHcCCE
Confidence            3478888888887777333789999999999999999887777776543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=83.11  E-value=1.5  Score=43.44  Aligned_cols=41  Identities=20%  Similarity=0.241  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      |+-.-+|...+..|..++..+++   .||.||.|+|||....+-
T Consensus        15 f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~l   58 (618)
T PRK14951         15 FSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRIL   58 (618)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            33334799999999999998743   599999999999655443

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

Probab=83.11  E-value=0.75  Score=41.31  Aligned_cols=42  Identities=19%  Similarity=0.276  Sum_probs=28.6

Q ss_pred             cCCC--CCCCHHHHHHHHHHHH----HHhcC--CceeeeCCCCCCchHHHH
Q psy14272         25 FPFP--FDAYDIQSNFMKNLYY----TLDNS--KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        25 ~~fP--y~py~iQ~e~M~~I~~----~L~~g--k~~I~ESPTGTGKTLS~L   67 (194)
                      |.|.  |.+ ..|.++...+..    .+-+|  ..++.-++||||||.+++
T Consensus        50 f~FD~vf~~-~~q~~vy~~~~~p~v~~~~~G~n~~i~ayG~tgSGKTyTm~   99 (334)
T cd01375          50 FKFDGVFHN-ASQEEVYETVAKPVVDSALDGYNGTIFAYGQTGAGKTFTMT   99 (334)
T ss_pred             EEcCcccCC-CCHHHHHHHHHHHHHHHHhCCCccceeeecCCCCCCeEEcc
Confidence            4444  557 888888766543    22344  457778999999998863

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

>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=82.95  E-value=1.3  Score=35.09  Aligned_cols=23  Identities=17%  Similarity=0.088  Sum_probs=16.6

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHH
Q psy14272         51 FGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      +++|.+|+|+|||-....-+..+
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~   24 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYL   24 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            57899999999997654443333

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.

>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=82.87  E-value=1.2  Score=36.70  Aligned_cols=26  Identities=23%  Similarity=0.475  Sum_probs=19.9

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ....+|-+|+|+|||-  |+-||.|+..
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            4578999999999995  5556776554

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 ....

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

Probab=82.76  E-value=0.99  Score=45.79  Aligned_cols=31  Identities=26%  Similarity=0.288  Sum_probs=22.2

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      ...++.+|.||||+|||-  |+=|++|+.-...
T Consensus        23 f~~gi~lI~G~nGsGKSS--IldAI~~ALyG~~   53 (908)
T COG0419          23 FDSGIFLIVGPNGAGKSS--ILDAITFALYGKT   53 (908)
T ss_pred             CCCCeEEEECCCCCcHHH--HHHHHHHHHcCCC
Confidence            356789999999999994  4555666654433

>TIGR00041 DTMP_kinase thymidylate kinase

Probab=82.72  E-value=0.66  Score=37.24  Aligned_cols=16  Identities=31%  Similarity=0.505  Sum_probs=14.4

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      |..++||++.|+|||-
T Consensus         3 g~~IvieG~~GsGKsT   18 (195)
T TIGR00041         3 GMFIVIEGIDGAGKTT   18 (195)
T ss_pred             ceEEEEECCCCCCHHH
Confidence            6789999999999983

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.

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=82.65  E-value=1.5  Score=42.51  Aligned_cols=34  Identities=15%  Similarity=0.350  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHhc-------CCceeeeCCCCCCchHHHHH
Q psy14272         35 QSNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        35 Q~e~M~~I~~~L~~-------gk~~I~ESPTGTGKTLS~L~   68 (194)
                      ...=+..|..||..       .+++|+-+|+|+|||-++-+
T Consensus        24 hkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~   64 (519)
T PF03215_consen   24 HKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKV   64 (519)
T ss_pred             cHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHH
Confidence            34445677777764       35799999999999976544

>KOG0390|consensus

Probab=82.64  E-value=2.1  Score=43.66  Aligned_cols=55  Identities=22%  Similarity=0.117  Sum_probs=42.8

Q ss_pred             cCCCC---CCCHHHHHHHHHHHHHHhcC-----Cc-eeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         25 FPFPF---DAYDIQSNFMKNLYYTLDNS-----KF-GIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        25 ~~fPy---~py~iQ~e~M~~I~~~L~~g-----k~-~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      +.+|+   .-||.|.+-...+|+||..-     .. +|+--..|+||||-.|.-+.+||+.++.
T Consensus       230 ~~dP~l~~~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~IsflwtlLrq~P~  293 (776)
T KOG0390|consen  230 VIDPLLKKILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQCISFIWTLLRQFPQ  293 (776)
T ss_pred             EecccHhhhcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHHHHHHHHHHHhCcC
Confidence            45675   38999999999999999642     22 4555567999999888888888888776

>KOG0743|consensus

Probab=82.63  E-value=1.6  Score=41.91  Aligned_cols=41  Identities=24%  Similarity=0.455  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..=.++|..+...+...           .--++-+|.||||| |+|.++..+|
T Consensus       208 ~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKS-S~IaAmAn~L  259 (457)
T KOG0743|consen  208 DLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKS-SFIAAMANYL  259 (457)
T ss_pred             hHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHH-HHHHHHHhhc
Confidence            45677888888777653           23678999999999 4555544454

>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=82.61  E-value=0.77  Score=36.64  Aligned_cols=35  Identities=20%  Similarity=0.366  Sum_probs=23.5

Q ss_pred             HHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         39 MKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        39 M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      +..|.+++..+  ..+++-||.|+|||- +|--++..+
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            34566667664  788999999999995 343344444

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=82.57  E-value=1.8  Score=45.49  Aligned_cols=39  Identities=15%  Similarity=0.116  Sum_probs=24.8

Q ss_pred             CCHHHHHHH-HHHHHHHhcC---CceeeeCCCCCCchHHHHHH
Q psy14272         31 AYDIQSNFM-KNLYYTLDNS---KFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        31 py~iQ~e~M-~~I~~~L~~g---k~~I~ESPTGTGKTLS~L~~   69 (194)
                      -|..|.+-+ ..|..+|...   .+++|-||||||||++...-
T Consensus       759 hREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~V  801 (1164)
T PTZ00112        759 CREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSV  801 (1164)
T ss_pred             ChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHH
Confidence            455555544 4455556533   23458999999999886543

>PRK14974 cell division protein FtsY; Provisional

Probab=82.53  E-value=2.4  Score=38.79  Aligned_cols=30  Identities=17%  Similarity=0.183  Sum_probs=21.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .+++|.+|+|+|||-+...-+ .|+...+.+
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA-~~l~~~g~~  170 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLA-YYLKKNGFS  170 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHH-HHHHHcCCe
Confidence            578899999999997644433 466655444

>KOG1802|consensus

Probab=82.48  E-value=1.4  Score=44.73  Aligned_cols=46  Identities=24%  Similarity=0.323  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      --..|......+   | +..+-|+.+|.|||||++.-.-++..++.+.-.
T Consensus       411 LN~SQ~~AV~~V---L-~rplsLIQGPPGTGKTvtsa~IVyhl~~~~~~~  456 (935)
T KOG1802|consen  411 LNASQSNAVKHV---L-QRPLSLIQGPPGTGKTVTSATIVYHLARQHAGP  456 (935)
T ss_pred             hchHHHHHHHHH---H-cCCceeeecCCCCCceehhHHHHHHHHHhcCCc
Confidence            346777744444   4 568999999999999987544444444544444

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=82.30  E-value=2.8  Score=41.42  Aligned_cols=31  Identities=23%  Similarity=0.342  Sum_probs=24.2

Q ss_pred             CHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      -+.|+.   ++..++. ..+.|+-+|.|||||...
T Consensus       154 ~d~Qk~---Av~~a~~-~~~~vItGgpGTGKTt~v  184 (615)
T PRK10875        154 VDWQKV---AAAVALT-RRISVISGGPGTGKTTTV  184 (615)
T ss_pred             CHHHHH---HHHHHhc-CCeEEEEeCCCCCHHHHH
Confidence            478988   5555554 579999999999999764

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=82.26  E-value=2.5  Score=38.58  Aligned_cols=37  Identities=11%  Similarity=0.168  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L   67 (194)
                      .||-|...-+.+..++.+|+   -.+|.||.|+||+....
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~   42 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIR   42 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHH
Confidence            47777888888888888874   35699999999986433

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=82.26  E-value=0.99  Score=41.66  Aligned_cols=27  Identities=22%  Similarity=0.431  Sum_probs=19.6

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ...+.+||-+|||||||-++ .+.+.|-
T Consensus       125 ~kRGLviiVGaTGSGKSTtm-AaMi~yR  151 (375)
T COG5008         125 AKRGLVIIVGATGSGKSTTM-AAMIGYR  151 (375)
T ss_pred             ccCceEEEECCCCCCchhhH-HHHhccc
Confidence            34578999999999999874 3334443

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=82.00  E-value=0.47  Score=46.93  Aligned_cols=23  Identities=22%  Similarity=0.236  Sum_probs=20.6

Q ss_pred             CCceeeeCCCCCCchHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      ..++++-||||+|||.++++|.|
T Consensus       224 ~~H~Lv~ApTgsGKt~g~VIPnL  246 (641)
T PRK13822        224 STHGLVFAGSGGFKTTSVVVPTA  246 (641)
T ss_pred             CceEEEEeCCCCCccceEehhhh
Confidence            36899999999999999999965

>TIGR00634 recN DNA repair protein RecN

Probab=81.94  E-value=1.3  Score=42.71  Aligned_cols=25  Identities=28%  Similarity=0.409  Sum_probs=19.4

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+..+|.+|||+|||.  |+-+|.|+.
T Consensus        22 ~g~~vitG~nGaGKS~--ll~al~~~~   46 (563)
T TIGR00634        22 RGLTVLTGETGAGKSM--IIDALSLLG   46 (563)
T ss_pred             CCeEEEECCCCCCHHH--HHHHHHHHh
Confidence            3578999999999985  455666665

All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=81.93  E-value=1.8  Score=42.02  Aligned_cols=42  Identities=26%  Similarity=0.305  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGI   70 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~a   70 (194)
                      |.---+|......+..++..++   ..||.||.|||||...-+-+
T Consensus        15 f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lA   59 (559)
T PRK05563         15 FEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFA   59 (559)
T ss_pred             HHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            3333478888999999998763   36889999999996655543

>cd01374 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis

Probab=81.92  E-value=0.97  Score=40.16  Aligned_cols=45  Identities=13%  Similarity=0.197  Sum_probs=28.7

Q ss_pred             CccCCC--CCCCHHHHHHHHHHH----HHHhcC--CceeeeCCCCCCchHHHH
Q psy14272         23 SEFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        23 ~~~~fP--y~py~iQ~e~M~~I~----~~L~~g--k~~I~ESPTGTGKTLS~L   67 (194)
                      ..|.|.  |.+-..|.++...+.    +.+-+|  ..++.-++||||||.++.
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  446667888766543    233345  346668999999999875

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

>TIGR01817 nifA Nif-specific regulatory protein

Probab=81.89  E-value=1.5  Score=41.52  Aligned_cols=26  Identities=19%  Similarity=0.257  Sum_probs=18.8

Q ss_pred             HHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         40 KNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        40 ~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +.+..+...+..++|.++|||||++.
T Consensus       210 ~~~~~~a~~~~pvli~Ge~GtGK~~l  235 (534)
T TIGR01817       210 DQARVVARSNSTVLLRGESGTGKELI  235 (534)
T ss_pred             HHHHHHhCcCCCEEEECCCCccHHHH
Confidence            33333334567899999999999963

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.

>PLN03188 kinesin-12 family protein; Provisional

Probab=81.78  E-value=0.58  Score=49.73  Aligned_cols=50  Identities=16%  Similarity=0.113  Sum_probs=33.2

Q ss_pred             CCCCCccCCC--CCCCHHHHHHHHHHHHH----HhcC--CceeeeCCCCCCchHHHHH
Q psy14272         19 AEVPSEFPFP--FDAYDIQSNFMKNLYYT----LDNS--KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        19 ~~~~~~~~fP--y~py~iQ~e~M~~I~~~----L~~g--k~~I~ESPTGTGKTLS~L~   68 (194)
                      .+.+..|.|.  |.|...|.++...+..-    +-+|  ..++.-|.||||||+++.-
T Consensus       128 ~I~~qtFtFD~VFdp~aTQedVFe~vv~PLV~svLdGyNaTIFAYGQTGSGKTYTM~G  185 (1320)
T PLN03188        128 TINGQTFTFDSIADPESTQEDIFQLVGAPLVENCLAGFNSSVFAYGQTGSGKTYTMWG  185 (1320)
T ss_pred             EEeCcEEeCCeeeCCCCCHHHHHHHHHHHHHHHHhcCCcceeecCCCCCCCCCEeeCC
Confidence            3344556666  56878888877765432    2334  3466688999999988753

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=81.76  E-value=0.79  Score=35.90  Aligned_cols=13  Identities=38%  Similarity=0.708  Sum_probs=11.4

Q ss_pred             eeeeCCCCCCchH
Q psy14272         52 GIFESPTGTGKSL   64 (194)
Q Consensus        52 ~I~ESPTGTGKTL   64 (194)
                      ++|.+|||+|||-
T Consensus         2 i~i~GpsGsGKst   14 (137)
T cd00071           2 IVLSGPSGVGKST   14 (137)
T ss_pred             EEEECCCCCCHHH
Confidence            6788999999994

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=81.64  E-value=2.8  Score=38.14  Aligned_cols=36  Identities=19%  Similarity=0.192  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSL   66 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~   66 (194)
                      +||-|...-+.+..++.+++   -.+|.||.|+||+...
T Consensus         4 ~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA   42 (319)
T PRK06090          4 DYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLV   42 (319)
T ss_pred             CcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH
Confidence            68888888889999998875   4889999999998543

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=81.63  E-value=0.81  Score=36.40  Aligned_cols=18  Identities=28%  Similarity=0.477  Sum_probs=14.5

Q ss_pred             CCceeeeCCCCCCchHHH
Q psy14272         49 SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~   66 (194)
                      |..+++.+|+|+|||-..
T Consensus         1 ~~~~~i~G~sGsGKttl~   18 (179)
T TIGR02322         1 GRLIYVVGPSGAGKDTLL   18 (179)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            357899999999998543

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.

>KOG0923|consensus

Probab=81.53  E-value=1.1  Score=45.54  Aligned_cols=25  Identities=24%  Similarity=0.367  Sum_probs=20.8

Q ss_pred             HHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         41 NLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        41 ~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      .|..++....++|+++.||+|||--
T Consensus       272 ell~av~e~QVLiI~GeTGSGKTTQ  296 (902)
T KOG0923|consen  272 ELLKAVKEHQVLIIVGETGSGKTTQ  296 (902)
T ss_pred             HHHHHHHhCcEEEEEcCCCCCcccc
Confidence            4555667889999999999999964

>KOG0239|consensus

Probab=81.50  E-value=1.5  Score=43.83  Aligned_cols=46  Identities=24%  Similarity=0.361  Sum_probs=33.1

Q ss_pred             ccCCCCCCCHHHHHHHHHHHH----HHhcCCceee-eCCCCCCchHHHHHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYY----TLDNSKFGIF-ESPTGTGKSLSLICG   69 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~----~L~~gk~~I~-ESPTGTGKTLS~L~~   69 (194)
                      .|.+-|.|-..|.+....|..    ||+.-.++|| -+.||||||++.--|
T Consensus       363 ~fdkVf~p~~sQ~~VF~e~~~lv~S~lDGYnVCIFAYGQTGSGKTyTM~G~  413 (670)
T KOG0239|consen  363 KFDKVFGPLASQDDVFEEVSPLVQSALDGYNVCIFAYGQTGSGKTYTMSGP  413 (670)
T ss_pred             eeeeecCCcccHHHHHHHHHHHHHHHhcCcceeEEEecccCCCccccccCC
Confidence            344457799999988877654    3444466666 789999999986654

>KOG0948|consensus

Probab=81.43  E-value=3  Score=42.98  Aligned_cols=51  Identities=18%  Similarity=0.202  Sum_probs=38.7

Q ss_pred             CccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        23 ~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ..-.|||+--|-|...    +.||+++..+++-|-|..|||...=.++..-|++.
T Consensus       122 pAk~YPF~LDpFQ~~a----I~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~k  172 (1041)
T KOG0948|consen  122 PAKTYPFTLDPFQSTA----IKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREK  172 (1041)
T ss_pred             cccCCCcccCchHhhh----hhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhc
Confidence            4456788877778774    35779999999999999999998777755555543

>cd01367 KISc_KIF2_like Kinesin motor domain, KIF2-like group

Probab=81.42  E-value=0.73  Score=41.15  Aligned_cols=44  Identities=18%  Similarity=0.285  Sum_probs=28.3

Q ss_pred             ccCCC--CCCCHHHHHHHHHH----HHHHhcC--CceeeeCCCCCCchHHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNS--KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I----~~~L~~g--k~~I~ESPTGTGKTLS~L   67 (194)
                      .|.|.  |.+..-|.++.+.+    .+.+-+|  ..++.-++||||||.++.
T Consensus        52 ~f~FD~vf~~~~~q~~vf~~~~~plv~~~~~G~n~~i~ayGqtGSGKTyTm~  103 (322)
T cd01367          52 TFRFDYVFDEAVTNEEVYRSTVKPLIPHVFEGGVATCFAYGQTGSGKTYTML  103 (322)
T ss_pred             eEecceEECCCCCHHHHHHHHHHHHHHHHhCCCceEEEeccCCCCCCceEec
Confidence            34444  45666787777663    3333345  345667899999999875

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

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=81.38  E-value=2.9  Score=37.81  Aligned_cols=47  Identities=13%  Similarity=0.094  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHh-----------cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         33 DIQSNFMKNLYYTLD-----------NSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~-----------~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .++.-+.+.|.+.|.           .+.+++|-+|+|+|||-+...-+ .++...+.+
T Consensus        87 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~vi~lvGpnGsGKTTt~~kLA-~~l~~~g~~  144 (318)
T PRK10416         87 ELKELLKEELAEILEPVEKPLNIEEKKPFVILVVGVNGVGKTTTIGKLA-HKYKAQGKK  144 (318)
T ss_pred             HHHHHHHHHHHHHhCcCCccccccCCCCeEEEEECCCCCcHHHHHHHHH-HHHHhcCCe
Confidence            345555556655553           24678888999999996544333 344444333

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=81.32  E-value=2.2  Score=38.20  Aligned_cols=33  Identities=18%  Similarity=0.123  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +.-..+.+.|..+...+..++|.+++||||++.
T Consensus        13 ~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~l   45 (326)
T PRK11608         13 NSFLEVLEQVSRLAPLDKPVLIIGERGTGKELI   45 (326)
T ss_pred             HHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHH
Confidence            444555666666667788999999999999863

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=81.27  E-value=1.4  Score=36.44  Aligned_cols=28  Identities=14%  Similarity=0.162  Sum_probs=19.6

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..|.+..+.+|+|||||.-.+--+...+
T Consensus        21 ~~g~i~~i~G~~GsGKT~l~~~la~~~~   48 (225)
T PRK09361         21 ERGTITQIYGPPGSGKTNICLQLAVEAA   48 (225)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3467899999999999865444333333

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=81.19  E-value=1.8  Score=42.08  Aligned_cols=38  Identities=18%  Similarity=0.240  Sum_probs=30.3

Q ss_pred             CHHHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~~   69 (194)
                      .-+|......+..++..|+  + .||.+|.|+|||....+-
T Consensus        18 iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~l   58 (576)
T PRK14965         18 LTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARIL   58 (576)
T ss_pred             ccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            3478888899999998874  3 589999999999765543

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=81.18  E-value=0.91  Score=35.86  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=13.9

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      ..+++|.+|.|||||-
T Consensus         3 ~~ii~i~G~~GsGKsT   18 (188)
T TIGR01360         3 CKIIFIVGGPGSGKGT   18 (188)
T ss_pred             CcEEEEECCCCCCHHH
Confidence            4578999999999985

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=80.98  E-value=1.6  Score=36.77  Aligned_cols=24  Identities=33%  Similarity=0.387  Sum_probs=19.9

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      |.+++|-||.|+|||.-.+.-+++
T Consensus         1 g~~~ll~g~~G~GKS~lal~la~~   24 (239)
T cd01125           1 GYVSALVAPGGTGKSSLLLVLALA   24 (239)
T ss_pred             CceeEEEcCCCCCHHHHHHHHHHH
Confidence            457899999999999877777665

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>KOG0951|consensus

Probab=80.96  E-value=2.3  Score=45.88  Aligned_cols=34  Identities=26%  Similarity=0.304  Sum_probs=28.3

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      +....++++.||||+|||-..+..+|.-+..+..
T Consensus       322 l~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r  355 (1674)
T KOG0951|consen  322 LRGDENMLLCAPTGAGKTNVAVLTILQELGNHLR  355 (1674)
T ss_pred             hcCcCcEEEeccCCCCchHHHHHHHHHHHhcccc
Confidence            3445789999999999999988888888777655

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=80.88  E-value=1.9  Score=43.62  Aligned_cols=36  Identities=25%  Similarity=0.338  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~   68 (194)
                      -+|....+.+..++..++  + .||.||.|+|||....+
T Consensus        21 iGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~Ari   59 (725)
T PRK07133         21 VGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKI   59 (725)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHH
Confidence            478888899999998874  3 48999999999965433

>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=80.88  E-value=1.1  Score=41.19  Aligned_cols=31  Identities=19%  Similarity=0.172  Sum_probs=21.6

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .+++++-+.||||||- +|-..|..+...+.+
T Consensus        15 ~~~~li~G~~GsGKT~-~i~~ll~~~~~~g~~   45 (386)
T PF10412_consen   15 NRHILIIGATGSGKTQ-AIRHLLDQIRARGDR   45 (386)
T ss_dssp             GG-EEEEE-TTSSHHH-HHHHHHHHHHHTT-E
T ss_pred             hCcEEEECCCCCCHHH-HHHHHHHHHHHcCCE
Confidence            4678999999999996 667777776665544

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.

>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=80.82  E-value=0.67  Score=34.90  Aligned_cols=24  Identities=25%  Similarity=0.383  Sum_probs=18.4

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ..|.++.|-+|+|+|||.  |+-+|.
T Consensus         9 ~~g~~~~i~G~nGsGKSt--Ll~~l~   32 (137)
T PF00005_consen    9 KPGEIVAIVGPNGSGKST--LLKALA   32 (137)
T ss_dssp             ETTSEEEEEESTTSSHHH--HHHHHT
T ss_pred             cCCCEEEEEccCCCcccc--ceeeec
Confidence            467899999999999995  344444

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 ....

>TIGR00602 rad24 checkpoint protein rad24

Probab=80.74  E-value=2  Score=42.77  Aligned_cols=34  Identities=18%  Similarity=0.372  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHHHHhc-------CCceeeeCCCCCCchHHH
Q psy14272         33 DIQSNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~-------gk~~I~ESPTGTGKTLS~   66 (194)
                      -+|...+..|..+|..       +.+++|-+|+|+|||-.+
T Consensus        87 ~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~  127 (637)
T TIGR00602        87 AVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTI  127 (637)
T ss_pred             cCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHH
Confidence            4677777788887764       345999999999999754

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

>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins

Probab=80.72  E-value=1.1  Score=40.05  Aligned_cols=39  Identities=18%  Similarity=0.219  Sum_probs=25.6

Q ss_pred             CCCCCHHHHHHHHHHH----HHHhcC--CceeeeCCCCCCchHHH
Q psy14272         28 PFDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~----~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      -|.+-..|.++-..+.    +.+-.|  ..++.-++||||||.++
T Consensus        55 vf~~~~~q~~vy~~~~~plv~~~~~G~n~~i~ayG~tgSGKTyTm   99 (333)
T cd01371          55 VYDPNSTQEDVYNETARPLVDSVLEGYNGTIFAYGQTGTGKTFTM   99 (333)
T ss_pred             ccCCCccHHHHHHHHHHHHHHHHhCCCceeEEecCCCCCCCcEee
Confidence            3566677877765433    233344  34666899999999775

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

>TIGR00368 Mg chelatase-related protein

Probab=80.69  E-value=0.96  Score=43.47  Aligned_cols=40  Identities=15%  Similarity=0.194  Sum_probs=32.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      +.|.-...|....+.+.-++..+.+++|-+|+|||||..+
T Consensus       189 ~d~~dv~Gq~~~~~al~~aa~~g~~vlliG~pGsGKTtla  228 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIAAAGGHNLLLFGPPGSGKTMLA  228 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhhccCCCEEEEEecCCCCHHHHH
Confidence            4455556688888888888888899999999999999643

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>cd01369 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup

Probab=80.66  E-value=0.75  Score=40.85  Aligned_cols=43  Identities=21%  Similarity=0.268  Sum_probs=27.5

Q ss_pred             ccCCC--CCCCHHHHHHHHHHH----HHHhcC--CceeeeCCCCCCchHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I~----~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      .|.|.  |.|-..|.++-..+.    +.+-.|  ..++.-++||||||.++
T Consensus        44 ~f~FD~vf~~~~~q~~vy~~~~~~~v~~~~~G~n~~i~ayG~tgSGKT~Tm   94 (325)
T cd01369          44 TFSFDRVFPPNTTQEDVYNFVAKPIVDDVLNGYNGTIFAYGQTGSGKTYTM   94 (325)
T ss_pred             EEEcCeEECCCCCHHHHHHHHHHHHHHHHHcCccceEEEeCCCCCCceEEe
Confidence            45554  456667777665542    223345  34567899999999885

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

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=80.53  E-value=3.1  Score=39.63  Aligned_cols=50  Identities=18%  Similarity=0.273  Sum_probs=35.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      -|...|+.++..|.-.+  -|... +.+.+-++-|||||+-.||++|.-..+.
T Consensus       223 vwGi~prn~eQ~~ALdl--Lld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~  273 (436)
T COG1875         223 VWGIRPRNAEQRVALDL--LLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLER  273 (436)
T ss_pred             hhccCcccHHHHHHHHH--hcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHH
Confidence            46677887777653222  23332 6788899999999999999988755443

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

Probab=80.50  E-value=1.4  Score=39.63  Aligned_cols=24  Identities=17%  Similarity=0.187  Sum_probs=18.2

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .++|+.+..|||||+-++.-+-..
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            578999999999998665554333

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

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=80.50  E-value=1.9  Score=40.81  Aligned_cols=16  Identities=50%  Similarity=0.592  Sum_probs=13.9

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      +.++|.+|+|||||+.
T Consensus       218 ~gVLL~GPPGTGKT~L  233 (438)
T PTZ00361        218 KGVILYGPPGTGKTLL  233 (438)
T ss_pred             cEEEEECCCCCCHHHH
Confidence            5688999999999975

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=80.44  E-value=1.9  Score=44.26  Aligned_cols=35  Identities=23%  Similarity=0.261  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L   67 (194)
                      =+|..+++.|..+|..++   ..||.+|.|||||....
T Consensus        19 IGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAr   56 (830)
T PRK07003         19 VGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSR   56 (830)
T ss_pred             cCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHH
Confidence            378999999999998874   35899999999996443

>cd01370 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup

Probab=80.44  E-value=1  Score=40.58  Aligned_cols=43  Identities=23%  Similarity=0.315  Sum_probs=28.7

Q ss_pred             ccCCC--CCCCHHHHHHHHHHH----HHHhcC--CceeeeCCCCCCchHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNLY----YTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I~----~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      .|.|.  |.|...|.++...+.    +.+-+|  .-++.-++||||||.++
T Consensus        55 ~f~Fd~vf~~~~~q~~vf~~~~~plv~~~~~G~n~~i~ayGqtGSGKTyTm  105 (338)
T cd01370          55 KYSFDRVFDETSTQEEVYENTTKPLVDGVLNGYNATVFAYGATGAGKTHTM  105 (338)
T ss_pred             EEEeccccCCCCCHHHHHHHHHHHHHHHHHCCCCceEEeeCCCCCCCeEEE
Confidence            34444  557777888776654    233345  34666899999999986

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

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=80.43  E-value=2  Score=43.25  Aligned_cols=30  Identities=13%  Similarity=0.305  Sum_probs=24.0

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.++++|+.+..|||||-..|-- ++||.-.
T Consensus       224 ek~~ilVVQGaAGSGKTtiALHR-vAyLlY~  253 (747)
T COG3973         224 EKNKILVVQGAAGSGKTTIALHR-VAYLLYG  253 (747)
T ss_pred             cCCCeEEEecCCCCCchhHHHHH-HHHHHhc
Confidence            34789999999999999888777 5666543

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=80.38  E-value=2.5  Score=38.43  Aligned_cols=39  Identities=10%  Similarity=0.058  Sum_probs=29.6

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      .||-|...-+.+...+.+|+   -.+|.||.|+||+...+.-
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~   44 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYAL   44 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHH
Confidence            56777777778888888874   3669999999998654443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=80.35  E-value=1.6  Score=35.58  Aligned_cols=22  Identities=18%  Similarity=0.234  Sum_probs=17.2

Q ss_pred             cCCceeeeCCCCCCchHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      .|.+..+.+|+|+|||.-.+-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~   32 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMIL   32 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            3578999999999999754433

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

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=80.31  E-value=2  Score=41.87  Aligned_cols=37  Identities=27%  Similarity=0.354  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHhcCCc---eeeeCCCCCCchHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKF---GIFESPTGTGKSLSLICG   69 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~---~I~ESPTGTGKTLS~L~~   69 (194)
                      =+|...+..+..++.++++   .||.||.|+|||.+..+-
T Consensus        19 iGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~l   58 (563)
T PRK06647         19 EGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAF   58 (563)
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHH
Confidence            3788888899999988744   589999999999765554

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=80.24  E-value=2.1  Score=38.64  Aligned_cols=26  Identities=19%  Similarity=0.215  Sum_probs=19.4

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      .+.+..+......++|.+++||||++
T Consensus        12 ~~~~~~~a~~~~pVLI~GE~GtGK~~   37 (329)
T TIGR02974        12 LEQVSRLAPLDRPVLIIGERGTGKEL   37 (329)
T ss_pred             HHHHHHHhCCCCCEEEECCCCChHHH
Confidence            33444444567889999999999996

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

>KOG0745|consensus

Probab=80.23  E-value=0.95  Score=44.00  Aligned_cols=22  Identities=32%  Similarity=0.531  Sum_probs=16.8

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ..++|+-+||||||||  |.-.|+
T Consensus       226 KSNvLllGPtGsGKTl--laqTLA  247 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTL--LAQTLA  247 (564)
T ss_pred             cccEEEECCCCCchhH--HHHHHH
Confidence            4689999999999996  444444

>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=80.15  E-value=1.7  Score=36.66  Aligned_cols=28  Identities=18%  Similarity=0.108  Sum_probs=22.2

Q ss_pred             HHHHHHHHHHhc----CCceeeeCCCCCCchH
Q psy14272         37 NFMKNLYYTLDN----SKFGIFESPTGTGKSL   64 (194)
Q Consensus        37 e~M~~I~~~L~~----gk~~I~ESPTGTGKTL   64 (194)
                      ..+..|.+.|..    ..++.+-|+.|+|||-
T Consensus         3 ~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~   34 (287)
T PF00931_consen    3 KEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTT   34 (287)
T ss_dssp             HHHHHHHHHHHTTTTSSEEEEEEESTTSSHHH
T ss_pred             HHHHHHHHHhhCCCCCeEEEEEEcCCcCCcce
Confidence            346677777866    3788999999999995

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.

---

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	194
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	5e-09
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	7e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	9e-05
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-04

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620

 Score = 53.9 bits (130), Expect = 5e-09
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW---------YYDHKI 79
          ++    Q   +  L  +L  S     ESPTG+GK++  +   L++         Y     
Sbjct: 2  YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTN 61

Query: 80 VGLEKIEAKIKDLE 93
             E++  +++ L 
Sbjct: 62 SQEEQVIKELRSLS 75

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540

 Score = 50.7 bits (121), Expect = 7e-08
 Identities = 8/54 (14%), Positives = 18/54 (33%), Gaps = 2/54 (3%)

Query: 27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV 80
                  Q+  +      L + K  +  +  G GK++ +    L      K++
Sbjct: 4  LKLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEV--LGMQLKKKVL 55

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 50.2 bits (119), Expect = 1e-07
 Identities = 30/213 (14%), Positives = 72/213 (33%), Gaps = 33/213 (15%)

Query: 3   SKTPNED-KEFNEQR-PLAEVPSEFPFPFDAYDIQS-NFMKNLYYTLDNSKFGIFESPTG 59
            + P+   + + EQR  L      F   ++   +Q    ++     L  +K  + +   G
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFA-KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG 160

Query: 60  TGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQID 119
           +GK+  +   +      +K+    K++ KI  L +    +        Q    ++     
Sbjct: 161 SGKT-WVALDVCL---SYKV--QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214

Query: 120 ALKDALKSQK-TYDELIENIRK--QNEKRKKSL---RN--DQEVKVHA--------LTYR 163
           +  D   + K     +   +R+  +++  +  L    N  + +   +A        LT R
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA-WNAFNLSCKILLTTR 273

Query: 164 NR-----MDEKNSKEKRKEEERDGL-ENETQEL 190
            +     +    +     +     L  +E + L
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306

>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 = 41.5 bits (97), Expect = 9e-05
 Identities = 11/42 (26%), Positives = 18/42 (42%)

Query: 32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW 73
           D Q      +   L N+      +PTG+GK+L  +   L+ 
Sbjct: 5  RDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV 46

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 38.6 bits (89), Expect = 4e-04
 Identities = 17/91 (18%), Positives = 38/91 (41%), Gaps = 18/91 (19%)

Query: 94  ISKNETVSED------WIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKK 147
           I++ + ++++      W E+Q   L+         DA  S+    E  E  +K  E+  +
Sbjct: 74  IAQADRLTQEPESIRKWREEQRKRLQE-------LDA-ASKVMEQEWREKAKKDLEEWNQ 125

Query: 148 SLRNDQEVKVHALTYRNRMDEKNSKEKRKEE 178
             +++Q  K       NR+ +K   ++   +
Sbjct: 126 R-QSEQVEKNKI---NNRIADKAFYQQPDAD 152

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	194
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.3
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.12
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.08
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	98.76
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	98.74
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	98.74
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.73
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	98.69
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	98.68
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	98.67
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	98.66
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	98.64
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	98.64
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	98.64
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	98.62
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	98.62
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	98.6
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	98.58
3bor_A	237	Human initiation factor 4A-II; translation initiat	98.58
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.55
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	98.55
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	98.53
3b6e_A	216	Interferon-induced helicase C domain-containing P;	98.53
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	98.52
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	98.5
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	98.5
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	98.49
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	98.48
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	98.46
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	98.46
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	98.45
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	98.44
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	98.44
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	98.42
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	98.38
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.36
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	98.34
4gl2_A	699	Interferon-induced helicase C domain-containing P;	98.26
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	98.26
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	98.23
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	98.23
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	98.16
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	98.15
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.14
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	98.14
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.11
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.1
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.06
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	98.06
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	98.03
3h1t_A	590	Type I site-specific restriction-modification syst	97.99
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	97.98
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	97.98
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	97.95
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	97.93
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	97.91
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	97.87
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	97.84
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	97.83
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	97.81
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	97.74
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	97.62
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	97.59
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	97.51
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	97.46
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	97.46
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	97.46
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	97.39
1yks_A	440	Genome polyprotein [contains: flavivirin protease	97.38
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	97.25
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	97.23
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	97.19
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	97.12
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.04
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	97.01
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	96.65
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	96.47
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.46
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	96.37
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.04
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	96.02
3jux_A	822	Protein translocase subunit SECA; protein transloc	95.41
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	95.33
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	95.24
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	95.2
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.19
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	95.1
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	94.98
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	94.93
2r44_A	331	Uncharacterized protein; putative ATPase, structur	94.92
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	94.86
3co5_A	143	Putative two-component system transcriptional RES	94.85
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	94.67
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	94.67
2chg_A	226	Replication factor C small subunit; DNA-binding pr	94.6
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.31
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	94.21
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	94.21
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	94.15
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	94.1
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	94.03
2chq_A	319	Replication factor C small subunit; DNA-binding pr	93.83
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	93.8
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	93.72
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	93.64
2qgz_A	308	Helicase loader, putative primosome component; str	93.62
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	93.58
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	93.46
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	93.45
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	93.25
3bos_A	242	Putative DNA replication factor; P-loop containing	93.25
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	93.12
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	92.94
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	92.86
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	92.85
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	92.81
1p9r_A	418	General secretion pathway protein E; bacterial typ	92.39
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	91.78
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	91.68
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	91.57
2eyu_A	261	Twitching motility protein PILT; pilus retraction	91.56
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	91.56
3pvs_A	447	Replication-associated recombination protein A; ma	91.39
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	91.34
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	91.29
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	91.27
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	91.22
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	90.96
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	90.96
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	90.91
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	90.67
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	90.67
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	90.64
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	90.62
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	90.41
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	90.37
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	90.12
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	90.05
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	89.97
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	89.95
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	89.84
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	89.81
1ry6_A	360	Internal kinesin; kinesin motor domain, nucleotide	89.77
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	89.73
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	89.69
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	89.69
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	89.56
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	89.46
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	89.45
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	89.1
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	89.08
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	88.96
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	88.89
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	88.84
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	88.83
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	88.58
1tue_A	212	Replication protein E1; helicase, replication, E1E	88.56
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	88.51
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	88.39
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	88.15
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	88.15
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	88.1
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	87.87
2ewv_A	372	Twitching motility protein PILT; pilus retraction	87.85
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	87.82
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	87.79
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	87.77
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	87.42
2fna_A	357	Conserved hypothetical protein; structural genomic	87.28
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	87.28
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	87.2
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	87.14
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	87.1
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	86.97
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	86.62
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	86.54
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	86.49
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	86.41
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	85.9
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	85.76
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	85.75
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	85.72
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	85.64
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	85.48
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	85.47
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	85.45
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	85.43
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	85.28
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	85.11
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	85.07
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	84.97
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	84.63
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	84.52
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	84.44
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	84.43
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	84.37
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	84.36
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	84.21
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	84.12
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	83.97
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	83.94
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	83.83
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	83.83
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	83.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	83.56
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	83.53
2cvh_A	220	DNA repair and recombination protein RADB; filamen	83.52
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	83.48
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	83.44
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	83.42
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	83.41
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	83.36
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	83.25
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	83.2
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	83.07
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	83.03
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	82.97
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	82.94
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	82.92
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	82.89
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	82.87
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	82.74
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	82.67
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	82.52
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	82.31
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	82.2
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	81.9
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	81.85
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	81.83
3kta_A	182	Chromosome segregation protein SMC; structural mai	81.77
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	81.71
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	81.68
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	81.48
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	81.44
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	81.43
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	81.31
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	81.24
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	81.23
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	81.19
3auy_A	371	DNA double-strand break repair RAD50 ATPase; DNA r	81.08
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	80.86
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	80.85
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	80.84
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	80.76
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	80.66
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	80.35
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	80.33
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	80.09
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	80.09
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	80.06
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	80.04
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	80.02

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.30  E-value=1.2e-12  Score=123.59  Aligned_cols=52  Identities=25%  Similarity=0.353  Sum_probs=45.6

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      |+|||.|.+||.+|+++|.+|+++|++||||||||++||+|++.|+...+.+
T Consensus         2 ~~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~~k   53 (620)
T 4a15_A            2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLK   53 (620)
T ss_dssp             ---CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHTCE
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcCCe
Confidence            7899999999999999999999999999999999999999999998764433

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.12  E-value=4.8e-11  Score=110.06  Aligned_cols=45  Identities=24%  Similarity=0.282  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      |+|||+|.+||..|+++|..|+++|++||||||||++||+|++.+
T Consensus         2 ~~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~   46 (551)
T 3crv_A            2 VKLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV   46 (551)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC
Confidence            789999999999999999999999999999999999999999873

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.08  E-value=7.4e-11  Score=108.86  Aligned_cols=47  Identities=13%  Similarity=0.145  Sum_probs=40.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .+|+|||+|.+||..|+.++.+|+++|++||||||||++||+|++.+
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            35789999999999999999999999999999999999999999875

>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=98.76  E-value=7.7e-09  Score=83.08  Aligned_cols=46  Identities=24%  Similarity=0.135  Sum_probs=39.0

Q ss_pred             CCC-CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPF-DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy-~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.| .|||+|.+.+..+.    +|+.+|+.||||+|||++|++|++.++..
T Consensus        38 ~g~~~~~~~Q~~~i~~~~----~~~~~l~~apTGsGKT~~~~l~~~~~l~~   84 (228)
T 3iuy_A           38 VGILKPTPIQSQAWPIIL----QGIDLIVVAQTGTGKTLSYLMPGFIHLDS   84 (228)
T ss_dssp             HTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            456 49999999887764    68899999999999999999999987754

>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=98.74  E-value=1.1e-08  Score=80.32  Aligned_cols=47  Identities=17%  Similarity=0.150  Sum_probs=40.0

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .++|. |||+|.+.+..+.    +++.+|+.+|||+|||++|++|++.++..
T Consensus        20 ~~g~~~~~~~Q~~~i~~~~----~~~~~lv~apTGsGKT~~~~~~~~~~~~~   67 (206)
T 1vec_A           20 EMGWEKPSPIQEESIPIAL----SGRDILARAKNGTGKSGAYLIPLLERLDL   67 (206)
T ss_dssp             TTTCCSCCHHHHHHHHHHH----TTCCEEEECCSSSTTHHHHHHHHHHHCCT
T ss_pred             HCCCCCCCHHHHHHHHHHc----cCCCEEEECCCCCchHHHHHHHHHHHhcc
Confidence            36675 9999999877764    67899999999999999999999987654

>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=98.74  E-value=1e-08  Score=83.64  Aligned_cols=47  Identities=19%  Similarity=0.092  Sum_probs=40.9

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+.|. |+|+|.+.+..+.    +|+.+|+.||||+|||++|++|++..+..
T Consensus        46 ~~g~~~~~~~Q~~~i~~~~----~g~~~l~~apTGsGKT~~~~l~~l~~l~~   93 (242)
T 3fe2_A           46 RQNFTEPTAIQAQGWPVAL----SGLDMVGVAQTGSGKTLSYLLPAIVHINH   93 (242)
T ss_dssp             TTTCCSCCHHHHHHHHHHH----HTCCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             HCCCCCCCHHHHHHHHHHh----CCCCEEEECCCcCHHHHHHHHHHHHHHHh
Confidence            35777 9999999887764    67899999999999999999999988764

>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=98.73  E-value=1.4e-08  Score=82.39  Aligned_cols=46  Identities=24%  Similarity=0.295  Sum_probs=39.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |||+|.+.+..+.    +|+.+|+.||||+|||++|++|++.++..
T Consensus        47 ~g~~~~~~~Q~~~i~~~~----~~~~~l~~a~TGsGKT~~~~l~~l~~l~~   93 (245)
T 3dkp_A           47 AGFQMPTPIQMQAIPVML----HGRELLASAPTGSGKTLAFSIPILMQLKQ   93 (245)
T ss_dssp             TTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCCcHHHHHHHHHHHHHhh
Confidence            4676 9999999887764    67889999999999999999999988764

>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=98.69  E-value=2.3e-08  Score=81.68  Aligned_cols=47  Identities=17%  Similarity=0.247  Sum_probs=40.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|. |+|+|.+.+..+.    +|+.+|+.+|||+|||++|++|++.++...
T Consensus        41 ~g~~~~~~~Q~~~i~~i~----~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~   88 (253)
T 1wrb_A           41 ASYQRPTPIQKNAIPAIL----EHRDIMACAQTGSGKTAAFLIPIINHLVCQ   88 (253)
T ss_dssp             TTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHHHhh
Confidence            4565 9999999887764    578999999999999999999999987654

>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=98.68  E-value=1.5e-08  Score=80.73  Aligned_cols=48  Identities=17%  Similarity=0.225  Sum_probs=40.5

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .++|. |||+|.+.+..+.    +++.+|+.+|||+|||++|++|++.++...
T Consensus        31 ~~g~~~~~~~Q~~~i~~~~----~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~   79 (224)
T 1qde_A           31 GYGFEEPSAIQQRAIMPII----EGHDVLAQAQSGTGKTGTFSIAALQRIDTS   79 (224)
T ss_dssp             HHTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHHCCTT
T ss_pred             HCCCCCCcHHHHHHHHHHh----cCCCEEEECCCCCcHHHHHHHHHHHHHhcc
Confidence            35675 9999999887764    678999999999999999999999887543

>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=98.67  E-value=2.4e-08  Score=78.27  Aligned_cols=46  Identities=24%  Similarity=0.147  Sum_probs=39.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+.    +++.+|+.+|||+|||++|++|++.++..
T Consensus        19 ~~~~~~~~~Q~~~i~~~~----~~~~~li~~~TGsGKT~~~~~~~~~~l~~   65 (207)
T 2gxq_A           19 RGLTTPTPIQAAALPLAL----EGKDLIGQARTGTGKTLAFALPIAERLAP   65 (207)
T ss_dssp             TTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHCCC
T ss_pred             cCCCCCCHHHHHHHHHHc----CCCCEEEECCCCChHHHHHHHHHHHHHhh
Confidence            4564 9999999887764    67899999999999999999999998753

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=98.66  E-value=2.9e-08  Score=80.07  Aligned_cols=46  Identities=22%  Similarity=0.282  Sum_probs=39.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+    .+|+.+|+.+|||+|||++|+.|++.++..
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            4565 999999987775    468899999999999999999999988754

>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=98.64  E-value=3.1e-08  Score=80.21  Aligned_cols=46  Identities=17%  Similarity=0.029  Sum_probs=39.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ++|. |||+|.+.+..+    .+|+.+|+.+|||+|||++|++|++..+..
T Consensus        42 ~g~~~~~~~Q~~~i~~~----~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~   88 (230)
T 2oxc_A           42 AGFERPSPVQLKAIPLG----RCGLDLIVQAKSGTGKTCVFSTIALDSLVL   88 (230)
T ss_dssp             TTCCSCCHHHHHHHHHH----HTTCCEEEECCTTSSHHHHHHHHHHHHCCT
T ss_pred             CCCCCCCHHHHHHHHHH----hCCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            5676 999999988775    468899999999999999999999887653

>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=98.64  E-value=3.8e-08  Score=81.46  Aligned_cols=48  Identities=19%  Similarity=0.135  Sum_probs=41.0

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +.|. ||++|.+.+..+.    +|+.+|+.+|||+|||++|++|++..+....
T Consensus        61 ~g~~~~~~~Q~~~i~~i~----~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~  109 (249)
T 3ber_A           61 LGWTKPTKIQIEAIPLAL----QGRDIIGLAETGSGKTGAFALPILNALLETP  109 (249)
T ss_dssp             TTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHHHHSC
T ss_pred             cCCCCCCHHHHHHHHHHh----CCCCEEEEcCCCCCchhHhHHHHHHHHhcCC
Confidence            5674 9999999887764    6789999999999999999999998776543

>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=98.64  E-value=3.2e-08  Score=78.82  Aligned_cols=46  Identities=13%  Similarity=0.195  Sum_probs=40.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+.    +++.+|+.+|||+|||++|++|++..+..
T Consensus        32 ~g~~~~~~~Q~~~i~~~~----~~~~~li~~~TGsGKT~~~~~~~~~~~~~   78 (220)
T 1t6n_A           32 CGFEHPSEVQHECIPQAI----LGMDVLCQAKSGMGKTAVFVLATLQQLEP   78 (220)
T ss_dssp             TTCCCCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCCchhhhhhHHHHHhhhc
Confidence            6777 9999999887764    57889999999999999999999988654

>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=98.62  E-value=3.8e-08  Score=82.01  Aligned_cols=46  Identities=20%  Similarity=0.330  Sum_probs=39.5

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+.    .++.+|+.||||+|||++|++|++..+..
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            3566 9999999887764    46889999999999999999999988765

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=98.62  E-value=2.2e-08  Score=80.09  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=39.5

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+.    +|+.+|+.+|||+|||++|++|++..+..
T Consensus        22 ~g~~~~~~~Q~~~i~~~~----~~~~~lv~a~TGsGKT~~~~~~~l~~l~~   68 (219)
T 1q0u_A           22 LRFYKPTEIQERIIPGAL----RGESMVGQSQTGTGKTHAYLLPIMEKIKP   68 (219)
T ss_dssp             TTCCSCCHHHHHHHHHHH----HTCCEEEECCSSHHHHHHHHHHHHHHCCT
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHHHh
Confidence            4554 9999999887764    57899999999999999999999988764

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=98.60  E-value=2.6e-08  Score=86.52  Aligned_cols=47  Identities=23%  Similarity=0.159  Sum_probs=39.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|+|+|+|+|.+.+..+.    +|+.+|+.||||+|||++|+.+++..+..
T Consensus        17 ~~~~~~~~~Q~~~i~~i~----~~~~~lv~apTGsGKT~~~l~~~~~~~~~   63 (414)
T 3oiy_A           17 KFGKDLTGYQRLWAKRIV----QGKSFTMVAPTGVGKTTFGMMTALWLARK   63 (414)
T ss_dssp             HHSSCCCHHHHHHHHHHT----TTCCEECCSCSSSSHHHHHHHHHHHHHTT
T ss_pred             hcCCCCCHHHHHHHHHHh----cCCCEEEEeCCCCCHHHHHHHHHHHHhcC
Confidence            368899999999887764    67899999999999999999998776633

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=98.58  E-value=6.2e-08  Score=82.99  Aligned_cols=48  Identities=17%  Similarity=0.249  Sum_probs=40.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +.|. |+|+|.+.+..+    ..|+.+|+.||||+|||++|++|++..+...+
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            4564 999999988765    47889999999999999999999998876543

>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=98.58  E-value=2.7e-08  Score=81.05  Aligned_cols=46  Identities=22%  Similarity=0.234  Sum_probs=39.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ++|. |+|+|.+.+..+.    +|+.+|+.+|||+|||++|++|++..+..
T Consensus        48 ~g~~~~~~~Q~~ai~~i~----~~~~~li~apTGsGKT~~~~l~~l~~l~~   94 (237)
T 3bor_A           48 YGFEKPSAIQQRAIIPCI----KGYDVIAQAQSGTGKTATFAISILQQLEI   94 (237)
T ss_dssp             HTCCSCCHHHHHHHHHHH----TTCCEEECCCSSHHHHHHHHHHHHHHCCT
T ss_pred             CCCCCCCHHHHHHHHHHh----CCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            5677 9999999887764    67889999999999999999999988754

>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=98.55  E-value=5e-08  Score=83.39  Aligned_cols=49  Identities=22%  Similarity=0.302  Sum_probs=39.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhc-CCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDN-SKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~-gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +.|. |+++|.+.+..+.   .. ++++|+.||||||||++|++|++..+....
T Consensus       110 ~g~~~pt~iQ~~ai~~il---~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~  160 (300)
T 3fmo_B          110 MGFNRPSKIQENALPLML---AEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN  160 (300)
T ss_dssp             TTCCSCCHHHHHHHHHHT---SSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTS
T ss_pred             cCCCCCCHHHHHHHHHHH---cCCCCeEEEECCCCCCccHHHHHHHHHhhhccC
Confidence            4565 9999999877663   22 389999999999999999999998876543

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=98.55  E-value=7.7e-08  Score=84.81  Aligned_cols=46  Identities=20%  Similarity=0.200  Sum_probs=40.8

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ||+|||+|.+.+..+.    .|+.+|+.+|||+|||++|++|++..+...
T Consensus         2 ~~~~~~~Q~~~i~~~~----~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~   47 (555)
T 3tbk_A            2 PLKPRNYQLELALPAK----KGKNTIICAPTGCGKTFVSLLICEHHLKKF   47 (555)
T ss_dssp             CCCCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCcHHHHHHHHHHh----CCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            7899999999887763    678999999999999999999999887764

>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=98.53  E-value=9.6e-08  Score=84.81  Aligned_cols=47  Identities=17%  Similarity=0.204  Sum_probs=41.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +.|. |+|+|.+.+..+    .+|+.+|+.||||||||++|++|++..+...
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 999999988775    4789999999999999999999999987654

>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=98.53  E-value=7.4e-08  Score=75.31  Aligned_cols=48  Identities=17%  Similarity=0.070  Sum_probs=40.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+.+.|||+|.+.+..+.    +++.+|+.+|||+|||++++++++.++...
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            345779999999887764    578899999999999999999988876543

>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=98.52  E-value=6.6e-08  Score=87.40  Aligned_cols=49  Identities=22%  Similarity=0.357  Sum_probs=42.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ++|. |+|+|.+.+..++   . .++.+|+.||||||||++|++|++.++...+
T Consensus        90 ~g~~~~~~~Q~~~i~~~l---~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~  140 (563)
T 3i5x_A           90 MEFPGLTPVQQKTIKPIL---SSEDHDVIARAKTGTGKTFAFLIPIFQHLINTK  140 (563)
T ss_dssp             TCCSSCCHHHHHHHHHHH---SSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCHHHHHHHHHHh---cCCCCeEEEECCCCCCccHHHHHHHHHHHHhcc
Confidence            6777 9999999887764   3 4689999999999999999999999887654

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=98.50  E-value=7.3e-08  Score=88.42  Aligned_cols=50  Identities=22%  Similarity=0.344  Sum_probs=42.5

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .++|. |+|+|.+.+..+.   . .++.+|+.||||+|||++|++|++..+...+
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            47887 9999999887764   3 4789999999999999999999999887653

>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=98.50  E-value=7.5e-08  Score=81.93  Aligned_cols=51  Identities=22%  Similarity=0.268  Sum_probs=40.7

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .+.|. |+|+|.+.+..+...  .++.+|+.+|||+|||++|++|++..+....
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            35675 999999988776421  2489999999999999999999998776443

>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=98.49  E-value=8.5e-08  Score=82.39  Aligned_cols=45  Identities=24%  Similarity=0.391  Sum_probs=39.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ++|. |+|+|.+.+..+.    +|+.+|+.+|||+|||++|++|++..+.
T Consensus        55 ~g~~~~~~~Q~~ai~~i~----~~~~~lv~a~TGsGKT~~~~~~~~~~l~  100 (410)
T 2j0s_A           55 YGFEKPSAIQQRAIKQII----KGRDVIAQSQSGTGKTATFSISVLQCLD  100 (410)
T ss_dssp             HTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHTCC
T ss_pred             cCCCCCCHHHHHHHHHHh----CCCCEEEECCCCCCchHHHHHHHHHHHh
Confidence            5676 9999999887764    6788999999999999999999998765

>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=98.48  E-value=1.6e-07  Score=77.62  Aligned_cols=42  Identities=24%  Similarity=0.349  Sum_probs=36.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ++|. |||+|.+.+..+.    +++.+|+.+|||+|||++|+.|++.
T Consensus        12 ~g~~~l~~~Q~~~i~~i~----~~~~~lv~~~TGsGKT~~~~~~~~~   54 (337)
T 2z0m_A           12 MGFKNFTEVQSKTIPLML----QGKNVVVRAKTGSGKTAAYAIPILE   54 (337)
T ss_dssp             TTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHh----cCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            5665 9999999877654    6789999999999999999999775

>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=98.46  E-value=1.1e-07  Score=80.08  Aligned_cols=48  Identities=23%  Similarity=0.254  Sum_probs=38.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+...  .++.+|+.+|||+|||++|+.+++..+..
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            4555 999999988776421  23899999999999999999999887653

>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=98.46  E-value=1.8e-07  Score=79.91  Aligned_cols=46  Identities=22%  Similarity=0.228  Sum_probs=39.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |+|+|.+.+..+.    .|+.+|+.+|||+|||++|+++++..+..
T Consensus        58 ~~~~~~~~~Q~~~i~~~~----~~~~~lv~a~TGsGKT~~~~~~~~~~~~~  104 (414)
T 3eiq_A           58 YGFEKPSAIQQRAILPCI----KGYDVIAQAQSGTGKTATFAISILQQIEL  104 (414)
T ss_dssp             TTCCSCCHHHHHHHHHHH----TTCCEEECCCSCSSSHHHHHHHHHHHCCT
T ss_pred             cCCCCCCHHHHHHhHHHh----CCCCEEEECCCCCcccHHHHHHHHHHHhh
Confidence            5675 9999999887764    57889999999999999999999987754

>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=98.45  E-value=1.1e-07  Score=80.45  Aligned_cols=46  Identities=13%  Similarity=0.195  Sum_probs=39.5

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ++|. |||+|.+.+..+.    .++.+|+.+|||+|||++|++|++..+..
T Consensus        26 ~g~~~~~~~Q~~~i~~~~----~~~~~lv~a~TGsGKT~~~~~~~~~~l~~   72 (391)
T 1xti_A           26 CGFEHPSEVQHECIPQAI----LGMDVLCQAKSGMGKTAVFVLATLQQLEP   72 (391)
T ss_dssp             HSCCSCCHHHHHHHHHHT----TTCCEEEECSSCSSHHHHHHHHHHHHCCC
T ss_pred             CCCCCCCHHHHHHHHHHh----cCCcEEEECCCCCcHHHHHHHHHHHhhcc
Confidence            5676 9999999877763    57899999999999999999999887654

>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=98.44  E-value=1.9e-07  Score=82.78  Aligned_cols=47  Identities=21%  Similarity=0.207  Sum_probs=37.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+|+|||+|.+.+..+.    +|+.+|+.+|||+|||++|+.|++..+...
T Consensus         4 ~~~~~~~~Q~~~i~~~~----~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~   50 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAI----NGKNALICAPTGSGKTFVSILICEHHFQNM   50 (556)
T ss_dssp             ----CCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHHH----cCCCEEEEcCCCChHHHHHHHHHHHHHHhC
Confidence            47889999999877763    578899999999999999999998887654

>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=98.44  E-value=1.8e-07  Score=79.82  Aligned_cols=46  Identities=17%  Similarity=0.170  Sum_probs=39.5

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |||+|.+.+..+.    +++.+|+.+|||+|||++|++|++..+..
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            4576 9999999887764    56889999999999999999999987754

>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=98.42  E-value=9.9e-08  Score=80.72  Aligned_cols=46  Identities=17%  Similarity=0.247  Sum_probs=39.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ++|. |||+|.+.+..+.    +++.+|+.+|||+|||++|++|++.++..
T Consensus        39 ~g~~~~~~~Q~~~i~~i~----~~~~~lv~~~TGsGKT~~~~~~~~~~l~~   85 (394)
T 1fuu_A           39 YGFEEPSAIQQRAIMPII----EGHDVLAQAQSGTGKTGTFSIAALQRIDT   85 (394)
T ss_dssp             HTCCSCCHHHHHHHHHHH----HTCCEEECCCSSHHHHHHHHHHHHHHCCT
T ss_pred             cCCCCCCHHHHHHHHHHh----CCCCEEEECCCCChHHHHHHHHHHHHhhc
Confidence            5664 9999999887764    47889999999999999999999988754

>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=98.38  E-value=2.8e-07  Score=76.75  Aligned_cols=47  Identities=21%  Similarity=0.316  Sum_probs=38.9

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|. |||+|.+.+..+   +..++.+|+.+|||+|||++++++++.++..
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            4554 999999977766   3445799999999999999999999887754

>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=98.36  E-value=1.3e-07  Score=83.88  Aligned_cols=50  Identities=22%  Similarity=0.290  Sum_probs=40.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +.|. |+|+|.+.+..+..  ..++++|+.||||||||++|++|++..+....
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            4565 99999998877642  12489999999999999999999988776543

>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=98.34  E-value=3e-07  Score=86.24  Aligned_cols=43  Identities=26%  Similarity=0.227  Sum_probs=37.8

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|+|. |+|+|.+.+..|.    +|+.+|+.+|||+|||++|++|++.
T Consensus        39 ~fg~~~~rp~Q~~~i~~il----~g~d~lv~~pTGsGKTl~~~lpal~   82 (591)
T 2v1x_A           39 VFKLEKFRPLQLETINVTM----AGKEVFLVMPTGGGKSLCYQLPALC   82 (591)
T ss_dssp             TSCCCSCCTTHHHHHHHHH----TTCCEEEECCTTSCTTHHHHHHHHT
T ss_pred             HhCCCCCCHHHHHHHHHHH----cCCCEEEEECCCChHHHHHHHHHHH
Confidence            47886 9999999888764    5889999999999999999999874

>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=98.26  E-value=6.9e-07  Score=82.60  Aligned_cols=46  Identities=17%  Similarity=0.076  Sum_probs=38.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +|.|||+|.+.+..+.    +|+.+|+.+|||+|||++|+.|++..+...
T Consensus         5 ~~~l~~~Q~~~i~~il----~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~   50 (699)
T 4gl2_A            5 MLQLRPYQMEVAQPAL----EGKNIIICLPTGCGKTRVAVYIAKDHLDKK   50 (699)
T ss_dssp             --CCCHHHHHHHHHHH----SSCCEEECCCTTSCHHHHHHHHHHHHHHHH
T ss_pred             CCCccHHHHHHHHHHH----hCCCEEEEcCCCCcHHHHHHHHHHHHHHhc
Confidence            5789999999877764    478999999999999999999998877665

>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=98.26  E-value=1e-06  Score=85.78  Aligned_cols=52  Identities=17%  Similarity=0.274  Sum_probs=46.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+||+|+++|.+.+..|...+..+  ..+|+.+|||||||++|+.|++..+...
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  4899999999999999999999877543

>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=98.23  E-value=4.3e-07  Score=83.47  Aligned_cols=43  Identities=23%  Similarity=0.293  Sum_probs=37.6

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|+|. |||+|.+.+..+.    +|+.+|+.+|||+|||++|++|++.
T Consensus        20 ~~g~~~~r~~Q~~~i~~il----~g~d~lv~apTGsGKTl~~~lp~l~   63 (523)
T 1oyw_A           20 TFGYQQFRPGQEEIIDTVL----SGRDCLVVMPTGGGKSLCYQIPALL   63 (523)
T ss_dssp             TTCCSSCCTTHHHHHHHHH----TTCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             HhCCCCCCHHHHHHHHHHH----cCCCEEEECCCCcHHHHHHHHHHHH
Confidence            47886 9999999887764    6789999999999999999999874

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=98.23  E-value=1.2e-06  Score=80.88  Aligned_cols=48  Identities=17%  Similarity=0.099  Sum_probs=39.7

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|+|. |||+|.+.+..+.    .|+++|+.+|||+|||++|+.|++..+...
T Consensus         8 ~~g~~~lr~~Q~~~i~~~l----~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~   56 (696)
T 2ykg_A            8 LYSPFKPRNYQLELALPAM----KGKNTIICAPTGCGKTFVSLLICEHHLKKF   56 (696)
T ss_dssp             TTC--CCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHHHHHS
T ss_pred             ccCCCCccHHHHHHHHHHH----cCCCEEEEcCCCchHHHHHHHHHHHHHHhC
Confidence            45654 9999999887763    588999999999999999999999887654

>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=98.16  E-value=2.2e-06  Score=86.04  Aligned_cols=52  Identities=15%  Similarity=0.236  Sum_probs=44.1

Q ss_pred             CccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        23 ~~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ....|||.|+|+|.+.+..|    .+|..+|+.||||+|||++|++|++..+...+
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            35568999999999977765    67899999999999999999999988775443

>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=98.15  E-value=2.3e-06  Score=86.12  Aligned_cols=52  Identities=15%  Similarity=0.181  Sum_probs=46.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|||+|+|+|.+.+..|...+.+++  .+|+.+|||+|||++++.+++..+...
T Consensus       599 ~f~~~~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~g  652 (1151)
T 2eyq_A          599 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH  652 (1151)
T ss_dssp             TCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT
T ss_pred             hCCCCCCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHhC
Confidence            5899999999999999999888886  899999999999999999988766544

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=98.14  E-value=2.8e-06  Score=84.57  Aligned_cols=50  Identities=16%  Similarity=0.234  Sum_probs=42.7

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ...|||+|+|+|.+.+..|    .+|+.+|+.+|||+|||++|+++++..+...
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            4568999999999987765    5688999999999999999999988877543

>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=98.14  E-value=9.9e-07  Score=74.93  Aligned_cols=42  Identities=17%  Similarity=0.057  Sum_probs=36.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      |.|||.|.+.+..+.    .+ .+|+.+|||+|||++++++++..+.
T Consensus         8 ~~l~~~Q~~~i~~~~----~~-~~ll~~~tG~GKT~~~~~~~~~~~~   49 (494)
T 1wp9_A            8 IQPRIYQEVIYAKCK----ET-NCLIVLPTGLGKTLIAMMIAEYRLT   49 (494)
T ss_dssp             HCCCHHHHHHHHHGG----GS-CEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHh----hC-CEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            789999999877664    34 8999999999999999999888765

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=98.11  E-value=3.5e-06  Score=83.77  Aligned_cols=49  Identities=16%  Similarity=0.194  Sum_probs=41.3

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ...|||+++|+|.+.+..|    .+|+.+|+.+|||+|||++|+.+++..+..
T Consensus        33 ~~~~~f~l~~~Q~~aI~~i----l~g~~vlv~apTGsGKTlv~~~~i~~~~~~   81 (997)
T 4a4z_A           33 ARSWPFELDTFQKEAVYHL----EQGDSVFVAAHTSAGKTVVAEYAIAMAHRN   81 (997)
T ss_dssp             SCCCSSCCCHHHHHHHHHH----HTTCEEEEECCTTSCSHHHHHHHHHHHHHT
T ss_pred             HHhCCCCCCHHHHHHHHHH----HcCCCEEEEECCCCcHHHHHHHHHHHHHhc
Confidence            4579999999999876655    578999999999999999999987776544

>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=98.10  E-value=3.2e-06  Score=74.69  Aligned_cols=45  Identities=24%  Similarity=0.299  Sum_probs=37.2

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .+.|+|.|||.|.+.+..+.    .+..+|+.+|||+|||++++.++..
T Consensus        87 ~~~~~~~l~~~Q~~ai~~i~----~~~~~ll~~~TGsGKT~~~l~~i~~  131 (472)
T 2fwr_A           87 YFDAEISLRDYQEKALERWL----VDKRGCIVLPTGSGKTHVAMAAINE  131 (472)
T ss_dssp             CCCCCCCBCHHHHHHHHHHT----TTTEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccCCCCcCHHHHHHHHHHH----hcCCEEEEeCCCCCHHHHHHHHHHH
Confidence            45678899999999777653    4567999999999999999988664

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=98.06  E-value=3.3e-06  Score=75.35  Aligned_cols=47  Identities=15%  Similarity=0.070  Sum_probs=39.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +|+|||.|.+.+..+..    +..+|+.+|||+|||++++.+++..+...+
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            67999999998877653    478999999999999999999887765443

>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=98.06  E-value=4.4e-06  Score=69.02  Aligned_cols=45  Identities=24%  Similarity=0.299  Sum_probs=35.8

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .+.|+|.++++|.+.+..+.    .+..+|+.+|||+|||+.++.++..
T Consensus        87 ~~~~~~~l~~~Q~~ai~~~~----~~~~~ll~~~tG~GKT~~a~~~~~~  131 (237)
T 2fz4_A           87 YFDAEISLRDYQEKALERWL----VDKRGCIVLPTGSGKTHVAMAAINE  131 (237)
T ss_dssp             CCCCCCCCCHHHHHHHHHHT----TTSEEEEEESSSTTHHHHHHHHHHH
T ss_pred             cccCCCCcCHHHHHHHHHHH----hCCCEEEEeCCCCCHHHHHHHHHHH
Confidence            45567789999999776643    4556999999999999998887654

>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=98.03  E-value=4.9e-06  Score=79.48  Aligned_cols=46  Identities=22%  Similarity=0.217  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ++.|||+|.+.+..+    ..|+.+|+.+|||+|||++|++|++..+...
T Consensus       246 ~~~l~~~Q~~~i~~~----l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~  291 (797)
T 4a2q_A          246 TKKARSYQIELAQPA----INGKNALICAPTGSGKTFVSILICEHHFQNM  291 (797)
T ss_dssp             --CCCHHHHHHHHHH----HTTCCEEEECCTTSCHHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHH----HhCCCEEEEeCCCChHHHHHHHHHHHHHHhc
Confidence            346999999977766    3578999999999999999999998887664

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=97.99  E-value=8.7e-06  Score=74.51  Aligned_cols=47  Identities=17%  Similarity=0.145  Sum_probs=37.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.|||+|.+.++.+.+++.++ ..+++.+|||||||++++..+...+.
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            379999999999999999876 55899999999999997765544443

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=97.98  E-value=5.2e-06  Score=83.40  Aligned_cols=47  Identities=23%  Similarity=0.159  Sum_probs=39.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .++|.|+|+|.+.+..+.    +|+.+|+.||||||||++||.+++..+..
T Consensus        74 ~~gf~pt~iQ~~ai~~il----~g~dvlv~ApTGSGKTl~~l~~il~~~~~  120 (1104)
T 4ddu_A           74 KFGKDLTGYQRLWAKRIV----QGKSFTMVAPTGVGKTTFGMMTALWLARK  120 (1104)
T ss_dssp             HSSSCCCHHHHHHHHHHT----TTCCEEECCSTTCCHHHHHHHHHHHHHTT
T ss_pred             hcCCCCCHHHHHHHHHHH----cCCCEEEEeCCCCcHHHHHHHHHHHHHhc
Confidence            478899999999877763    57899999999999999998888776643

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=97.98  E-value=4.2e-06  Score=78.45  Aligned_cols=47  Identities=26%  Similarity=0.290  Sum_probs=39.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ++|. +||+|.+.+..+   +.+++++|+.||||+|||+++..+++..+..
T Consensus        26 ~g~~~l~~~Q~~~i~~~---~~~~~~~lv~apTGsGKT~~~~l~il~~~~~   73 (715)
T 2va8_A           26 RGIKKLNPPQTEAVKKG---LLEGNRLLLTSPTGSGKTLIAEMGIISFLLK   73 (715)
T ss_dssp             TSCCBCCHHHHHHHHTT---TTTTCCEEEECCTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH---hcCCCcEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence            6884 999999977662   4568999999999999999999999876653

>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=97.95  E-value=1.1e-05  Score=67.24  Aligned_cols=44  Identities=16%  Similarity=0.089  Sum_probs=35.8

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +.|+|+|.+.+..+..    +..+|+.+|||+|||++++.++..++..
T Consensus       112 ~~l~~~Q~~ai~~~l~----~~~~ll~~~tGsGKT~~~~~~~~~~~~~  155 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLV----NRRRILNLPTSAGRSLIQALLARYYLEN  155 (282)
T ss_dssp             CCCCHHHHHHHHHHHH----HSEEEECCCTTSCHHHHHHHHHHHHHHH
T ss_pred             cCccHHHHHHHHHHHh----cCCeEEEcCCCCCcHHHHHHHHHHHHHc
Confidence            6899999998776543    3567889999999999998887776653

>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=97.93  E-value=4.1e-06  Score=78.86  Aligned_cols=48  Identities=19%  Similarity=0.236  Sum_probs=40.1

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ++|. |||+|.+.+..+   +.+++++|+.+|||+|||+++..+++..+...
T Consensus        19 ~g~~~l~~~Q~~~i~~~---~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~   67 (720)
T 2zj8_A           19 RGIESFYPPQAEALKSG---ILEGKNALISIPTASGKTLIAEIAMVHRILTQ   67 (720)
T ss_dssp             TTCCBCCHHHHHHHTTT---GGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH---hcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC
Confidence            6784 999999977652   35689999999999999999999998776643

>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=97.87  E-value=1.1e-05  Score=65.84  Aligned_cols=46  Identities=17%  Similarity=0.263  Sum_probs=36.9

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ++..+++|.+.+..|    ..|+++++.||||||||..+.++++..+...
T Consensus        59 ~~p~~~~q~~~i~~i----~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~  104 (235)
T 3llm_A           59 LLPVKKFESEILEAI----SQNSVVIIRGATGCGKTTQVPQFILDDFIQN  104 (235)
T ss_dssp             TSGGGGGHHHHHHHH----HHCSEEEEECCTTSSHHHHHHHHHHHHHHHT
T ss_pred             cCChHHHHHHHHHHH----hcCCEEEEEeCCCCCcHHhHHHHHhcchhhc
Confidence            455788888877765    5789999999999999998888877755443

>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=97.84  E-value=4.3e-06  Score=78.53  Aligned_cols=46  Identities=15%  Similarity=0.168  Sum_probs=37.7

Q ss_pred             CCC-CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPF-DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy-~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ++| .|||+|.+.+..+    .+++++|+.+|||+|||+++..+++..+..
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            677 4999999987774    468999999999999999999998876653

>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=97.83  E-value=1.1e-05  Score=79.23  Aligned_cols=46  Identities=22%  Similarity=0.217  Sum_probs=38.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ++.|+|+|.+.+..+    .+|+.+|+.+|||+|||++|+.|++..+...
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            456999999987776    3578999999999999999999998876653

>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=97.81  E-value=1.5e-05  Score=79.47  Aligned_cols=46  Identities=17%  Similarity=0.117  Sum_probs=38.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      |+|.| |+|.+.+..+.    +|+++|+.||||||||+ |++|++.++...+
T Consensus        54 ~g~~p-~iQ~~ai~~il----~g~dvlv~apTGSGKTl-~~lp~l~~~~~~~   99 (1054)
T 1gku_B           54 VGEPR-AIQKMWAKRIL----RKESFAATAPTGVGKTS-FGLAMSLFLALKG   99 (1054)
T ss_dssp             TCSCC-HHHHHHHHHHH----TTCCEECCCCBTSCSHH-HHHHHHHHHHTTS
T ss_pred             cCCCH-HHHHHHHHHHH----hCCCEEEEcCCCCCHHH-HHHHHHHHHhhcC
Confidence            56668 99999888764    68899999999999999 8888888776544

>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=97.74  E-value=2.4e-05  Score=77.33  Aligned_cols=41  Identities=22%  Similarity=0.131  Sum_probs=34.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      ..|.|||+|..-+..+.    +|+  |.+|+||+||||+|++|++..
T Consensus        80 lG~~pt~VQ~~~ip~ll----~G~--Iaea~TGeGKTlaf~LP~~l~  120 (844)
T 1tf5_A           80 TGMFPFKVQLMGGVALH----DGN--IAEMKTGEGKTLTSTLPVYLN  120 (844)
T ss_dssp             HSCCCCHHHHHHHHHHH----TTS--EEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCcHHHHHhhHHHh----CCC--EEEccCCcHHHHHHHHHHHHH
Confidence            45689999999777653    566  999999999999999998843

>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=97.62  E-value=9.6e-05  Score=77.44  Aligned_cols=49  Identities=27%  Similarity=0.386  Sum_probs=41.1

Q ss_pred             CCC-CC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFP-FD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fP-y~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|| |+ +.++|......+   +..++++++.||||+|||+++.++++..+..+
T Consensus        73 ~f~g~~~ln~iQs~~~~~a---l~~~~N~lv~APTGsGKTlva~l~il~~l~~~  123 (1724)
T 4f92_B           73 GFEGFKTLNRIQSKLYRAA---LETDENLLLCAPTGAGKTNVALMCMLREIGKH  123 (1724)
T ss_dssp             TCTTCSBCCHHHHHTHHHH---HTCCCCEEEECCTTSCCHHHHHHHHHHHHGGG
T ss_pred             hcCCCCCCCHHHHHHHHHH---HcCCCcEEEEeCCcchHHHHHHHHHHHHHHhh
Confidence            365 77 899999966554   57889999999999999999999999887653

>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=97.59  E-value=7.4e-05  Score=78.27  Aligned_cols=47  Identities=23%  Similarity=0.430  Sum_probs=39.5

Q ss_pred             CCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         28 PFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        28 Py~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|. +.|+|.+.+..||   ..+.++++.||||+|||+++.+|++..+...
T Consensus       923 ~f~~fnpiQ~q~~~~l~---~~~~nvlv~APTGSGKTliaelail~~l~~~  970 (1724)
T 4f92_B          923 KFPFFNPIQTQVFNTVY---NSDDNVFVGAPTGSGKTICAEFAILRMLLQS  970 (1724)
T ss_dssp             TCSBCCHHHHHHHHHHH---SCCSCEEEECCTTSCCHHHHHHHHHHHHHHC
T ss_pred             cCCCCCHHHHHHHHHHh---cCCCcEEEEeCCCCCchHHHHHHHHHHHHhC
Confidence            355 8899999777764   6678999999999999999999999877654

>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=97.51  E-value=0.00022  Score=63.35  Aligned_cols=48  Identities=13%  Similarity=-0.042  Sum_probs=38.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .+...+||.|.+.+..+......+..+|+-.|||+|||+..|+.+...
T Consensus        33 ~~~~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i~~~   80 (500)
T 1z63_A           33 NIKANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDA   80 (500)
T ss_dssp             SCSSCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHHHH
T ss_pred             hhhccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHHHHH
Confidence            344569999999988887777778889999999999999977654443

>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=97.46  E-value=8.6e-05  Score=74.05  Aligned_cols=41  Identities=22%  Similarity=0.203  Sum_probs=34.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      +.|.|||+|..-+..+.    +|+  |.+++||+||||++++|++..
T Consensus       108 lG~rP~~VQ~~~ip~Ll----~G~--Iaem~TGeGKTLa~~LP~~l~  148 (922)
T 1nkt_A          108 LDQRPFDVQVMGAAALH----LGN--VAEMKTGEGKTLTCVLPAYLN  148 (922)
T ss_dssp             HSCCCCHHHHHHHHHHH----TTE--EEECCTTSCHHHHTHHHHHHH
T ss_pred             cCCCCCHHHHHHHHhHh----cCC--EEEecCCCccHHHHHHHHHHH
Confidence            56789999999776653    565  999999999999999998643

>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=97.46  E-value=0.0001  Score=73.00  Aligned_cols=41  Identities=27%  Similarity=0.210  Sum_probs=33.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      +.+.|||+|..-+..+    .+|+  |.+++||||||++|++|++..
T Consensus        71 lg~~p~~VQ~~~i~~l----l~G~--Iaem~TGsGKTlaf~LP~l~~  111 (853)
T 2fsf_A           71 FGMRHFDVQLLGGMVL----NERC--IAEMRTGEGKTLTATLPAYLN  111 (853)
T ss_dssp             HSCCCCHHHHHHHHHH----HSSE--EEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCChHHHhhcccc----cCCe--eeeecCCchHHHHHHHHHHHH
Confidence            4467999999976655    3565  999999999999999998853

>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=97.46  E-value=3e-05  Score=69.87  Aligned_cols=35  Identities=17%  Similarity=0.330  Sum_probs=29.6

Q ss_pred             HHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         44 YTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        44 ~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .+|.+++++|+.+|||||||++|+.|++..+...+
T Consensus        16 ~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~~   50 (459)
T 2z83_A           16 NMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQR   50 (459)
T ss_dssp             GGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHTT
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhCC
Confidence            45677899999999999999999999998765443

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=97.39  E-value=8.5e-06  Score=77.95  Aligned_cols=49  Identities=16%  Similarity=0.247  Sum_probs=36.0

Q ss_pred             CCCHHHH-----HHHHHHH--HHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         30 DAYDIQS-----NFMKNLY--YTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        30 ~py~iQ~-----e~M~~I~--~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .|.++|.     ..+..+.  .++..++++|+.||||||||++|++|++..+...+
T Consensus       215 ~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~~  270 (673)
T 2wv9_A          215 YVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQKR  270 (673)
T ss_dssp             EEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHTT
T ss_pred             ccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhCC
Confidence            4788998     5444433  33457899999999999999999999998765544

>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=97.38  E-value=4.8e-05  Score=68.26  Aligned_cols=34  Identities=18%  Similarity=0.245  Sum_probs=29.0

Q ss_pred             HHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ++.+|+++|+.||||||||++|++|++..+...+
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~~   37 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRR   37 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhcC
Confidence            4567899999999999999999999988665544

>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=97.25  E-value=0.00019  Score=71.98  Aligned_cols=46  Identities=15%  Similarity=0.170  Sum_probs=37.7

Q ss_pred             CCCHHHHHHHHHHHHHHhc----------CCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDN----------SKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~----------gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .|||+|...+..+..++..          ++.+|+.+|||||||+++ ++++.++..
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            4999999999999988754          367999999999999997 565666543

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=97.23  E-value=0.00023  Score=71.42  Aligned_cols=40  Identities=28%  Similarity=0.275  Sum_probs=33.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ..|.|||+|..-+..+    -+|+  |.++.||+|||+++++|++.
T Consensus        76 lG~~Pt~VQ~~~ip~L----lqG~--IaeakTGeGKTLvf~Lp~~L  115 (997)
T 2ipc_A           76 LGMRHFDVQLIGGAVL----HEGK--IAEMKTGEGKTLVATLAVAL  115 (997)
T ss_dssp             TCCCCCHHHHHHHHHH----HTTS--EEECCSTHHHHHHHHHHHHH
T ss_pred             hCCCCcHHHHhhcccc----cCCc--eeeccCCCchHHHHHHHHHH
Confidence            5678999999977665    3566  99999999999999999854

>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=97.19  E-value=9.5e-05  Score=66.31  Aligned_cols=33  Identities=15%  Similarity=0.323  Sum_probs=26.6

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +..+.++|+.+|||||||++|++|+|..+...+
T Consensus        16 l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~   48 (451)
T 2jlq_A           16 FRKKRLTIMDLHPGAGKTKRILPSIVREALLRR   48 (451)
T ss_dssp             GSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTT
T ss_pred             HhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcC
Confidence            455566799999999999999999987665544

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=97.12  E-value=0.00018  Score=64.30  Aligned_cols=30  Identities=10%  Similarity=0.298  Sum_probs=25.3

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      |+++|+.+|||||||++|+.|++..+...+
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l~~~~~~g   31 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLVREAVKKR   31 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHhCC
Confidence            678999999999999999999986554444

>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=97.04  E-value=0.0011  Score=59.59  Aligned_cols=55  Identities=20%  Similarity=0.201  Sum_probs=42.7

Q ss_pred             ccCCCCC-CCHHHHHHHHHHHHHHhcCC-ceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         24 EFPFPFD-AYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        24 ~~~fPy~-py~iQ~e~M~~I~~~L~~gk-~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      -.+.+|. .-+.|.+.+..+..+|..+. +++|.||.|||||. +|...+.|+...+.
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            3556676 77999999999998888775 99999999999995 45666777766554

>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=97.01  E-value=0.00019  Score=67.82  Aligned_cols=44  Identities=11%  Similarity=0.169  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      |.|+|..   . ..++.+++++|+.||||||||++|++|+|..+...+
T Consensus       172 ~lpiq~~---~-i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~~  215 (618)
T 2whx_A          172 GEPDYEV---D-EDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKRR  215 (618)
T ss_dssp             CCCCCCC---C-GGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT
T ss_pred             CCCcccc---C-HHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhCC
Confidence            5666654   2 556678999999999999999999999998776543

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=96.65  E-value=0.0032  Score=60.52  Aligned_cols=46  Identities=17%  Similarity=0.164  Sum_probs=39.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      ....||.|.+.++.+......+..+|+-.+||+|||+..|+.+...
T Consensus       234 ~~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l  279 (800)
T 3mwy_W          234 GGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWL  279 (800)
T ss_dssp             SSCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHH
Confidence            4569999999999998888889999999999999999877765433

>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=96.47  E-value=0.0033  Score=62.04  Aligned_cols=49  Identities=10%  Similarity=0.005  Sum_probs=36.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..++++||.|.+.+..+..  ..+..+|+-.|||+|||+.++..+...+..
T Consensus       149 ~~~~~LrpyQ~eav~~~l~--~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~  197 (968)
T 3dmq_A          149 GQRTSLIPHQLNIAHDVGR--RHAPRVLLADEVGLGKTIEAGMILHQQLLS  197 (968)
T ss_dssp             CCSSCCCHHHHHHHHHHHH--SSSCEEEECCCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCCCCcHHHHHHHHHHHH--hcCCCEEEECCCCCcHHHHHHHHHHHHHHh
Confidence            3558899999997665542  124678999999999999998886665543

>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=96.46  E-value=0.0013  Score=63.61  Aligned_cols=36  Identities=19%  Similarity=0.296  Sum_probs=28.1

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      |.++|.+   .|..+|..+.++|+.||||+|||+  ++|++
T Consensus        94 P~~~q~~---~i~~~l~~~~~vii~gpTGSGKTt--llp~l  129 (773)
T 2xau_A           94 PVHAQRD---EFLKLYQNNQIMVFVGETGSGKTT--QIPQF  129 (773)
T ss_dssp             GGGGGHH---HHHHHHHHCSEEEEECCTTSSHHH--HHHHH
T ss_pred             ChHHHHH---HHHHHHhCCCeEEEECCCCCCHHH--HHHHH
Confidence            4456666   566677888999999999999998  56655

>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=96.37  E-value=0.003  Score=59.29  Aligned_cols=48  Identities=25%  Similarity=0.113  Sum_probs=39.3

Q ss_pred             CCCCHHHHHHHHHHHHHHh-----cCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLD-----NSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~-----~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ...||.|.+-+..++.++.     .+..+|+-.+||+|||+..|+.+...+..
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            3589999999999998874     45678999999999999988876655443

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.04  E-value=0.0068  Score=56.73  Aligned_cols=46  Identities=20%  Similarity=0.383  Sum_probs=34.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      --+.|.+   +|..+|....+.|+.||.|||||.+++ -++.++...+.+
T Consensus       190 LN~~Q~~---AV~~al~~~~~~lI~GPPGTGKT~ti~-~~I~~l~~~~~~  235 (646)
T 4b3f_X          190 LDTSQKE---AVLFALSQKELAIIHGPPGTGKTTTVV-EIILQAVKQGLK  235 (646)
T ss_dssp             CCHHHHH---HHHHHHHCSSEEEEECCTTSCHHHHHH-HHHHHHHHTTCC
T ss_pred             CCHHHHH---HHHHHhcCCCceEEECCCCCCHHHHHH-HHHHHHHhCCCe
Confidence            3478988   677778777899999999999998754 445555555544

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=96.02  E-value=0.0022  Score=61.52  Aligned_cols=17  Identities=29%  Similarity=0.491  Sum_probs=15.9

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      +++++|+.||||+|||+
T Consensus       154 ~rk~vlv~apTGSGKT~  170 (677)
T 3rc3_A          154 QRKIIFHSGPTNSGKTY  170 (677)
T ss_dssp             CCEEEEEECCTTSSHHH
T ss_pred             CCCEEEEEcCCCCCHHH
Confidence            57899999999999998

>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=95.41  E-value=0.015  Score=57.50  Aligned_cols=44  Identities=25%  Similarity=0.287  Sum_probs=33.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ...+.||++|.-=.  +  +|..|+  |.|+.||+||||++.+|++..+.
T Consensus        71 ~lg~r~~dvQligg--~--~L~~G~--iaEM~TGEGKTLva~lp~~lnAL  114 (822)
T 3jux_A           71 TLGMRPFDVQVMGG--I--ALHEGK--VAEMKTGEGKTLAATMPIYLNAL  114 (822)
T ss_dssp             HTSCCCCHHHHHHH--H--HHHTTC--EEECCTTSCHHHHTHHHHHHHHT
T ss_pred             HhCCCCcHHHHHHH--H--HHhCCC--hhhccCCCCccHHHHHHHHHHHh
Confidence            35677899987533  3  345675  88999999999999999875443

>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=95.33  E-value=0.0056  Score=58.97  Aligned_cols=31  Identities=19%  Similarity=0.210  Sum_probs=25.4

Q ss_pred             HHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         42 LYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        42 I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      |..+|.+++++|+.||||||||++|+.+++.
T Consensus       225 i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~  255 (666)
T 3o8b_A          225 PPAVPQSFQVAHLHAPTGSGKSTKVPAAYAA  255 (666)
T ss_dssp             CCCCCSSCEEEEEECCTTSCTTTHHHHHHHH
T ss_pred             HHHHHHcCCeEEEEeCCchhHHHHHHHHHHH
Confidence            3344567889999999999999999988764

>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=95.24  E-value=0.013  Score=54.83  Aligned_cols=37  Identities=19%  Similarity=0.265  Sum_probs=28.8

Q ss_pred             CHHHHHHHHHHHHHHhcCCceeeeCCCCCCch--HHHHHHHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKS--LSLICGILK   72 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKT--LS~L~~al~   72 (194)
                      -+.|...+..+   + .++++|+.||+|||||  +++|++.+.
T Consensus       151 ~~~Q~~Ai~~~---l-~~~~~vi~G~pGTGKTt~l~~ll~~l~  189 (608)
T 1w36_D          151 INWQKVAAAVA---L-TRRISVISGGPGTGKTTTVAKLLAALI  189 (608)
T ss_dssp             CCHHHHHHHHH---H-TBSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHH---h-cCCCEEEEeCCCCCHHHHHHHHHHHHH
Confidence            47899866554   3 5789999999999999  666776655

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=95.20  E-value=0.016  Score=42.92  Aligned_cols=37  Identities=14%  Similarity=0.153  Sum_probs=26.4

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      |...-++.+.+..+...+..+  ..++|.+|+|||||..
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHH
T ss_pred             ccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHH
Confidence            333344555666777777654  6789999999999964

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.19  E-value=0.025  Score=43.96  Aligned_cols=33  Identities=15%  Similarity=0.031  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHhcC------CceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNS------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g------k~~I~ESPTGTGKTLS   65 (194)
                      +.|...+..+...+...      ..++|.+|+|||||.-
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           32 DGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             HHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHH
T ss_pred             hhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHH
Confidence            46777788887777754      6899999999999964

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=95.10  E-value=0.018  Score=43.29  Aligned_cols=27  Identities=15%  Similarity=0.112  Sum_probs=19.7

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      ...+..+...+..++|.+|+|||||..
T Consensus        14 ~~~~~~~a~~~~~vll~G~~GtGKt~l   40 (145)
T 3n70_A           14 RRRLQQLSETDIAVWLYGAPGTGRMTG   40 (145)
T ss_dssp             HHHHHHHTTCCSCEEEESSTTSSHHHH
T ss_pred             HHHHHHHhCCCCCEEEECCCCCCHHHH
Confidence            334444445678899999999999953

>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=94.98  E-value=0.01  Score=45.30  Aligned_cols=33  Identities=21%  Similarity=0.217  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS   65 (194)
                      -++...+..|..++..+.   .++|.+|+|+|||..
T Consensus        26 ~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l   61 (250)
T 1njg_A           26 VGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSI   61 (250)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHH
T ss_pred             hCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHH
Confidence            345666778888887765   689999999999954

>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=94.93  E-value=0.045  Score=41.96  Aligned_cols=34  Identities=18%  Similarity=0.108  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHHHHHHh-----cCCceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLD-----NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~-----~gk~~I~ESPTGTGKTLS   65 (194)
                      .+.|...+..+...+.     .|..++|-+|+|||||.-
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           16 NVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             SHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHH
T ss_pred             CHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHH
Confidence            4688888888877664     468899999999999953

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=94.92  E-value=0.0088  Score=50.37  Aligned_cols=34  Identities=21%  Similarity=0.187  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +-+|.+.+..+..++..+..++|.+|+|||||..
T Consensus        29 i~g~~~~~~~l~~~l~~~~~vll~G~pGtGKT~l   62 (331)
T 2r44_A           29 VVGQKYMINRLLIGICTGGHILLEGVPGLAKTLS   62 (331)
T ss_dssp             CCSCHHHHHHHHHHHHHTCCEEEESCCCHHHHHH
T ss_pred             eeCcHHHHHHHHHHHHcCCeEEEECCCCCcHHHH
Confidence            4457778888888888899999999999999953

>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=94.86  E-value=0.026  Score=48.30  Aligned_cols=39  Identities=10%  Similarity=0.089  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~   69 (194)
                      +||.|.+.++.+..++.+|+   ..+|.||.|+|||.....-
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            58999999999999998875   3899999999998654433

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.85  E-value=0.02  Score=43.07  Aligned_cols=28  Identities=4%  Similarity=-0.008  Sum_probs=20.1

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +...+..+...+..++|.+|+|||||..
T Consensus        16 l~~~~~~~~~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           16 MNREVEAAAKRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             HHHHHHHHHTCSSCEEEEEETTCCHHHH
T ss_pred             HHHHHHHHhCCCCcEEEECCCCccHHHH
Confidence            3334444445678899999999999953

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=94.67  E-value=0.021  Score=42.45  Aligned_cols=37  Identities=16%  Similarity=0.150  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhc--CCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS   65 (194)
                      |...-++...+..+...+..  ...++|.+|+|||||..
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~l   59 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAI   59 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHH
T ss_pred             cchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHH
Confidence            33334455566677777765  46789999999999954

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=94.67  E-value=0.066  Score=45.21  Aligned_cols=36  Identities=11%  Similarity=0.070  Sum_probs=25.5

Q ss_pred             CCHHHHHHHHHHHHHHhcC----CceeeeCCCCCCchHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~g----k~~I~ESPTGTGKTLS~   66 (194)
                      -.+.....+..+...+..+    ..++|.+|+|||||...
T Consensus        48 G~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           48 GQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHH
Confidence            3455555555677777665    36899999999999753

>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=94.60  E-value=0.018  Score=43.71  Aligned_cols=32  Identities=25%  Similarity=0.403  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      ++.+.+..|..++..+  ..++|.+|+|||||..
T Consensus        21 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l   54 (226)
T 2chg_A           21 GQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTAT   54 (226)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHH
T ss_pred             CcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHH
Confidence            4556667888888766  3599999999999964

>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=94.31  E-value=0.033  Score=45.68  Aligned_cols=38  Identities=24%  Similarity=0.348  Sum_probs=29.4

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      |.-.-+|...+..+..++..+.  +++|.||+|||||...
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la   63 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAA   63 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHH
Confidence            3333457778888888888774  6999999999999653

>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=94.21  E-value=0.024  Score=46.23  Aligned_cols=17  Identities=35%  Similarity=0.423  Sum_probs=14.7

Q ss_pred             CCceeeeCCCCCCchHH
Q psy14272         49 SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS   65 (194)
                      ...++|.+|+|||||..
T Consensus        50 ~~~vll~G~~GtGKT~l   66 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEI   66 (310)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             CceEEEECCCCCCHHHH
Confidence            46799999999999964

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=94.21  E-value=0.037  Score=45.80  Aligned_cols=32  Identities=22%  Similarity=0.245  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHh-------cCCceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLD-------NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~-------~gk~~I~ESPTGTGKTLS   65 (194)
                      ++...|..+..++.       ....++|.+|+|||||..
T Consensus        16 g~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~l   54 (324)
T 1hqc_A           16 GQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTL   54 (324)
T ss_dssp             SCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHH
T ss_pred             CHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHH
Confidence            34444555555553       236799999999999964

>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=94.15  E-value=0.027  Score=48.34  Aligned_cols=32  Identities=28%  Similarity=0.248  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHh-----------------cCCceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLD-----------------NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~-----------------~gk~~I~ESPTGTGKTLS   65 (194)
                      +|...+..|..++.                 ....++|.+|+|||||..
T Consensus        19 G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~l   67 (363)
T 3hws_A           19 GQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLL   67 (363)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHH
Confidence            35566666666662                 346799999999999974

>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=94.10  E-value=0.019  Score=47.93  Aligned_cols=35  Identities=29%  Similarity=0.402  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHH
Q psy14272         32 YDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      .-+|.+.+..|..++..+  .+++|.+|+|||||...
T Consensus        39 i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la   75 (353)
T 1sxj_D           39 VTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTI   75 (353)
T ss_dssp             CCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHH
T ss_pred             hhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHH
Confidence            345777788999999887  66999999999999653

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.03  E-value=0.047  Score=46.36  Aligned_cols=35  Identities=26%  Similarity=0.467  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHhcCCc--eeeeCCCCCCchHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSKF--GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk~--~I~ESPTGTGKTLS~L~   68 (194)
                      +|...+..|..++..|.+  ++|.||.|||||....+
T Consensus        29 g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~   65 (340)
T 1sxj_C           29 GQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVA   65 (340)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHH
T ss_pred             CcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHH
Confidence            477888899999998876  99999999999965443

>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=93.83  E-value=0.027  Score=46.06  Aligned_cols=34  Identities=24%  Similarity=0.353  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      -+|...+..|..++..+.  +++|.||+|||||...
T Consensus        20 ~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la   55 (319)
T 2chq_A           20 VGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATA   55 (319)
T ss_dssp             CSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHH
T ss_pred             hCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHH
Confidence            356777888888887764  6999999999999643

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=93.80  E-value=0.026  Score=46.43  Aligned_cols=33  Identities=21%  Similarity=0.241  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTLS~   66 (194)
                      +|...|..|..++..+           .+++|.+|+|||||...
T Consensus        21 G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la   64 (311)
T 4fcw_A           21 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELA   64 (311)
T ss_dssp             SCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHH
Confidence            5666667777777653           47899999999999654

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=93.72  E-value=0.029  Score=51.95  Aligned_cols=33  Identities=18%  Similarity=0.123  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      -+|.+.+..+..++..+.+++|.+|+|||||..
T Consensus        25 vGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           25 YERSHAIRLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             SSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCeeEeecCchHHHHHH
Confidence            356677888888888899999999999999964

>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=93.64  E-value=0.064  Score=43.59  Aligned_cols=29  Identities=21%  Similarity=0.185  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      .+...+..+...+..++|.+|+|||||..
T Consensus        17 ~~~~~~~~~~~~~~~vll~G~~GtGKt~l   45 (265)
T 2bjv_A           17 EVLEQVSHLAPLDKPVLIIGERGTGKELI   45 (265)
T ss_dssp             HHHHHHHHHTTSCSCEEEECCTTSCHHHH
T ss_pred             HHHHHHHHHhCCCCCEEEECCCCCcHHHH
Confidence            33444444455678899999999999953

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=93.62  E-value=0.1  Score=44.62  Aligned_cols=32  Identities=16%  Similarity=0.093  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHhc-----CCceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~-----gk~~I~ESPTGTGKTLS   65 (194)
                      .+...+..+..++..     +..++|-+|||||||.-
T Consensus       132 ~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~L  168 (308)
T 2qgz_A          132 SRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYL  168 (308)
T ss_dssp             HHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHH
T ss_pred             HHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHH
Confidence            566666677777775     57899999999999964

>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=93.58  E-value=0.025  Score=47.26  Aligned_cols=39  Identities=31%  Similarity=0.259  Sum_probs=24.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHh--cCCceeeeCCCCCCchHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~--~gk~~I~ESPTGTGKTLS   65 (194)
                      ++|.-.-+|..++..+..++.  ....++|.+|+|||||..
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            444433344445555444443  346799999999999964

>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=93.46  E-value=0.061  Score=50.34  Aligned_cols=40  Identities=20%  Similarity=0.281  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .-+.|.+.+..+   + .+.+.++.||+|||||..+..- +.++.
T Consensus       181 ln~~Q~~av~~~---l-~~~~~li~GppGTGKT~~~~~~-i~~l~  220 (624)
T 2gk6_A          181 LNHSQVYAVKTV---L-QRPLSLIQGPPGTGKTVTSATI-VYHLA  220 (624)
T ss_dssp             CCHHHHHHHHHH---H-TCSEEEEECCTTSCHHHHHHHH-HHHHH
T ss_pred             CCHHHHHHHHHH---h-cCCCeEEECCCCCCHHHHHHHH-HHHHH
Confidence            458899866654   3 3678999999999999875444 44443

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=93.45  E-value=0.075  Score=43.73  Aligned_cols=34  Identities=21%  Similarity=0.147  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      |-.|+.+.+   .|..++..+.++++.+|.|+|||.-
T Consensus        14 ~~gR~~el~---~L~~~l~~~~~v~i~G~~G~GKT~L   47 (350)
T 2qen_A           14 IFDREEESR---KLEESLENYPLTLLLGIRRVGKSSL   47 (350)
T ss_dssp             SCSCHHHHH---HHHHHHHHCSEEEEECCTTSSHHHH
T ss_pred             cCChHHHHH---HHHHHHhcCCeEEEECCCcCCHHHH
Confidence            445666665   4555566678999999999999953

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=93.25  E-value=0.034  Score=45.40  Aligned_cols=17  Identities=41%  Similarity=0.518  Sum_probs=14.6

Q ss_pred             CCceeeeCCCCCCchHH
Q psy14272         49 SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS   65 (194)
                      ...++|.+|+|||||..
T Consensus        51 ~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           51 PKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CSEEEEESSSSSSHHHH
T ss_pred             CCeEEEECCCCCcHHHH
Confidence            46799999999999964

>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=93.25  E-value=0.079  Score=41.11  Aligned_cols=31  Identities=10%  Similarity=0.125  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHHHhc--CCceeeeCCCCCCchHH
Q psy14272         35 QSNFMKNLYYTLDN--SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        35 Q~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS   65 (194)
                      +...+..+..++..  +..++|.+|+|||||..
T Consensus        36 ~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~l   68 (242)
T 3bos_A           36 NDELIGALKSAASGDGVQAIYLWGPVKSGRTHL   68 (242)
T ss_dssp             CHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHH
Confidence            35666677777764  57899999999999964

>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=93.12  E-value=0.1  Score=48.84  Aligned_cols=47  Identities=15%  Similarity=0.175  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      ++..-+.|.+.+..+.    .+.++++.+|.|||||.. +..++..+...+.
T Consensus       187 ~~~L~~~Q~~Av~~~~----~~~~~~I~G~pGTGKTt~-i~~l~~~l~~~g~  233 (574)
T 3e1s_A          187 RKGLSEEQASVLDQLA----GHRLVVLTGGPGTGKSTT-TKAVADLAESLGL  233 (574)
T ss_dssp             TTTCCHHHHHHHHHHT----TCSEEEEECCTTSCHHHH-HHHHHHHHHHTTC
T ss_pred             cCCCCHHHHHHHHHHH----hCCEEEEEcCCCCCHHHH-HHHHHHHHHhcCC
Confidence            6667789998766653    568999999999999965 4444555544443

>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=92.94  E-value=0.082  Score=44.36  Aligned_cols=36  Identities=19%  Similarity=0.175  Sum_probs=27.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSL   66 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~   66 (194)
                      ..-+|...+..+..++..+.   .++|.||.|||||...
T Consensus        17 ~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           17 DVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIA   55 (373)
T ss_dssp             TSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHH
T ss_pred             hccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHH
Confidence            34457777788888887775   3789999999999653

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=92.86  E-value=0.036  Score=46.52  Aligned_cols=34  Identities=29%  Similarity=0.395  Sum_probs=25.3

Q ss_pred             CHHHHHHHHHHHHHHhcC-------CceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDNS-------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~g-------k~~I~ESPTGTGKTLS   65 (194)
                      .-+|...|..|..++...       ..++|.+|+|||||..
T Consensus        31 iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~l   71 (338)
T 3pfi_A           31 YIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTL   71 (338)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHH
T ss_pred             hCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHH
Confidence            345666677777777542       4799999999999964

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=92.85  E-value=0.057  Score=45.07  Aligned_cols=33  Identities=21%  Similarity=0.232  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHh------cCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLD------NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~------~gk~~I~ESPTGTGKTLS   65 (194)
                      .++..-+..|..+|.      .+..++|-||+|||||..
T Consensus        22 ~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l   60 (387)
T 2v1u_A           22 PHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAV   60 (387)
T ss_dssp             TTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHH
Confidence            445555556666662      346799999999999964

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=92.81  E-value=0.067  Score=46.87  Aligned_cols=30  Identities=17%  Similarity=0.120  Sum_probs=21.6

Q ss_pred             HHHHHHHHHhcC--CceeeeCCCCCCchHHHH
Q psy14272         38 FMKNLYYTLDNS--KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        38 ~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L   67 (194)
                      +...|..++..+  ..++|-+|+|||||.+.-
T Consensus        32 i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~   63 (318)
T 3te6_A           32 IFLPIYDSLMSSQNKLFYITNADDSTKFQLVN   63 (318)
T ss_dssp             HHHHHHHHHHTTCCCEEEEECCCSHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCeEEEECCCCCCHHHHHH
Confidence            334566666544  678999999999997643

>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=92.39  E-value=0.093  Score=47.44  Aligned_cols=40  Identities=20%  Similarity=0.248  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         34 IQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+...+..+  ....+.+++|-+|||+|||-. |-.++.++..
T Consensus       154 ~~~~~L~~l--~~~~ggii~I~GpnGSGKTTl-L~allg~l~~  193 (418)
T 1p9r_A          154 HNHDNFRRL--IKRPHGIILVTGPTGSGKSTT-LYAGLQELNS  193 (418)
T ss_dssp             HHHHHHHHH--HTSSSEEEEEECSTTSCHHHH-HHHHHHHHCC
T ss_pred             HHHHHHHHH--HHhcCCeEEEECCCCCCHHHH-HHHHHhhcCC
Confidence            455555555  234567899999999999953 4444555543

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=91.78  E-value=0.11  Score=44.13  Aligned_cols=27  Identities=19%  Similarity=0.322  Sum_probs=19.3

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +..+..+......++|.+|||||||+.
T Consensus        15 ~~~~~~~a~~~~~vLi~Ge~GtGKt~l   41 (304)
T 1ojl_A           15 LNEIAMVAPSDATVLIHGDSGTGKELV   41 (304)
T ss_dssp             HHHHHHHCSTTSCEEEESCTTSCHHHH
T ss_pred             HHHHHHHhCCCCcEEEECCCCchHHHH
Confidence            333433344567899999999999964

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=91.68  E-value=0.089  Score=43.25  Aligned_cols=18  Identities=33%  Similarity=0.423  Sum_probs=15.1

Q ss_pred             CCceeeeCCCCCCchHHH
Q psy14272         49 SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~   66 (194)
                      ...++|.+|+|||||...
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            467999999999999643

>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=91.57  E-value=0.22  Score=39.64  Aligned_cols=34  Identities=21%  Similarity=0.253  Sum_probs=22.1

Q ss_pred             CHHHHHHHHHHHHHHhc-----------CCceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~-----------gk~~I~ESPTGTGKTLS   65 (194)
                      ++...+.+..+...+..           ...++|.+|+|||||..
T Consensus        11 ~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A           11 MHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHH
T ss_pred             HHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHH
Confidence            34455555555554432           24578999999999964

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=91.56  E-value=0.13  Score=43.19  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=19.2

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..|.  +..|.+++|-+|||+|||-
T Consensus        17 l~~i~--i~~g~~v~i~Gp~GsGKST   40 (261)
T 2eyu_A           17 VLELC--HRKMGLILVTGPTGSGKST   40 (261)
T ss_dssp             HHHGG--GCSSEEEEEECSTTCSHHH
T ss_pred             HHHHh--hCCCCEEEEECCCCccHHH
Confidence            34443  6788899999999999984

>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=91.56  E-value=0.097  Score=42.36  Aligned_cols=16  Identities=44%  Similarity=0.584  Sum_probs=13.6

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      ..++|.+|+|||||..
T Consensus        45 ~~vll~G~~GtGKT~l   60 (268)
T 2r62_A           45 KGVLLVGPPGTGKTLL   60 (268)
T ss_dssp             SCCCCBCSSCSSHHHH
T ss_pred             ceEEEECCCCCcHHHH
Confidence            4588999999999964

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=91.39  E-value=0.097  Score=47.42  Aligned_cols=37  Identities=27%  Similarity=0.392  Sum_probs=30.1

Q ss_pred             CCCCHHHHHHH---HHHHHHHhcCCc--eeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFM---KNLYYTLDNSKF--GIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M---~~I~~~L~~gk~--~I~ESPTGTGKTLS   65 (194)
                      |.-+-+|...+   ..+..++..+..  +||.+|+|||||..
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtl   66 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTL   66 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHH
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHH
Confidence            44556788888   788888888864  99999999999964

>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=91.34  E-value=0.18  Score=49.10  Aligned_cols=41  Identities=22%  Similarity=0.340  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .-+.|.+.+..+   + .+.+.++.||.|||||..+.. ++.++..
T Consensus       357 Ln~~Q~~Av~~~---l-~~~~~lI~GppGTGKT~ti~~-~i~~l~~  397 (800)
T 2wjy_A          357 LNHSQVYAVKTV---L-QRPLSLIQGPPGTGKTVTSAT-IVYHLAR  397 (800)
T ss_dssp             CCHHHHHHHHHH---H-TSSEEEEECCTTSCHHHHHHH-HHHHHHT
T ss_pred             CCHHHHHHHHHh---c-cCCeEEEEcCCCCCHHHHHHH-HHHHHHH
Confidence            458898866554   3 357899999999999987544 4454443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=91.29  E-value=0.15  Score=44.54  Aligned_cols=25  Identities=20%  Similarity=0.267  Sum_probs=22.1

Q ss_pred             HHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         40 KNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        40 ~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      ..|.-++..|..++|-+|||+|||-
T Consensus       166 ~~l~~~i~~G~~i~ivG~sGsGKST  190 (361)
T 2gza_A          166 SFLRRAVQLERVIVVAGETGSGKTT  190 (361)
T ss_dssp             HHHHHHHHTTCCEEEEESSSSCHHH
T ss_pred             HHHHHHHhcCCEEEEECCCCCCHHH
Confidence            6777778899999999999999984

>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=91.27  E-value=0.21  Score=47.31  Aligned_cols=41  Identities=22%  Similarity=0.246  Sum_probs=34.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCC-ceeeeCCCCCCchHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk-~~I~ESPTGTGKTLS~L   67 (194)
                      -||.|.+.|-..+..+...+..|. ..++.+.||||||+.+.
T Consensus         5 ~~~~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a   46 (664)
T 1c4o_A            5 RGPSPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMA   46 (664)
T ss_dssp             CSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH
T ss_pred             CCCCCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHH
Confidence            468899999999999999998874 46688999999998654

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=91.22  E-value=0.16  Score=49.45  Aligned_cols=40  Identities=23%  Similarity=0.334  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .-+.|.+.+..+   + .+.+.++.||.|||||..+..- +.++.
T Consensus       361 Ln~~Q~~Av~~~---l-~~~~~lI~GppGTGKT~~i~~~-i~~l~  400 (802)
T 2xzl_A          361 LNSSQSNAVSHV---L-QRPLSLIQGPPGTGKTVTSATI-VYHLS  400 (802)
T ss_dssp             CCHHHHHHHHHH---T-TCSEEEEECSTTSSHHHHHHHH-HHHHH
T ss_pred             CCHHHHHHHHHH---h-cCCCEEEECCCCCCHHHHHHHH-HHHHH
Confidence            458999866554   3 3668999999999999875443 44443

>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=90.96  E-value=0.13  Score=42.09  Aligned_cols=33  Identities=18%  Similarity=0.211  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      +|...+..+..++..+.  +++|.||+|+|||...
T Consensus        25 g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la   59 (323)
T 1sxj_B           25 GNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSV   59 (323)
T ss_dssp             SCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHH
Confidence            56677778888888764  5999999999999643

>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=90.96  E-value=0.17  Score=42.20  Aligned_cols=38  Identities=16%  Similarity=0.115  Sum_probs=28.3

Q ss_pred             CCCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHH
Q psy14272         30 DAYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L   67 (194)
                      +-.-+|...+..|..++..+.   .+++.+|+|||||...-
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~   66 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAK   66 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHH
Confidence            334467777888888998764   45777889999997543

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=90.91  E-value=0.16  Score=41.76  Aligned_cols=17  Identities=29%  Similarity=0.313  Sum_probs=14.4

Q ss_pred             CceeeeCCCCCCchHHH
Q psy14272         50 KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~   66 (194)
                      ..++|.+|+|||||...
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46899999999999654

>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=90.67  E-value=0.18  Score=42.28  Aligned_cols=16  Identities=31%  Similarity=0.484  Sum_probs=14.1

Q ss_pred             ceeeeCCCCCCchHHH
Q psy14272         51 FGIFESPTGTGKSLSL   66 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~   66 (194)
                      +++|.||+|||||..+
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            7999999999999654

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=90.67  E-value=0.13  Score=44.80  Aligned_cols=37  Identities=22%  Similarity=0.200  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHHHHHHHHh--------------cCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLD--------------NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~--------------~gk~~I~ESPTGTGKTLS   65 (194)
                      |.-.-+|...++.|...+.              ....++|.+|+|||||+.
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~l  164 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTML  164 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHH
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHH
Confidence            4444566677777776662              236799999999999964

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=90.64  E-value=0.24  Score=39.94  Aligned_cols=34  Identities=29%  Similarity=0.309  Sum_probs=22.2

Q ss_pred             CHHHHHHHHHHHHHHhc-----------CCceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~-----------gk~~I~ESPTGTGKTLS   65 (194)
                      ++.+.+-+..+...+..           ...++|.+|+|||||..
T Consensus        17 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~l   61 (257)
T 1lv7_A           17 CDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLL   61 (257)
T ss_dssp             CHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHH
T ss_pred             cHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHH
Confidence            45555555555554432           34588999999999953

>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=90.62  E-value=0.28  Score=41.07  Aligned_cols=29  Identities=21%  Similarity=0.100  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHhcC----CceeeeCCCCCCchHH
Q psy14272         37 NFMKNLYYTLDNS----KFGIFESPTGTGKSLS   65 (194)
Q Consensus        37 e~M~~I~~~L~~g----k~~I~ESPTGTGKTLS   65 (194)
                      ..+..+...+...    ..++|-||+|||||..
T Consensus        21 ~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~l   53 (324)
T 1l8q_A           21 LAYEVVKEALENLGSLYNPIFIYGSVGTGKTHL   53 (324)
T ss_dssp             HHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHH
T ss_pred             HHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHH
Confidence            3344455555443    5799999999999954

>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=90.41  E-value=0.17  Score=42.54  Aligned_cols=18  Identities=33%  Similarity=0.396  Sum_probs=14.8

Q ss_pred             CCceeeeCCCCCCchHHH
Q psy14272         49 SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~   66 (194)
                      ...++|.+|+|||||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            356999999999999643

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=90.37  E-value=0.18  Score=45.44  Aligned_cols=38  Identities=16%  Similarity=0.160  Sum_probs=29.4

Q ss_pred             CCCCHHHHHHHHHHHHHHhc--CCceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS~   66 (194)
                      +.|--+|...|..+...|..  ..+++|.+|+|||||...
T Consensus       179 ld~iiGr~~~i~~l~~~l~r~~~~~~LL~G~pG~GKT~la  218 (468)
T 3pxg_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIA  218 (468)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHHH
T ss_pred             CCCccCcHHHHHHHHHHHhccCCCCeEEECCCCCCHHHHH
Confidence            44555677788888888854  367899999999999753

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=90.12  E-value=0.25  Score=45.96  Aligned_cols=34  Identities=18%  Similarity=0.140  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      -.|...+..|..++..+.+++|.+|+|||||..+
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            3678888999999999999999999999999643

>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=90.05  E-value=0.31  Score=46.16  Aligned_cols=44  Identities=20%  Similarity=0.296  Sum_probs=36.9

Q ss_pred             CccCCCCCCCHHHHHHHHHHHHHHhcCC-ceeeeCCCCCCchHHH
Q psy14272         23 SEFPFPFDAYDIQSNFMKNLYYTLDNSK-FGIFESPTGTGKSLSL   66 (194)
Q Consensus        23 ~~~~fPy~py~iQ~e~M~~I~~~L~~gk-~~I~ESPTGTGKTLS~   66 (194)
                      ....-||.|+.-|...+..+...|..|. ..++-+.||+|||+.+
T Consensus         5 ~~~~~~~~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~   49 (661)
T 2d7d_A            5 FELVSKYQPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTV   49 (661)
T ss_dssp             CCCCCSCCCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH
T ss_pred             ceeecCCCCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHH
Confidence            4466789999999999999999998874 4667899999999864

>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=89.97  E-value=0.2  Score=41.65  Aligned_cols=30  Identities=20%  Similarity=0.230  Sum_probs=22.6

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      -..|.+.++-+|+|+|||.++|-.+..+..
T Consensus         9 ~~~G~i~litG~mGsGKTT~ll~~~~r~~~   38 (223)
T 2b8t_A            9 KKIGWIEFITGPMFAGKTAELIRRLHRLEY   38 (223)
T ss_dssp             --CCEEEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            356789999999999999887766555543

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=89.95  E-value=0.22  Score=46.10  Aligned_cols=36  Identities=17%  Similarity=0.361  Sum_probs=26.1

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ++..|.-++..|.+++|-+|||+|||-. |-.++.++
T Consensus       249 ~l~~l~~~v~~g~~i~I~GptGSGKTTl-L~aL~~~i  284 (511)
T 2oap_1          249 VLAYLWLAIEHKFSAIVVGETASGKTTT-LNAIMMFI  284 (511)
T ss_dssp             HHHHHHHHHHTTCCEEEEESTTSSHHHH-HHHHGGGS
T ss_pred             HHHHHHHHHhCCCEEEEECCCCCCHHHH-HHHHHhhC
Confidence            4556667788899999999999999943 33333444

>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=89.84  E-value=0.29  Score=43.20  Aligned_cols=30  Identities=23%  Similarity=0.433  Sum_probs=20.7

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ...+++++|-+|||+|||-. |-.++.++..
T Consensus       120 ~~~~g~i~I~GptGSGKTTl-L~~l~g~~~~  149 (356)
T 3jvv_A          120 DVPRGLVLVTGPTGSGKSTT-LAAMLDYLNN  149 (356)
T ss_dssp             HCSSEEEEEECSTTSCHHHH-HHHHHHHHHH
T ss_pred             hCCCCEEEEECCCCCCHHHH-HHHHHhcccC
Confidence            34567899999999999853 3344455544

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=89.81  E-value=0.15  Score=48.39  Aligned_cols=32  Identities=25%  Similarity=0.255  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHhcCC-----------ceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDNSK-----------FGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk-----------~~I~ESPTGTGKTLS   65 (194)
                      +|...|..|..++....           +++|.+|||||||..
T Consensus       495 Gq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~l  537 (758)
T 3pxi_A          495 GQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTEL  537 (758)
T ss_dssp             SCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHH
Confidence            46777777777776421           599999999999964

>1ry6_A Internal kinesin; kinesin motor domain, nucleotide-free, transport protein; 1.60A {Plasmodium falciparum} SCOP: c.37.1.9

Probab=89.77  E-value=0.16  Score=45.32  Aligned_cols=43  Identities=21%  Similarity=0.275  Sum_probs=30.6

Q ss_pred             cCCC--CCCCHHHHHHHHH-----HHHHHhcCCc--eeeeCCCCCCchHHHH
Q psy14272         25 FPFP--FDAYDIQSNFMKN-----LYYTLDNSKF--GIFESPTGTGKSLSLI   67 (194)
Q Consensus        25 ~~fP--y~py~iQ~e~M~~-----I~~~L~~gk~--~I~ESPTGTGKTLS~L   67 (194)
                      |.|.  |.|...|.++...     |..+|.+|.+  ++.-+.||||||.+.+
T Consensus        52 F~FD~Vf~~~~~Q~~Vy~~~~~plv~~~~~~G~n~tifAYGqTGSGKTyTM~  103 (360)
T 1ry6_A           52 FIVDKVFDDTVDNFTVYENTIKPLIIDLYENGCVCSCFAYGQTGSGKTYTML  103 (360)
T ss_dssp             EECSEEECTTCCHHHHHHHHTHHHHHHHHHHCCEEEEEEECCTTSSHHHHHH
T ss_pred             EEeeeEecCCCCHHHHHHHHhhhhhhhhccCCceeEEEeeCCCCCCCCEEEe
Confidence            4444  5677788887665     3355666755  4778999999999874

>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=89.73  E-value=0.42  Score=42.67  Aligned_cols=32  Identities=16%  Similarity=0.230  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHhcC----CceeeeCCCCCCchHHH
Q psy14272         35 QSNFMKNLYYTLDNS----KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        35 Q~e~M~~I~~~L~~g----k~~I~ESPTGTGKTLS~   66 (194)
                      ..+.+..+...+..+    ..++|.+|+|||||...
T Consensus        45 ~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la   80 (456)
T 2c9o_A           45 AREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALA   80 (456)
T ss_dssp             HHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHH
Confidence            333333444555554    46999999999999643

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=89.69  E-value=0.19  Score=47.75  Aligned_cols=37  Identities=16%  Similarity=0.172  Sum_probs=30.0

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      +.|.-+|...|+.+..+|...  .+++|.+|+|||||..
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~~~~vLL~G~pGtGKT~l  217 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAI  217 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSSSCEEEEESCTTTTTHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCCCCCeEEECCCCCCHHHH
Confidence            445667888888999988653  5899999999999974

>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=89.69  E-value=0.18  Score=43.64  Aligned_cols=28  Identities=21%  Similarity=0.179  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchH
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      .....|.-++..|+++++-+|||+|||-
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            3566777778889999999999999994

>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=89.56  E-value=0.23  Score=41.63  Aligned_cols=17  Identities=47%  Similarity=0.616  Sum_probs=14.6

Q ss_pred             CCceeeeCCCCCCchHH
Q psy14272         49 SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS   65 (194)
                      +..++|.+|+|||||+.
T Consensus        49 ~~~vLL~Gp~GtGKT~l   65 (301)
T 3cf0_A           49 SKGVLFYGPPGCGKTLL   65 (301)
T ss_dssp             CSEEEEECSSSSSHHHH
T ss_pred             CceEEEECCCCcCHHHH
Confidence            46789999999999964

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=89.46  E-value=0.12  Score=39.79  Aligned_cols=19  Identities=26%  Similarity=0.637  Sum_probs=15.8

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..|.+++|-+|+|+|||-
T Consensus         4 m~~g~ii~l~Gp~GsGKST   22 (205)
T 3tr0_A            4 MNKANLFIISAPSGAGKTS   22 (205)
T ss_dssp             -CCCCEEEEECCTTSCHHH
T ss_pred             CCCCcEEEEECcCCCCHHH
Confidence            3467889999999999984

>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=89.45  E-value=0.27  Score=42.15  Aligned_cols=17  Identities=35%  Similarity=0.534  Sum_probs=14.5

Q ss_pred             CCceeeeCCCCCCchHH
Q psy14272         49 SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS   65 (194)
                      ...++|.+|+|||||..
T Consensus        72 ~~~ill~Gp~GtGKT~l   88 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLM   88 (376)
T ss_dssp             CCCEEEECCTTSSHHHH
T ss_pred             CCCEEEECCCCCCHHHH
Confidence            35799999999999964

>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=89.10  E-value=0.27  Score=44.68  Aligned_cols=33  Identities=21%  Similarity=0.237  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHhc-------------------CCceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDN-------------------SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~-------------------gk~~I~ESPTGTGKTLS~   66 (194)
                      +|...+..|..+|..                   ...++|.+|+|||||...
T Consensus        43 G~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla   94 (516)
T 1sxj_A           43 GNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   94 (516)
T ss_dssp             SCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHH
Confidence            456667777777764                   257999999999999653

>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=89.08  E-value=0.23  Score=42.83  Aligned_cols=17  Identities=41%  Similarity=0.501  Sum_probs=14.5

Q ss_pred             CCceeeeCCCCCCchHH
Q psy14272         49 SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS   65 (194)
                      ...++|.+|+|||||..
T Consensus       117 ~~~vLl~GppGtGKT~l  133 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLI  133 (357)
T ss_dssp             CSEEEEESSTTSSHHHH
T ss_pred             CceEEEECCCCCCHHHH
Confidence            36789999999999964

>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=88.96  E-value=0.21  Score=42.29  Aligned_cols=38  Identities=18%  Similarity=0.128  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHHHHHHHHh----------c----CCceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLD----------N----SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~----------~----gk~~I~ESPTGTGKTLS~   66 (194)
                      |.-..+|...++.|...+.          .    ...++|.+|+|||||+..
T Consensus        17 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           17 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            4444556666666666662          1    245899999999999643

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=88.89  E-value=0.52  Score=52.73  Aligned_cols=37  Identities=19%  Similarity=0.184  Sum_probs=29.3

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +-|..-=..+...+..+|..++.+++.||||||||..
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            4477655566666777788999999999999999953

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=88.84  E-value=0.14  Score=39.31  Aligned_cols=19  Identities=21%  Similarity=0.468  Sum_probs=15.8

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..|.+++|.+|+|+|||-
T Consensus         3 i~~g~~i~l~G~~GsGKST   21 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGT   21 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHH
T ss_pred             CCCCCEEEEECCCCCCHHH
Confidence            3568899999999999984

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=88.83  E-value=0.23  Score=41.24  Aligned_cols=31  Identities=19%  Similarity=0.216  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHhc------CCceeeeCCCCCCchHH
Q psy14272         35 QSNFMKNLYYTLDN------SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        35 Q~e~M~~I~~~L~~------gk~~I~ESPTGTGKTLS   65 (194)
                      +..-+..|..++..      +..++|-+|+|||||..
T Consensus        25 r~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl   61 (386)
T 2qby_A           25 REDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAV   61 (386)
T ss_dssp             CHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHH
Confidence            33344455555543      46799999999999964

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=88.58  E-value=0.55  Score=51.70  Aligned_cols=37  Identities=22%  Similarity=0.198  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      +-|..--..+.-.+..++..++.+++.||||||||..
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            3477666666667777788999999999999999974

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=88.56  E-value=0.39  Score=40.39  Aligned_cols=30  Identities=30%  Similarity=0.358  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHhcC---CceeeeCCCCCCchHHH
Q psy14272         37 NFMKNLYYTLDNS---KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        37 e~M~~I~~~L~~g---k~~I~ESPTGTGKTLS~   66 (194)
                      .|+..+...+..-   ..++|-+|.|||||...
T Consensus        43 ~f~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a   75 (212)
T 1tue_A           43 TFLGALKSFLKGTPKKNCLVFCGPANTGKSYFG   75 (212)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHHHH
T ss_pred             HHHHHHHHHHhcCCcccEEEEECCCCCCHHHHH
Confidence            3466776666642   25899999999999654

>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=88.51  E-value=0.34  Score=44.18  Aligned_cols=39  Identities=18%  Similarity=0.098  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .-+.|.+.+..      .++.+++.||.|||||.+++.-+...+.
T Consensus        10 Ln~~Q~~av~~------~~~~~lV~a~aGsGKT~~l~~ri~~l~~   48 (647)
T 3lfu_A           10 LNDKQREAVAA------PRSNLLVLAGAGSGKTRVLVHRIAWLMS   48 (647)
T ss_dssp             CCHHHHHHHTC------CSSCEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC------CCCCEEEEECCCCCHHHHHHHHHHHHHH
Confidence            34788885542      3578899999999999887666444443

>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=88.39  E-value=0.3  Score=41.62  Aligned_cols=32  Identities=28%  Similarity=0.400  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHhcC-------CceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDNS-------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g-------k~~I~ESPTGTGKTLS   65 (194)
                      +|......|..++..+       .+++|-+|+|+|||..
T Consensus        29 g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTL   67 (334)
T 1in4_A           29 GQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTL   67 (334)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHH
T ss_pred             CcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHH
Confidence            3445556666666544       6899999999999853

>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=88.15  E-value=0.18  Score=47.58  Aligned_cols=32  Identities=25%  Similarity=0.287  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHHHhc---C--------CceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDN---S--------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~---g--------k~~I~ESPTGTGKTLS   65 (194)
                      +|.+.+..|..++..   |        ..++|.+|||||||..
T Consensus       462 g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~l  504 (758)
T 1r6b_X          462 GQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEV  504 (758)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHH
Confidence            455666666666643   1        2589999999999964

>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=88.15  E-value=0.55  Score=40.42  Aligned_cols=31  Identities=13%  Similarity=-0.097  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHhcC----CceeeeCCCCCCchHHHH
Q psy14272         37 NFMKNLYYTLDNS----KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        37 e~M~~I~~~L~~g----k~~I~ESPTGTGKTLS~L   67 (194)
                      .|...++.+|...    ..++|-+|.|||||+-..
T Consensus        88 ~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           88 YAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             HHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            4556788888754    258999999999997544

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=88.10  E-value=0.19  Score=38.90  Aligned_cols=17  Identities=18%  Similarity=0.212  Sum_probs=14.9

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|++++|-+|+|+|||-
T Consensus         4 ~g~~i~i~GpsGsGKST   20 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRH   20 (180)
T ss_dssp             CCCEEEEECCTTSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            46789999999999984

>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=87.87  E-value=0.17  Score=48.96  Aligned_cols=32  Identities=22%  Similarity=0.261  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHhcC-----------CceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDNS-----------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g-----------k~~I~ESPTGTGKTLS   65 (194)
                      +|...|..|..++...           ..++|.+|||||||..
T Consensus       562 G~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~l  604 (854)
T 1qvr_A          562 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTEL  604 (854)
T ss_dssp             SCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHH
T ss_pred             CcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHH
Confidence            4566777777777542           3689999999999964

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=87.85  E-value=0.28  Score=43.18  Aligned_cols=30  Identities=23%  Similarity=0.454  Sum_probs=20.7

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +..|++++|-+|||+|||-. |-.++.++..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTl-l~~l~~~~~~  162 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTT-IASMIDYINQ  162 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHH-HHHHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHH-HHHHHhhcCc
Confidence            45678899999999999843 3333444443

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=87.82  E-value=0.19  Score=39.79  Aligned_cols=17  Identities=24%  Similarity=0.518  Sum_probs=15.2

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|.+++|-+|+|+|||-
T Consensus         7 ~g~~i~l~GpsGsGKsT   23 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGT   23 (208)
T ss_dssp             CCCEEEEECCTTSCHHH
T ss_pred             CCcEEEEECcCCCCHHH
Confidence            57889999999999984

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=87.79  E-value=0.18  Score=38.52  Aligned_cols=20  Identities=25%  Similarity=0.326  Sum_probs=16.6

Q ss_pred             HHhcCCceeeeCCCCCCchH
Q psy14272         45 TLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTL   64 (194)
                      .+..+.+++|.+|.|+|||-
T Consensus         8 ~~~~~~~I~l~G~~GsGKsT   27 (199)
T 2bwj_A            8 DLRKCKIIFIIGGPGSGKGT   27 (199)
T ss_dssp             HHHHSCEEEEEECTTSSHHH
T ss_pred             ccCCCCEEEEECCCCCCHHH
Confidence            34567889999999999984

>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=87.77  E-value=0.36  Score=41.41  Aligned_cols=35  Identities=6%  Similarity=-0.071  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~L~   68 (194)
                      +|.+.+..+...+.+++  +.+|.+|.|+|||-...+
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~   37 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLE   37 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHH
Confidence            47778889999998875  789999999999754443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=87.42  E-value=0.36  Score=37.24  Aligned_cols=24  Identities=21%  Similarity=0.310  Sum_probs=18.2

Q ss_pred             HHhcCCceeeeCCCCCCchHHHHH
Q psy14272         45 TLDNSKFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTLS~L~   68 (194)
                      .+..|.++++-+|+|+|||.-+.+
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~   42 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLH   42 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHH
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHH
Confidence            345678899999999999954333

>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=87.28  E-value=0.48  Score=38.80  Aligned_cols=32  Identities=22%  Similarity=0.115  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS   65 (194)
                      |-.|..+.+   .|.. +.. .+++|.+|.|+|||--
T Consensus        15 ~~gR~~el~---~L~~-l~~-~~v~i~G~~G~GKT~L   46 (357)
T 2fna_A           15 FFDREKEIE---KLKG-LRA-PITLVLGLRRTGKSSI   46 (357)
T ss_dssp             SCCCHHHHH---HHHH-TCS-SEEEEEESTTSSHHHH
T ss_pred             hcChHHHHH---HHHH-hcC-CcEEEECCCCCCHHHH
Confidence            445666655   4444 555 6899999999999953

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=87.28  E-value=0.32  Score=38.16  Aligned_cols=30  Identities=23%  Similarity=0.101  Sum_probs=20.2

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..|.++++.|++|+|||.-.+--+...+..
T Consensus        28 ~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~   57 (251)
T 2zts_A           28 PEGTTVLLTGGTGTGKTTFAAQFIYKGAEE   57 (251)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHHHHh
Confidence            346899999999999995433333333333

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=87.20  E-value=0.21  Score=38.21  Aligned_cols=17  Identities=29%  Similarity=0.351  Sum_probs=15.4

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+..++|-+|+|+|||.
T Consensus        35 ~g~~~~l~G~~G~GKTt   51 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSH   51 (149)
T ss_dssp             CCSEEEEESSSTTTTCH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            68889999999999985

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=87.14  E-value=0.26  Score=43.72  Aligned_cols=45  Identities=33%  Similarity=0.353  Sum_probs=29.5

Q ss_pred             CCccCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         22 PSEFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        22 ~~~~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      ...|.|-  |.|...|.++...+    .+.+-+|.  -++.-+.||||||.+.
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            3445555  56877888877653    23333343  3556899999999986

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=87.10  E-value=0.32  Score=38.12  Aligned_cols=29  Identities=14%  Similarity=0.140  Sum_probs=20.9

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      |..|.++++-+|+|+|||.-.+.-+...+
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            45678999999999999975444434433

>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=86.97  E-value=0.3  Score=40.90  Aligned_cols=15  Identities=27%  Similarity=0.297  Sum_probs=13.2

Q ss_pred             CCceeeeCCCCCCch
Q psy14272         49 SKFGIFESPTGTGKS   63 (194)
Q Consensus        49 gk~~I~ESPTGTGKT   63 (194)
                      +..++|-+|||+|||
T Consensus        34 g~~ilI~GpsGsGKS   48 (205)
T 2qmh_A           34 GLGVLITGDSGVGKS   48 (205)
T ss_dssp             TEEEEEECCCTTTTH
T ss_pred             CEEEEEECCCCCCHH
Confidence            566889999999997

>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=86.62  E-value=0.34  Score=39.51  Aligned_cols=16  Identities=25%  Similarity=0.351  Sum_probs=14.0

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      ..++|.+|+|||||..
T Consensus        65 ~~vLl~G~~GtGKT~l   80 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTAL   80 (272)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECCCCCcHHHH
Confidence            5699999999999964

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=86.54  E-value=0.61  Score=51.36  Aligned_cols=39  Identities=18%  Similarity=0.236  Sum_probs=32.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      .+.|-+.+..-+-.+|+++.....+++-||||+|||.++
T Consensus       902 ~l~~~~~~~~K~~ql~e~~~~r~gvmlvGptgsGKTt~~  940 (2695)
T 4akg_A          902 GFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATW  940 (2695)
T ss_dssp             TCCCCHHHHHHHHHHHHHHHHCSEEEEECSTTSSHHHHH
T ss_pred             CCcccHHHHHHHHHHHHHHHhcceEEEECCCCCCHHHHH
Confidence            455667777777788999988888999999999999764

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=86.49  E-value=0.58  Score=41.53  Aligned_cols=43  Identities=16%  Similarity=0.246  Sum_probs=28.8

Q ss_pred             ccCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      .|.|-  |.|-..|.++...+    .+.+-+|.  .++.-++||||||.+.
T Consensus        45 ~F~FD~Vf~~~~tQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           45 SFNFDRVFHGNETTKNVYEEIAAPIIDSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             EEECSCEECTTSCHHHHHHHTTHHHHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             EEECCEEECCCCCHHHHHHHHHHHHHHHHHcCCccceeeecCCCCCCCeEE
Confidence            34444  56777888877654    23333453  3556899999999997

>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=86.41  E-value=0.24  Score=36.19  Aligned_cols=20  Identities=30%  Similarity=0.419  Sum_probs=15.2

Q ss_pred             CceeeeCCCCCCchHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al   71 (194)
                      .+++|.+|+|+|||-  ++-.|
T Consensus         2 ~~I~l~G~~GsGKsT--~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSE--FAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHH--HHHHH
T ss_pred             cEEEEECCCCCCHHH--HHHHH
Confidence            368899999999994  44444

>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=85.90  E-value=1.7  Score=34.80  Aligned_cols=34  Identities=24%  Similarity=0.289  Sum_probs=21.3

Q ss_pred             CCHHHHHHHHHHHHHHhc-----------CCceeeeCCCCCCchH
Q psy14272         31 AYDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSL   64 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~-----------gk~~I~ESPTGTGKTL   64 (194)
                      -++.+..-+..+...+..           .+-++|.+|+|||||.
T Consensus        20 g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTt   64 (254)
T 1ixz_A           20 GAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTH   64 (254)
T ss_dssp             SCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHH
T ss_pred             CcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHH
Confidence            345555555555544432           1237899999999995

>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=85.76  E-value=0.66  Score=43.20  Aligned_cols=40  Identities=13%  Similarity=0.016  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .-+.|.+.+..      .++.+++.|+.|||||.+++.-+...+..
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            34778885543      35788999999999999877765555544

>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=85.75  E-value=0.86  Score=42.26  Aligned_cols=44  Identities=11%  Similarity=0.187  Sum_probs=34.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .||.++|.|..+|..+.    ....+++..|-|+|||.....-++.++
T Consensus       160 ~~~~l~p~Q~~i~~~l~----~~r~~~i~~~Rq~GKS~~~a~~~l~~~  203 (592)
T 3cpe_A          160 IKVQLRDYQRDMLKIMS----SKRMTVCNLSRQLGKTTVVAIFLAHFV  203 (592)
T ss_dssp             BBCCCCHHHHHHHHHHH----HCSEEEEEECSSSCHHHHHHHHHHHHH
T ss_pred             ccCcCCHHHHHHHHhhc----cccEEEEEEcCccChHHHHHHHHHHHH
Confidence            67889999999998872    357799999999999986554444333

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=85.72  E-value=0.3  Score=38.16  Aligned_cols=19  Identities=16%  Similarity=0.104  Sum_probs=15.3

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..+++++|.+|+|+|||-
T Consensus        22 ~~~~~~i~l~G~~GsGKsT   40 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTT   40 (199)
T ss_dssp             --CCCEEEEECCTTSCHHH
T ss_pred             cCCCCEEEEEcCCCCCHHH
Confidence            3467899999999999984

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=85.64  E-value=0.29  Score=41.00  Aligned_cols=33  Identities=18%  Similarity=0.170  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHH-hcC--CceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTL-DNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L-~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      +|...+..+..++ ..+  .+++|-||+|+|||..+
T Consensus        18 g~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~   53 (354)
T 1sxj_E           18 HNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRC   53 (354)
T ss_dssp             SCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHH
Confidence            5667777888877 554  35899999999999654

>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=85.48  E-value=0.36  Score=41.74  Aligned_cols=17  Identities=35%  Similarity=0.362  Sum_probs=14.0

Q ss_pred             CceeeeCCCCCCchHHH
Q psy14272         50 KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~   66 (194)
                      ..++|.+|+|||||+..
T Consensus        85 ~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCEEEECSTTSCHHHHH
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            45889999999999643

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=85.47  E-value=0.3  Score=38.56  Aligned_cols=17  Identities=29%  Similarity=0.571  Sum_probs=13.7

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|+.++|-+|+|+|||-
T Consensus         3 ~g~~i~lvGpsGaGKST   19 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKST   19 (198)
T ss_dssp             --CCEEEECCTTSSHHH
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            57889999999999984

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=85.45  E-value=0.3  Score=36.75  Aligned_cols=16  Identities=19%  Similarity=0.339  Sum_probs=14.2

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      +.+++|.+|.|+|||-
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            5689999999999994

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=85.43  E-value=0.38  Score=36.52  Aligned_cols=19  Identities=21%  Similarity=0.338  Sum_probs=16.1

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..+.+++|.+|.|+|||-
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            4456789999999999994

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=85.28  E-value=0.58  Score=39.88  Aligned_cols=16  Identities=38%  Similarity=0.438  Sum_probs=13.9

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      +.++|.+|+|||||+.
T Consensus        46 ~~iLL~GppGtGKT~l   61 (322)
T 1xwi_A           46 RGILLFGPPGTGKSYL   61 (322)
T ss_dssp             SEEEEESSSSSCHHHH
T ss_pred             ceEEEECCCCccHHHH
Confidence            5688999999999964

>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=85.11  E-value=0.4  Score=41.98  Aligned_cols=18  Identities=39%  Similarity=0.564  Sum_probs=15.8

Q ss_pred             CCceeeeCCCCCCchHHH
Q psy14272         49 SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~   66 (194)
                      ..++++-||||+|||.++
T Consensus        53 ~~h~~i~G~tGsGKs~~~   70 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLL   70 (437)
T ss_dssp             GGCEEEEECTTSSHHHHH
T ss_pred             cceEEEECCCCCCHHHHH
Confidence            468999999999999975

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=85.07  E-value=0.23  Score=39.58  Aligned_cols=19  Identities=26%  Similarity=0.445  Sum_probs=12.1

Q ss_pred             hcCCceeeeCCCCCCchHH
Q psy14272         47 DNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS   65 (194)
                      ..|.++.|-+|+|+|||-.
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            4578899999999999843

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=84.97  E-value=0.28  Score=38.42  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=16.3

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..+.+++|.+|+|+|||-
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            4567899999999999984

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=84.63  E-value=0.4  Score=43.30  Aligned_cols=39  Identities=21%  Similarity=0.301  Sum_probs=26.7

Q ss_pred             CCCCHHHHHHHHHHHHHH---hcCC--ceeeeCCCCCCchHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTL---DNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L---~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      |.|-..|.++...|...+   -+|.  -++.-+.||||||.+.+
T Consensus       116 F~~~~~Q~~Vf~~v~~lv~~~l~G~N~tifAYGqTGSGKTyTM~  159 (403)
T 4etp_A          116 FDQQDTNVDVFKEVGQLVQSSLDGYNVAIFAYGQTGSGKTFTML  159 (403)
T ss_dssp             ECTTCCHHHHHHHHHHHHHHHHTTCCEEEEEESCTTSSHHHHHH
T ss_pred             ECCCCchHHHHHHHHHHHHHHhCCcceEEEEECCCCCCCceEeC
Confidence            667777877766654333   2453  35568999999999973

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=84.52  E-value=0.29  Score=37.53  Aligned_cols=17  Identities=24%  Similarity=0.393  Sum_probs=14.9

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+..++|++|.|+|||-
T Consensus         3 ~~~~I~l~G~~GsGKsT   19 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTT   19 (204)
T ss_dssp             CCCEEEEECCTTSSHHH
T ss_pred             CCcEEEEEcCCCCCHHH
Confidence            46789999999999984

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=84.44  E-value=0.39  Score=38.54  Aligned_cols=23  Identities=22%  Similarity=0.236  Sum_probs=15.6

Q ss_pred             HHHHHhcCCceeeeCCCCCCchH
Q psy14272         42 LYYTLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        42 I~~~L~~gk~~I~ESPTGTGKTL   64 (194)
                      |--.+..|.++.|-+|+|+|||-
T Consensus        16 isl~i~~G~~~~lvGpsGsGKST   38 (218)
T 1z6g_A           16 PRGSMNNIYPLVICGPSGVGKGT   38 (218)
T ss_dssp             ------CCCCEEEECSTTSSHHH
T ss_pred             CceecCCCCEEEEECCCCCCHHH
Confidence            33345678999999999999983

>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=84.43  E-value=0.56  Score=41.94  Aligned_cols=33  Identities=21%  Similarity=0.063  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHHHh--------------cCCceeeeCCCCCCchHH
Q psy14272         33 DIQSNFMKNLYYTLD--------------NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~--------------~gk~~I~ESPTGTGKTLS   65 (194)
                      -++...+..|..++.              ..+.++|.+|+|||||+.
T Consensus       137 ~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~l  183 (444)
T 2zan_A          137 AGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYL  183 (444)
T ss_dssp             CSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHH
T ss_pred             cCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHH
Confidence            345555666665552              125689999999999964

>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=84.37  E-value=0.45  Score=37.31  Aligned_cols=26  Identities=12%  Similarity=0.014  Sum_probs=19.8

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHH
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      |..|.+++|-+|+|+|||.-+++-+.
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHH
Confidence            44578999999999999975554443

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=84.21  E-value=0.47  Score=41.99  Aligned_cols=39  Identities=21%  Similarity=0.356  Sum_probs=27.9

Q ss_pred             CCCCHHHHHHHHHHHHHHh---cCC--ceeeeCCCCCCchHHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLD---NSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~---~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      |.|-..|.++...|...+.   +|.  -++.-+.||||||.+.+
T Consensus        60 f~~~~~Q~~Vy~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTM~  103 (347)
T 1f9v_A           60 FDQQDTNVDVFKEVGQLVQSSLDGYNVCIFAYGQTGSGKTFTML  103 (347)
T ss_dssp             ECTTCCHHHHHHHHHHHHGGGGGTCCEEEEEECCTTSSHHHHHH
T ss_pred             ECCCCCHHHHHHHHHHHHHHhcCCceeEEEEECCCCCCCcEecc
Confidence            5577788888777655443   343  35668999999999873

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=84.12  E-value=0.39  Score=36.46  Aligned_cols=16  Identities=19%  Similarity=0.063  Sum_probs=14.0

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      .+++++.+|+|+|||-
T Consensus         5 ~~~i~l~G~~GsGKst   20 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTS   20 (185)
T ss_dssp             CCEEEEECSTTSSHHH
T ss_pred             CCEEEEECCCCCCHHH
Confidence            5678999999999984

>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=83.97  E-value=0.24  Score=37.73  Aligned_cols=19  Identities=21%  Similarity=0.237  Sum_probs=16.3

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..|.++++-+|+|+|||-
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            3568889999999999984

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=83.94  E-value=0.7  Score=38.97  Aligned_cols=37  Identities=16%  Similarity=0.259  Sum_probs=23.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHhc------CCceeeeCCCCCCchH
Q psy14272         28 PFDAYDIQSNFMKNLYYTLDN------SKFGIFESPTGTGKSL   64 (194)
Q Consensus        28 Py~py~iQ~e~M~~I~~~L~~------gk~~I~ESPTGTGKTL   64 (194)
                      +|.+..++..+=..+...|..      +..+||-||.|+|||-
T Consensus         6 ~~s~~~~~~~~~~~~~~~l~~~~~~~~~~livl~G~sGsGKST   48 (287)
T 1gvn_B            6 NFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTS   48 (287)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHH
T ss_pred             CCCHHHHHHHHHHHHHHHhccccCCCCCeEEEEECCCCCCHHH
Confidence            455655555444444444432      3568999999999984

>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=83.83  E-value=0.41  Score=37.65  Aligned_cols=20  Identities=20%  Similarity=0.373  Sum_probs=15.8

Q ss_pred             HHhcCCceeeeCCCCCCchH
Q psy14272         45 TLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTL   64 (194)
                      .+..|.++.|-+|+|+|||-
T Consensus        16 ~i~~Gei~~l~GpnGsGKST   35 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKST   35 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHH
T ss_pred             CCCCCCEEEEECCCCCCHHH
Confidence            46789999999999999984

>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=83.83  E-value=0.45  Score=42.73  Aligned_cols=43  Identities=19%  Similarity=0.303  Sum_probs=29.8

Q ss_pred             cCCC--CCCCHHHHHHHHHHHHHHh---cCC--ceeeeCCCCCCchHHHH
Q psy14272         25 FPFP--FDAYDIQSNFMKNLYYTLD---NSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        25 ~~fP--y~py~iQ~e~M~~I~~~L~---~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      |.|-  |.|...|.++...|...+.   +|.  -++.-+.||||||.+.+
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  5577889888877654443   342  35568999999999873

>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=83.73  E-value=0.32  Score=43.58  Aligned_cols=38  Identities=18%  Similarity=0.294  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHHHH---HHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNL---YYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I---~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      |.|...|.++...+   .+.+-+|.  -++.-+.||||||.+.
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            56777888776543   22333453  3555899999999997

>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=83.56  E-value=0.75  Score=43.36  Aligned_cols=37  Identities=14%  Similarity=0.124  Sum_probs=27.7

Q ss_pred             CCCCHHHHHHHHHHHHHHhc--CCceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDN--SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~--gk~~I~ESPTGTGKTLS   65 (194)
                      |.+.-++...+..+.+.|..  +..++|.+|+|||||..
T Consensus       185 ~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~GtGKT~l  223 (758)
T 1r6b_X          185 IDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAI  223 (758)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHH
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCeEEEcCCCCCHHHH
Confidence            34444566677788888864  46799999999999964

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=83.53  E-value=0.79  Score=37.38  Aligned_cols=30  Identities=20%  Similarity=0.231  Sum_probs=20.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .|..++||+|.|+|||-. +-....|+...+
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            467889999999999843 233345665544

>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=83.52  E-value=0.58  Score=36.04  Aligned_cols=21  Identities=14%  Similarity=0.172  Sum_probs=17.2

Q ss_pred             HhcCCceeeeCCCCCCchHHH
Q psy14272         46 LDNSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~   66 (194)
                      |..|.++++-+|+|+|||.-.
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~   37 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLA   37 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHH
T ss_pred             CcCCEEEEEECCCCCCHHHHH
Confidence            446789999999999999543

>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=83.48  E-value=0.75  Score=37.03  Aligned_cols=28  Identities=29%  Similarity=0.266  Sum_probs=22.3

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ..|++.++-+|.|+|||.++|--+..+.
T Consensus         6 ~~g~i~v~~G~mgsGKTT~ll~~a~r~~   33 (191)
T 1xx6_A            6 DHGWVEVIVGPMYSGKSEELIRRIRRAK   33 (191)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3468899999999999988776655554

>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=83.44  E-value=0.48  Score=39.13  Aligned_cols=36  Identities=19%  Similarity=0.242  Sum_probs=25.2

Q ss_pred             HHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        39 M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ++.|.-.|..|.++++-+|+|+|||.-+++-+....
T Consensus        25 Ld~i~~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~   60 (296)
T 1cr0_A           25 INDKTLGARGGEVIMVTSGSGMGKSTFVRQQALQWG   60 (296)
T ss_dssp             HHHHHCSBCTTCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            345554567789999999999999965544443333

>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=83.41  E-value=0.43  Score=38.99  Aligned_cols=17  Identities=24%  Similarity=0.346  Sum_probs=15.2

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|+.++|-+|+|+|||-
T Consensus        18 ~g~~ivl~GPSGaGKsT   34 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSH   34 (197)
T ss_dssp             SCCEEEEECCTTSSHHH
T ss_pred             CCCEEEEECcCCCCHHH
Confidence            57899999999999984

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=83.36  E-value=0.31  Score=36.95  Aligned_cols=17  Identities=35%  Similarity=0.520  Sum_probs=14.6

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|..++|.+|.|||||-
T Consensus         3 ~g~~I~l~G~~GsGKST   19 (186)
T 3cm0_A            3 VGQAVIFLGPPGAGKGT   19 (186)
T ss_dssp             CEEEEEEECCTTSCHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            45678999999999984

>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=83.25  E-value=0.72  Score=44.55  Aligned_cols=37  Identities=14%  Similarity=0.132  Sum_probs=29.2

Q ss_pred             CCCCHHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLS   65 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS   65 (194)
                      |+|.-++.+.+..+.+.|..+  ..++|.+|+|||||..
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~~~~vlL~G~pG~GKT~l  207 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAI  207 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCCCCceEEEcCCCCCHHHH
Confidence            455666778888888888764  4689999999999964

>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=83.20  E-value=0.42  Score=35.33  Aligned_cols=14  Identities=36%  Similarity=0.275  Sum_probs=12.5

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      +++|.+|.|+|||-
T Consensus         3 ~i~l~G~~GsGKsT   16 (173)
T 3kb2_A            3 LIILEGPDCCFKST   16 (173)
T ss_dssp             EEEEECSSSSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57899999999984

>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=83.07  E-value=0.37  Score=44.22  Aligned_cols=16  Identities=38%  Similarity=0.538  Sum_probs=14.0

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      ..++|.+|+|||||+.
T Consensus       239 ~~vLL~GppGtGKT~l  254 (489)
T 3hu3_A          239 RGILLYGPPGTGKTLI  254 (489)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CcEEEECcCCCCHHHH
Confidence            5689999999999974

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=83.03  E-value=0.32  Score=45.59  Aligned_cols=15  Identities=27%  Similarity=0.186  Sum_probs=13.6

Q ss_pred             ceeeeCCCCCCchHH
Q psy14272         51 FGIFESPTGTGKSLS   65 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS   65 (194)
                      +++|.+|+|||||..
T Consensus       329 ~vLL~GppGtGKT~L  343 (595)
T 3f9v_A          329 HILIIGDPGTAKSQM  343 (595)
T ss_dssp             CEEEEESSCCTHHHH
T ss_pred             ceEEECCCchHHHHH
Confidence            799999999999963

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=82.97  E-value=0.47  Score=42.00  Aligned_cols=38  Identities=13%  Similarity=0.288  Sum_probs=27.5

Q ss_pred             CCCCHHHHHHHHHHHHHHh---cCC--ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNLYYTLD---NSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~---~gk--~~I~ESPTGTGKTLS~   66 (194)
                      |.|-..|.++...|...+.   +|.  -++.-+.||||||.+.
T Consensus        61 f~~~~~Q~~vf~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           61 FEPSHTNKEIFEEIRQLVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             ECTTCCHHHHHHHHHHHHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             ECCCccHHHHHHHHHHHHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            5677788887777655443   343  3556899999999987

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=82.94  E-value=0.86  Score=35.90  Aligned_cols=27  Identities=19%  Similarity=0.327  Sum_probs=20.7

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .|.+.++-+|.|+|||..++--+..+.
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~   28 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYK   28 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            367889999999999987765554444

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=82.92  E-value=0.37  Score=42.85  Aligned_cols=16  Identities=44%  Similarity=0.547  Sum_probs=14.0

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      ++++||-+|||+|||-
T Consensus        40 ~~lIvI~GPTgsGKTt   55 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSR   55 (339)
T ss_dssp             CEEEEEECSTTSSHHH
T ss_pred             CceEEEECCCCCCHHH
Confidence            4689999999999994

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=82.89  E-value=0.3  Score=37.58  Aligned_cols=19  Identities=21%  Similarity=0.310  Sum_probs=16.2

Q ss_pred             hcCCceeeeCCCCCCchHH
Q psy14272         47 DNSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS   65 (194)
                      ..|.++.+-+|+|+|||--
T Consensus         7 ~~gei~~l~G~nGsGKSTl   25 (171)
T 4gp7_A            7 PELSLVVLIGSSGSGKSTF   25 (171)
T ss_dssp             ESSEEEEEECCTTSCHHHH
T ss_pred             CCCEEEEEECCCCCCHHHH
Confidence            4678899999999999853

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=82.87  E-value=0.57  Score=39.32  Aligned_cols=16  Identities=25%  Similarity=0.136  Sum_probs=13.0

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      ..++|.+|+|||||..
T Consensus        37 ~~lLl~GppGtGKT~l   52 (293)
T 3t15_A           37 LILGIWGGKGQGKSFQ   52 (293)
T ss_dssp             SEEEEEECTTSCHHHH
T ss_pred             eEEEEECCCCCCHHHH
Confidence            3577889999999963

>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=82.74  E-value=0.59  Score=41.23  Aligned_cols=38  Identities=13%  Similarity=0.060  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      |.|...|.++...+    .+.+-+|.  -++.-++||||||.+.
T Consensus        58 f~~~~~Q~~vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           58 LAEDAGQEAVYQACVQPLLEAFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             ECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             EecCcchhHHHHHHHHHHHHHHHhhcCeeEEEecccCCCceEee
Confidence            56777888776653    33333453  3566899999999986

>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=82.67  E-value=1  Score=45.50  Aligned_cols=40  Identities=18%  Similarity=0.154  Sum_probs=30.7

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      ..+.|.+.+..      .++.+++.|+-|||||.+++--++..+..
T Consensus        11 ~t~eQ~~~i~~------~~~~~~v~a~AGSGKT~vl~~ri~~ll~~   50 (1232)
T 3u4q_A           11 WTDDQWNAIVS------TGQDILVAAAAGSGKTAVLVERMIRKITA   50 (1232)
T ss_dssp             CCHHHHHHHHC------CSSCEEEEECTTCCHHHHHHHHHHHHHSC
T ss_pred             CCHHHHHHHhC------CCCCEEEEecCCCcHHHHHHHHHHHHHhc
Confidence            57899986543      47789999999999999877665555444

>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=82.52  E-value=0.77  Score=37.32  Aligned_cols=29  Identities=24%  Similarity=0.315  Sum_probs=20.2

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .|..++||+|.|+|||-. +--...|+...
T Consensus         5 ~g~~i~~eG~~gsGKsT~-~~~l~~~l~~~   33 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTN-RDYLAERLRER   33 (213)
T ss_dssp             CCEEEEEECSTTSSHHHH-HHHHHHHHHTT
T ss_pred             CceEEEEEcCCCCCHHHH-HHHHHHHHHHc
Confidence            577899999999999842 23334566543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=82.31  E-value=0.55  Score=35.11  Aligned_cols=17  Identities=29%  Similarity=0.442  Sum_probs=14.4

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+.+++|-+|.|+|||-
T Consensus         3 ~~~~i~l~G~~GsGKST   19 (173)
T 1kag_A            3 EKRNIFLVGPMGAGKST   19 (173)
T ss_dssp             CCCCEEEECCTTSCHHH
T ss_pred             CCCeEEEECCCCCCHHH
Confidence            35789999999999984

>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=82.20  E-value=0.48  Score=35.96  Aligned_cols=17  Identities=18%  Similarity=0.171  Sum_probs=14.8

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+.+++|.+|.|+|||-
T Consensus        10 ~~~~i~i~G~~GsGKst   26 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTT   26 (180)
T ss_dssp             CCCCEEEECSTTSSHHH
T ss_pred             cCCeEEEEeCCCCCHHH
Confidence            45789999999999995

>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=81.90  E-value=1.6  Score=39.18  Aligned_cols=42  Identities=12%  Similarity=0.176  Sum_probs=33.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .||.++|.|..+|..+.    ....+++..|-+.|||....+-++.
T Consensus       160 ~p~~L~p~Qk~il~~l~----~~R~~vi~~sRq~GKT~l~a~~~l~  201 (385)
T 2o0j_A          160 IKVQLRDYQRDMLKIMS----SKRMTVCNLSRQLGKTTVVAIFLAH  201 (385)
T ss_dssp             EECCCCHHHHHHHHHHH----HSSEEEEEECSSSCHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHhhc----cCcEEEEEEcCcCChhHHHHHHHHH
Confidence            67889999999998774    3467999999999999865544443

>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=81.85  E-value=0.44  Score=42.29  Aligned_cols=16  Identities=31%  Similarity=0.430  Sum_probs=13.7

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      +++++|-+|||+|||-
T Consensus         3 ~~~i~i~GptgsGKt~   18 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTK   18 (322)
T ss_dssp             CEEEEEECCTTSCHHH
T ss_pred             CcEEEEECCCcCCHHH
Confidence            4578899999999994

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=81.83  E-value=0.47  Score=36.28  Aligned_cols=17  Identities=35%  Similarity=0.444  Sum_probs=14.6

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+..++|++|.|||||-
T Consensus         3 ~~~~I~i~G~~GsGKsT   19 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSS   19 (213)
T ss_dssp             CCEEEEEECCTTSSHHH
T ss_pred             CCeEEEEEcCCCCCHHH
Confidence            35689999999999984

>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=81.77  E-value=0.82  Score=34.60  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=18.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+.+|-+|+|+|||-  |+-+|.|+.
T Consensus        27 g~~~i~G~NGsGKSt--ll~ai~~~l   50 (182)
T 3kta_A           27 GFTAIVGANGSGKSN--IGDAILFVL   50 (182)
T ss_dssp             SEEEEEECTTSSHHH--HHHHHHHHT
T ss_pred             CcEEEECCCCCCHHH--HHHHHHHHH
Confidence            378899999999994  445566654

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=81.71  E-value=0.56  Score=41.70  Aligned_cols=43  Identities=28%  Similarity=0.305  Sum_probs=28.0

Q ss_pred             cCCC--CCCCHHHHHHHHH----HHHHHhcCC--ceeeeCCCCCCchHHHH
Q psy14272         25 FPFP--FDAYDIQSNFMKN----LYYTLDNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        25 ~~fP--y~py~iQ~e~M~~----I~~~L~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      |.|-  |.|...|.++...    +.+.+-+|.  .++.-+.||||||.+.+
T Consensus        49 f~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~   99 (355)
T 1goj_A           49 FTFDRVFDMSCKQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMM   99 (355)
T ss_dssp             EECSEEECTTCCHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHT
T ss_pred             EeeCeEECCCCccHHHHHHHHHHHHHHHhCCCcceEEEECCCCCCcceEee
Confidence            4444  5577788877664    233333453  35568999999999873

>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=81.68  E-value=1.5  Score=36.99  Aligned_cols=35  Identities=17%  Similarity=0.230  Sum_probs=22.6

Q ss_pred             CCHHHHHHHHHHH-HHH-h----cCCceee--eCCCCCCchHH
Q psy14272         31 AYDIQSNFMKNLY-YTL-D----NSKFGIF--ESPTGTGKSLS   65 (194)
Q Consensus        31 py~iQ~e~M~~I~-~~L-~----~gk~~I~--ESPTGTGKTLS   65 (194)
                      -|..+.+.+...+ ..+ .    .+..+++  .+|.|+|||..
T Consensus        26 gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L   68 (412)
T 1w5s_A           26 VRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTL   68 (412)
T ss_dssp             SSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHH
T ss_pred             ChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHH
Confidence            4566666554443 332 2    2357888  99999999964

>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=81.48  E-value=0.97  Score=36.04  Aligned_cols=28  Identities=11%  Similarity=-0.059  Sum_probs=20.3

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .+++|-+|.|+|||- ++...+.++...+
T Consensus         5 ~~i~i~G~sGsGKTT-l~~~L~~~l~~~g   32 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTT-LMEKWVAAAVREG   32 (169)
T ss_dssp             CEEEEECCTTSSHHH-HHHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHH-HHHHHHHhhHhcC
Confidence            467788999999984 5556666766544

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=81.44  E-value=0.33  Score=42.71  Aligned_cols=38  Identities=16%  Similarity=0.204  Sum_probs=25.8

Q ss_pred             CCCCHHHHHHHHHHH---HHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNLY---YTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I~---~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      |.|...|.++...|.   +.+-+|.  -++.-+.||||||.+.
T Consensus        56 f~~~~~Q~~Vy~~v~~lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           56 FSPQASQQDVFQEVQALVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             ECTTCCHHHHHTTTHHHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             eCCCCCcHhHHHHHHHHHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            557778887765532   2223453  3556899999999987

>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=81.43  E-value=0.36  Score=36.58  Aligned_cols=17  Identities=24%  Similarity=0.284  Sum_probs=14.5

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+.+++|.+|.|+|||-
T Consensus         4 ~~~~I~l~G~~GsGKST   20 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTT   20 (193)
T ss_dssp             CCEEEEEEESTTSSHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            35678999999999985

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=81.31  E-value=0.52  Score=35.11  Aligned_cols=15  Identities=33%  Similarity=0.308  Sum_probs=12.9

Q ss_pred             CceeeeCCCCCCchH
Q psy14272         50 KFGIFESPTGTGKSL   64 (194)
Q Consensus        50 k~~I~ESPTGTGKTL   64 (194)
                      .+++|.+|.|+|||-
T Consensus         3 ~~I~i~G~~GsGKST   17 (181)
T 1ly1_A            3 KIILTIGCPGSGKST   17 (181)
T ss_dssp             EEEEEECCTTSSHHH
T ss_pred             eEEEEecCCCCCHHH
Confidence            368899999999984

>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=81.24  E-value=0.58  Score=35.14  Aligned_cols=16  Identities=25%  Similarity=0.358  Sum_probs=13.9

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      +.++++-+|.|+|||-
T Consensus         3 ~~~i~l~G~~GsGKST   18 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSG   18 (178)
T ss_dssp             CCEEEEECCTTSSHHH
T ss_pred             ceEEEEECCCCCCHHH
Confidence            4678999999999984

>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=81.23  E-value=0.91  Score=38.71  Aligned_cols=22  Identities=32%  Similarity=0.371  Sum_probs=16.9

Q ss_pred             CCceeeeCCCCCCchHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGI   70 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~a   70 (194)
                      +.+++|-+|+|+|||-...+-+
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA  126 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLA  126 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            5688889999999996544443

>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=81.19  E-value=0.57  Score=38.18  Aligned_cols=20  Identities=30%  Similarity=0.551  Sum_probs=15.7

Q ss_pred             HHhcCCceeeeCCCCCCchH
Q psy14272         45 TLDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTL   64 (194)
                      .+..|.+++|-+|+|+|||-
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            45678999999999999984

>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=81.08  E-value=0.74  Score=39.92  Aligned_cols=23  Identities=22%  Similarity=0.205  Sum_probs=18.5

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      ++.+|-+|||+|||.  |+-|+.|+
T Consensus        26 gl~vi~G~NGaGKT~--ileAI~~~   48 (371)
T 3auy_A           26 GIVAIIGENGSGKSS--IFEAVFFA   48 (371)
T ss_dssp             EEEEEEECTTSSHHH--HHHHHHHH
T ss_pred             CeEEEECCCCCCHHH--HHHHHHHH
Confidence            578999999999995  45567774

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=80.86  E-value=0.64  Score=41.28  Aligned_cols=38  Identities=24%  Similarity=0.304  Sum_probs=26.3

Q ss_pred             CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         29 FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        29 y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      |.|...|.++...+    .+.+-+|.  -++.-+.||||||.+.
T Consensus        80 f~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A           80 FDETSTQSEVFEHTTKPILRSFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             ECTTCCHHHHHHTTHHHHHHHHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             ECCCCChHHHHHHHHHHHHHHHhCCCceEEEEeCCCCCCceeee
Confidence            56777888776543    33333453  3566899999999987

>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=80.85  E-value=1.3  Score=41.99  Aligned_cols=39  Identities=15%  Similarity=0.085  Sum_probs=28.2

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .-|.|.+.+..      .++.+++.|+.|||||.+++.-+...+.
T Consensus        12 Ln~~Q~~av~~------~~g~~lV~AgAGSGKT~vL~~ri~~ll~   50 (724)
T 1pjr_A           12 LNKEQQEAVRT------TEGPLLIMAGAGSGKTRVLTHRIAYLMA   50 (724)
T ss_dssp             SCHHHHHHHHC------CSSCEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC------CCCCEEEEEcCCCCHHHHHHHHHHHHHH
Confidence            45788885443      3568899999999999987766444443

>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=80.84  E-value=1  Score=35.58  Aligned_cols=26  Identities=23%  Similarity=0.301  Sum_probs=18.7

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .+++|-+|+|+|||- ++..++.++..
T Consensus         7 ~~i~i~G~sGsGKTT-l~~~l~~~l~~   32 (174)
T 1np6_A            7 PLLAFAAWSGTGKTT-LLKKLIPALCA   32 (174)
T ss_dssp             CEEEEECCTTSCHHH-HHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHH-HHHHHHHhccc
Confidence            568889999999984 45555555544

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=80.76  E-value=1.5  Score=49.11  Aligned_cols=47  Identities=15%  Similarity=0.063  Sum_probs=35.1

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHH--HHHHHHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSL--ICGILKW   73 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~--L~~al~w   73 (194)
                      ..+.|-|.+..=+-.+|+++.-..-+++-||||+|||-++  |+.+++-
T Consensus       884 ~~L~~~~~~v~KviQLye~~~vRhGvmlVGp~gsGKTt~~~~L~~al~~  932 (3245)
T 3vkg_A          884 RHLVTKQEWVEKILQLHQILNINHGVMMVGPSGGGKTTSWEVYLEAIEQ  932 (3245)
T ss_dssp             TTCCCCHHHHHHHHHHHHHHTTCSEEEEECSSSSSHHHHHHHHHHHHTT
T ss_pred             cCCccCHHHHHHHHHHHHHHHheeeEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3456677777777788888877777899999999999875  3344443

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=80.66  E-value=2.6  Score=34.45  Aligned_cols=35  Identities=23%  Similarity=0.261  Sum_probs=22.0

Q ss_pred             CCHHHHHHHHHHHHHHhc-----------CCceeeeCCCCCCchHH
Q psy14272         31 AYDIQSNFMKNLYYTLDN-----------SKFGIFESPTGTGKSLS   65 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~-----------gk~~I~ESPTGTGKTLS   65 (194)
                      -++.+..-+..+...+..           .+.++|.+|+|||||..
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            345555555555554432           12378999999999953

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=80.35  E-value=0.82  Score=40.83  Aligned_cols=45  Identities=13%  Similarity=0.101  Sum_probs=29.9

Q ss_pred             CCccCCC--CCCCHHHHHHHHHHH----HHHhcCC--ceeeeCCCCCCchHHH
Q psy14272         22 PSEFPFP--FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        22 ~~~~~fP--y~py~iQ~e~M~~I~----~~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      +..|.|-  |.|...|.++...+.    +.+-+|.  .++.-+.||||||.+.
T Consensus        50 ~~~f~FD~Vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           50 GKVYLFDKVFKPNASQEKVYNEAAKSIVTDVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             TEEEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             CEEEeCceEecCCCCHHHHHHHhhhhHHHHHhCCCceEEEeecCCCCCCceEE
Confidence            3345554  668888888766542    3333453  3556899999999997

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=80.33  E-value=0.63  Score=41.37  Aligned_cols=39  Identities=21%  Similarity=0.173  Sum_probs=26.9

Q ss_pred             CCCCHHHHHHHHHHH----HHHhcCC--ceeeeCCCCCCchHHHH
Q psy14272         29 FDAYDIQSNFMKNLY----YTLDNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        29 y~py~iQ~e~M~~I~----~~L~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      |.|...|.++...+.    +.+-+|.  -++.-+.||||||.+.+
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            567788888776543    2333453  35568999999999874

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=80.09  E-value=0.47  Score=35.62  Aligned_cols=14  Identities=43%  Similarity=0.639  Sum_probs=12.4

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      .++|++|.|+|||-
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            58899999999984

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=80.09  E-value=0.58  Score=37.13  Aligned_cols=17  Identities=18%  Similarity=0.263  Sum_probs=14.2

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      ....++|.+|+|+|||-
T Consensus         6 ~~~~I~l~G~~GsGKsT   22 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGT   22 (227)
T ss_dssp             -CCEEEEEECTTSSHHH
T ss_pred             cCcEEEEECCCCCCHHH
Confidence            45679999999999984

>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=80.06  E-value=0.76  Score=40.32  Aligned_cols=45  Identities=13%  Similarity=0.152  Sum_probs=29.7

Q ss_pred             CccCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHHH
Q psy14272         23 SEFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        23 ~~~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      ..|.|-  |.|...|.++...+    .+.+-+|.  -++.-+.||||||.+.+
T Consensus        44 ~~f~FD~Vf~~~~sQ~~Vy~~~~~plv~~~l~G~n~tifAYGqTGSGKTyTm~   96 (325)
T 1bg2_A           44 KPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTME   96 (325)
T ss_dssp             EEEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             EEEECCeEeCCCCCHHHHHHHHhhhhHHHHhCCCeEEEEEECCCCCCCceEec
Confidence            344454  56777888876554    33333453  35668999999999974

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=80.04  E-value=0.58  Score=35.20  Aligned_cols=16  Identities=19%  Similarity=0.177  Sum_probs=13.7

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      +.+++|.+|.|||||-
T Consensus         3 ~~~I~l~G~~GsGKsT   18 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGT   18 (196)
T ss_dssp             CEEEEEECCTTSSHHH
T ss_pred             ceEEEEECCCCCCHHH
Confidence            4578999999999984

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.02  E-value=0.85  Score=41.62  Aligned_cols=16  Identities=44%  Similarity=0.638  Sum_probs=13.8

Q ss_pred             CceeeeCCCCCCchHH
Q psy14272         50 KFGIFESPTGTGKSLS   65 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS   65 (194)
                      +-++|-+|+|||||+.
T Consensus       216 rGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          216 KGALMYGPPGTGKTLL  231 (434)
T ss_dssp             CEEEEESCTTSSHHHH
T ss_pred             CeeEEECcCCCCHHHH
Confidence            4589999999999964

---

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	194
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.91
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.88
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.83
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.81
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.81
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	98.74
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.7
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.68
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.67
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	98.57
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	98.52
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	98.39
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.35
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	97.95
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.9
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	97.82
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	97.81
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	97.74
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.56
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	96.51
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.1
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	95.92
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	95.57
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.53
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	95.42
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.37
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	95.34
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	95.19
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.07
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	95.02
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	94.92
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.75
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	94.58
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	94.54
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.07
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	93.87
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	93.59
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	93.57
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.55
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	93.38
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	93.32
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	93.32
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	92.9
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	92.77
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	92.74
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	92.54
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.53
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	92.42
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	92.13
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	91.93
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	91.87
d1okkd2	207	GTPase domain of the signal recognition particle r	91.77
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	91.75
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	91.74
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	91.42
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	91.18
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	90.98
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	90.68
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	90.66
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	90.62
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	90.53
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	90.48
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	90.45
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	90.36
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	89.89
d1vmaa2	213	GTPase domain of the signal recognition particle r	89.76
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	89.67
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	89.57
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	89.41
d1j8yf2	211	GTPase domain of the signal sequence recognition p	89.32
d1ls1a2	207	GTPase domain of the signal sequence recognition p	89.24
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	89.23
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	89.08
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	88.23
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	87.84
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	87.79
d2qy9a2	211	GTPase domain of the signal recognition particle r	87.64
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	87.6
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	87.27
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	87.16
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	87.02
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	86.66
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	86.52
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	86.39
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	86.37
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	86.35
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	86.32
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	86.02
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	85.85
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	85.82
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	85.48
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	85.46
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	85.19
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	85.07
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	85.01
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	84.53
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	84.53
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	84.43
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	84.29
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	83.96
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	83.89
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	83.55
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	83.53
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	83.42
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	83.18
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	83.05
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	82.88
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	82.76
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	82.53
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	82.35
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	81.42
d1tuea_	205	Replication protein E1 helicase domain {Human papi	81.32
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	81.03
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	80.77
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	80.6

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.91  E-value=3e-10  Score=89.34  Aligned_cols=48  Identities=21%  Similarity=0.243  Sum_probs=40.7

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +.|. |+|+|.+.+..+    -+|+++|+.||||||||+||++|++..+....
T Consensus        19 ~g~~~pt~iQ~~aip~~----l~G~dvii~a~TGSGKTlayllp~l~~~~~~~   67 (209)
T d1q0ua_          19 LRFYKPTEIQERIIPGA----LRGESMVGQSQTGTGKTHAYLLPIMEKIKPER   67 (209)
T ss_dssp             TTCCSCCHHHHHHHHHH----HHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS
T ss_pred             CCCCCCCHHHHHHHHHH----HCCCCeEeecccccccceeeeeeecccccccc
Confidence            5676 999999987765    46899999999999999999999988775443

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=7.7e-10  Score=88.49  Aligned_cols=50  Identities=18%  Similarity=0.114  Sum_probs=42.4

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      ...|+ |+|+|...+..+    -+|+++|+.||||||||+||++|++..+...+.
T Consensus        20 ~~g~~~pt~iQ~~aip~i----l~g~dvl~~a~TGsGKTlayllP~l~~~~~~~~   70 (206)
T d1veca_          20 EMGWEKPSPIQEESIPIA----LSGRDILARAKNGTGKSGAYLIPLLERLDLKKD   70 (206)
T ss_dssp             TTTCCSCCHHHHHHHHHH----HTTCCEEEECCSSSTTHHHHHHHHHHHCCTTSC
T ss_pred             HCCCCCCCHHHHHHHHHH----HcCCCEEeeccCccccccccccchhhccccccc
Confidence            46786 999999987776    479999999999999999999999987765443

>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=98.83  E-value=1.2e-09  Score=87.34  Aligned_cols=48  Identities=13%  Similarity=0.174  Sum_probs=41.6

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ..|+ |+|+|...+..+.    +|+++|+.||||||||++|++|++..+....
T Consensus        19 ~g~~~pt~iQ~~aip~il----~g~dvl~~A~TGsGKTla~~lp~l~~~~~~~   67 (207)
T d1t6na_          19 CGFEHPSEVQHECIPQAI----LGMDVLCQAKSGMGKTAVFVLATLQQLEPVT   67 (207)
T ss_dssp             TTCCCCCHHHHHHHHHHH----TTCCEEEECCTTSCHHHHHHHHHHHHCCCCT
T ss_pred             CCCCCCCHHHHHHHHHHH----cCCCeEEEeccccccccccccceeeeecccC
Confidence            4676 9999999888874    7899999999999999999999998876544

>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=98.81  E-value=2.2e-09  Score=87.87  Aligned_cols=48  Identities=17%  Similarity=0.226  Sum_probs=41.9

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ...|. |+|+|...+..+.    +|+++|+.||||||||+||++|+|..+...
T Consensus        38 ~~g~~~pt~iQ~~~ip~il----~g~dvvi~a~TGsGKTlayllp~l~~l~~~   86 (238)
T d1wrba1          38 LASYQRPTPIQKNAIPAIL----EHRDIMACAQTGSGKTAAFLIPIINHLVCQ   86 (238)
T ss_dssp             TTTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             HCCCCCCCHHHHHHhhhhh----CCCCEEEECCCCCCcceeeHHHHHHHHHhc
Confidence            45787 9999999887764    799999999999999999999999987543

>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=98.81  E-value=1.4e-09  Score=88.66  Aligned_cols=50  Identities=22%  Similarity=0.295  Sum_probs=42.4

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ..|. |+|+|...+..+.    +|+++|+.||||||||+||++|++..+......
T Consensus        35 ~g~~~pt~IQ~~aIp~il----~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~   85 (222)
T d2j0sa1          35 YGFEKPSAIQQRAIKQII----KGRDVIAQSQSGTGKTATFSISVLQCLDIQVRE   85 (222)
T ss_dssp             HTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCS
T ss_pred             CCCCCCCHHHHHHHHHHH----CCCCeEEEcCcchhhhhhhcccccccccccccC
Confidence            3576 9999999877764    689999999999999999999999988665443

>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=98.74  E-value=1.9e-09  Score=84.33  Aligned_cols=44  Identities=23%  Similarity=0.251  Sum_probs=37.4

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .|+|+ +||+|.+.++.+    .+|+++|+.+|||+|||++|++|++..
T Consensus        20 ~fg~~~~rp~Q~~ai~~~----l~g~~vlv~apTGsGKT~~~~~~~~~~   64 (206)
T d1oywa2          20 TFGYQQFRPGQEEIIDTV----LSGRDCLVVMPTGGGKSLCYQIPALLL   64 (206)
T ss_dssp             TTCCSSCCTTHHHHHHHH----HTTCCEEEECSCHHHHHHHHHHHHHHS
T ss_pred             hcCCCCCCHHHHHHHHHH----HcCCCEEEEcCCCCCCcchhhhhhhhc
Confidence            46776 899999988775    468899999999999999999998753

>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=98.70  E-value=6.3e-09  Score=83.69  Aligned_cols=50  Identities=16%  Similarity=0.191  Sum_probs=42.7

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      ...|+ |+|+|...+..+.    .|+++|+.||||||||++|++|++..+.....
T Consensus        27 ~~g~~~pt~iQ~~aip~il----~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~~   77 (212)
T d1qdea_          27 GYGFEEPSAIQQRAIMPII----EGHDVLAQAQSGTGKTGTFSIAALQRIDTSVK   77 (212)
T ss_dssp             HHTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHHCCTTCC
T ss_pred             HCCCCCCCHHHHHHHHHHH----cCCCEEeecccccchhhhhHhhhHhhhhccCC
Confidence            35677 9999999888764    79999999999999999999999998865433

>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=98.68  E-value=7.1e-09  Score=82.11  Aligned_cols=48  Identities=17%  Similarity=0.153  Sum_probs=40.8

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      ..|. |+|+|...+..+.    +|+++|+.||||||||++|+.|++..+....
T Consensus        19 ~g~~~pt~iQ~~aip~il----~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~   67 (206)
T d1s2ma1          19 AGFEKPSPIQEEAIPVAI----TGRDILARAKNGTGKTAAFVIPTLEKVKPKL   67 (206)
T ss_dssp             TTCCSCCHHHHHHHHHHH----HTCCEEEECCTTSCHHHHHHHHHHHHCCTTS
T ss_pred             CCCCCCCHHHHHHHHHHH----cCCCEEEecCCcchhhhhhcccccccccccc
Confidence            4676 9999999888764    6899999999999999999999988765443

>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=98.67  E-value=8e-09  Score=83.50  Aligned_cols=48  Identities=21%  Similarity=0.202  Sum_probs=41.1

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      .+.|. |+|+|...+..+    ..|+++|+.||||||||++|++|++..+...
T Consensus        29 ~~g~~~pt~iQ~~aip~i----l~g~dvl~~a~TGsGKTlayllp~l~~i~~~   77 (218)
T d2g9na1          29 AYGFEKPSAIQQRAILPC----IKGYDVIAQAQSGTGKTATFAISILQQIELD   77 (218)
T ss_dssp             HHTCCSCCHHHHHHHHHH----HHTCCEEEECCTTSSHHHHHHHHHHHHCCTT
T ss_pred             HCCCCCCCHHHHHHHHHH----HcCCCEEEEcccchhhhhhhhhhhhheeccc
Confidence            45776 999999977765    3789999999999999999999999887543

>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=98.57  E-value=2.4e-08  Score=79.72  Aligned_cols=44  Identities=20%  Similarity=0.122  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      +||++|...+..+    -.|+.+|+.||||+|||++++++++..+...
T Consensus        43 ~p~~~Q~~~i~~~----l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~   86 (237)
T d1gkub1          43 EPRAIQKMWAKRI----LRKESFAATAPTGVGKTSFGLAMSLFLALKG   86 (237)
T ss_dssp             SCCHHHHHHHHHH----HTTCCEECCCCBTSCSHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHH----HCCCCEEEEecCCChHHHHHHHHHHHHHHhc
Confidence            4999999977765    3789999999999999999999988766544

>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=98.52  E-value=2.8e-08  Score=76.36  Aligned_cols=47  Identities=15%  Similarity=-0.027  Sum_probs=36.5

Q ss_pred             CCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        29 y~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ++||+.|.+.+..++     ++++|+.+|||+|||+.++.++...+...+.+
T Consensus         8 ~~pr~~Q~~~~~~~~-----~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~   54 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-----ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGK   54 (200)
T ss_dssp             HCCCHHHHHHHHHGG-----GSCEEEECCTTSCHHHHHHHHHHHHHHHSCSC
T ss_pred             CCCCHHHHHHHHHHh-----cCCeEEEeCCCCcHHHHHHHHHHHHHHhcCCc
Confidence            469999999777652     45689999999999998888877666554443

>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=98.39  E-value=1.6e-07  Score=74.43  Aligned_cols=46  Identities=22%  Similarity=0.303  Sum_probs=37.3

Q ss_pred             CCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         27 FPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        27 fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ..|. |+|+|.+.+..+   |..+..+|+.||||||||++|+.|++....
T Consensus        22 ~g~~~pt~iQ~~~ip~~---l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~   68 (208)
T d1hv8a1          22 KGFEKPTDIQMKVIPLF---LNDEYNIVAQARTGSGKTASFAIPLIELVN   68 (208)
T ss_dssp             HTCCSCCHHHHHHHHHH---HHTCSEEEEECCSSSSHHHHHHHHHHHHSC
T ss_pred             CCCCCCCHHHHHHHHHH---HcCCCCeeeechhcccccceeecccccccc
Confidence            4575 999999976665   444568999999999999999999887543

>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=98.35  E-value=5.1e-08  Score=76.01  Aligned_cols=44  Identities=16%  Similarity=0.199  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         30 DAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        30 ~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      ++||+|.+.+..+    .+|+.+|+.+|||+|||++++++++..+...
T Consensus        25 ~l~~~Q~~ai~~l----~~~~~~il~apTGsGKT~~a~l~i~~~~~~~   68 (202)
T d2p6ra3          25 ELFPPQAEAVEKV----FSGKNLLLAMPTAAGKTLLAEMAMVREAIKG   68 (202)
T ss_dssp             CCCCCCHHHHHHH----TTCSCEEEECSSHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHH----HcCCCEEEEcCCCCchhHHHHHHHHHHhhcc
Confidence            3889999977665    4688999999999999999988877665543

>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=97.95  E-value=4.8e-06  Score=65.49  Aligned_cols=42  Identities=26%  Similarity=0.335  Sum_probs=31.8

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      .+..++++||.|.+.++.+   + +++.+|+.+|||+|||+..+..
T Consensus        64 ~~~~~~~Lr~yQ~eav~~~---~-~~~~~ll~~~tG~GKT~~a~~~  105 (206)
T d2fz4a1          64 YFDAEISLRDYQEKALERW---L-VDKRGCIVLPTGSGKTHVAMAA  105 (206)
T ss_dssp             CCCCCCCCCHHHHHHHHHH---T-TTSEEEEEESSSTTHHHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHH---H-hCCCcEEEeCCCCCceehHHhH
Confidence            4456678999999966543   3 4567889999999999876544

>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=97.90  E-value=1.8e-06  Score=60.97  Aligned_cols=35  Identities=17%  Similarity=0.251  Sum_probs=29.1

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      |+.|+.+|+.+|||+|||+.++..++..+...+..
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~~~   38 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLR   38 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTTCC
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhcCce
Confidence            56789999999999999999888877777665544

>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=97.82  E-value=1.7e-06  Score=69.33  Aligned_cols=34  Identities=15%  Similarity=0.281  Sum_probs=27.3

Q ss_pred             HHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      +|..|+++|+.||||+|||++||.+++.-....+
T Consensus         5 ~~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~   38 (305)
T d2bmfa2           5 IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRG   38 (305)
T ss_dssp             SSSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHT
T ss_pred             HhhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcC
Confidence            4567899999999999999999888776444433

>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=97.81  E-value=6.1e-06  Score=68.63  Aligned_cols=45  Identities=22%  Similarity=0.300  Sum_probs=33.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      .||+||+.|.+   ++..+|.+ +.+|+.+|||+|||+..++. +.++..
T Consensus       110 ~~~~~rdyQ~~---av~~~l~~-~~~il~~pTGsGKT~i~~~i-~~~~~~  154 (282)
T d1rifa_         110 KRIEPHWYQKD---AVFEGLVN-RRRILNLPTSAGRSLIQALL-ARYYLE  154 (282)
T ss_dssp             EECCCCHHHHH---HHHHHHHH-SEEEECCCTTSCHHHHHHHH-HHHHHH
T ss_pred             CccccchHHHH---HHHHHHhc-CCceeEEEcccCccHHHHHH-HHHhhh
Confidence            47899999999   55556665 46899999999999875443 444433

>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=97.74  E-value=2.4e-05  Score=64.37  Aligned_cols=53  Identities=17%  Similarity=0.198  Sum_probs=46.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHHHHHHHHHHhhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILKWYYDHK   78 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~L~~al~wl~~~~   78 (194)
                      .|||...+.|..-+..|...+..+.  ..++.+.||||||..|+.+++..+...+
T Consensus        51 ~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~  105 (233)
T d2eyqa3          51 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHK  105 (233)
T ss_dssp             TCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTTC
T ss_pred             ccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcCC
Confidence            6999999999999999999999875  6799999999999999999877665433

>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=97.56  E-value=6.1e-05  Score=62.98  Aligned_cols=54  Identities=19%  Similarity=0.260  Sum_probs=47.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .|||+..+.|...+..|+..+..+.  .-++.|.||||||..|+.+++..+....+
T Consensus        79 ~LPFeLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q  134 (264)
T d1gm5a3          79 SLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQ  134 (264)
T ss_dssp             HSSSCCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSC
T ss_pred             hccccCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhcccc
Confidence            5999999999999999999998774  67999999999999999998877765443

>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=96.51  E-value=0.00049  Score=49.40  Aligned_cols=19  Identities=32%  Similarity=0.567  Sum_probs=16.0

Q ss_pred             cCCceeeeCCCCCCchHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~   66 (194)
                      ..+++|+.+|||+|||+.+
T Consensus         7 ~~~~~ll~apTGsGKT~~~   25 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKV   25 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            4578999999999999753

>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=96.10  E-value=0.0029  Score=48.76  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=30.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcC------CceeeeCCCCCCchHH
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNS------KFGIFESPTGTGKSLS   65 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~g------k~~I~ESPTGTGKTLS   65 (194)
                      .-|+++..|-.+...|-..+...      +.++|-+|+|||||..
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~l   48 (273)
T d1gvnb_           4 VNFTDKQFENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSL   48 (273)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHH
T ss_pred             cccChHHHHHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHH
Confidence            35788899999998886665432      3478999999999963

>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=95.92  E-value=0.0065  Score=47.14  Aligned_cols=41  Identities=15%  Similarity=-0.019  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      .||.|.+-+..++.....+.-+|+--++|+|||+..|..+.
T Consensus        13 L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~~~~   53 (230)
T d1z63a1          13 LRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFS   53 (230)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHHhhh
Confidence            68999999888887777777789999999999998765543

>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=95.57  E-value=0.0057  Score=46.47  Aligned_cols=36  Identities=25%  Similarity=0.157  Sum_probs=22.6

Q ss_pred             CCHHHHH-HHHHHHHHHhc----CCceeeeCCCCCCchHHH
Q psy14272         31 AYDIQSN-FMKNLYYTLDN----SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        31 py~iQ~e-~M~~I~~~L~~----gk~~I~ESPTGTGKTLS~   66 (194)
                      -|..|.+ ++..|..++.+    ..+++|.+|+|||||...
T Consensus        20 ~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          20 HREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             TCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHH
Confidence            4566654 33333333332    157999999999999643

>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=95.53  E-value=0.0039  Score=47.93  Aligned_cols=34  Identities=24%  Similarity=0.326  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHH
Q psy14272         33 DIQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      -+|....+.|..++.++  .++||.||+|||||...
T Consensus        27 ig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          27 VGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHH
T ss_pred             cCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHH
Confidence            35678888899999887  56899999999998654

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=95.42  E-value=0.0078  Score=46.72  Aligned_cols=40  Identities=10%  Similarity=0.072  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHHHHHHHhcCC---ceeeeCCCCCCchHHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNSK---FGIFESPTGTGKSLSLICGI   70 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~gk---~~I~ESPTGTGKTLS~L~~a   70 (194)
                      .||.|....+.+...+.+++   ..||.+|.|+|||....+-+
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            57888888889999998875   38999999999997655543

>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=95.37  E-value=0.0058  Score=46.71  Aligned_cols=32  Identities=28%  Similarity=0.422  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHHHHhcCC--ceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--FGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~~I~ESPTGTGKTLS   65 (194)
                      +|.+....|..++.++.  ++||.||+|||||..
T Consensus        18 g~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl   51 (227)
T d1sxjc2          18 GQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTST   51 (227)
T ss_dssp             SCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHH
Confidence            35567778888888875  589999999999954

>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=95.34  E-value=0.0086  Score=45.68  Aligned_cols=38  Identities=11%  Similarity=-0.068  Sum_probs=25.3

Q ss_pred             CCHHH-HHHHHHHHHHHhcCC-------ceeeeCCCCCCchHHHHH
Q psy14272         31 AYDIQ-SNFMKNLYYTLDNSK-------FGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        31 py~iQ-~e~M~~I~~~L~~gk-------~~I~ESPTGTGKTLS~L~   68 (194)
                      -|+.| ..++..++..+.+|.       +++|-+|+|||||...-.
T Consensus        20 ~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~   65 (287)
T d1w5sa2          20 VRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKF   65 (287)
T ss_dssp             SSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHH
Confidence            34555 455566667776652       356789999999976433

>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=95.19  E-value=0.0037  Score=48.20  Aligned_cols=33  Identities=27%  Similarity=0.369  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHhc----C---CceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDN----S---KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~----g---k~~I~ESPTGTGKTLS~   66 (194)
                      +|....+.|..++..    +   .++||.||+|||||...
T Consensus        13 Gqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          13 GQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             SCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHH
Confidence            466666666665542    2   46999999999999753

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.07  E-value=0.0068  Score=43.08  Aligned_cols=30  Identities=20%  Similarity=0.297  Sum_probs=22.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +++++-+|+|||||- ++..++..+...+..
T Consensus         2 k~v~ItG~~GtGKTt-l~~~i~~~l~~~~~~   31 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTT-LIHKASEVLKSSGVP   31 (189)
T ss_dssp             CCEEEESCCSSCHHH-HHHHHHHHHHHTTCC
T ss_pred             cEEEEECCCCCcHHH-HHHHHHHHHHHCCCE
Confidence            578999999999997 555556666655443

>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=95.02  E-value=0.007  Score=46.45  Aligned_cols=33  Identities=18%  Similarity=0.197  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHhcC--CceeeeCCCCCCchHHH
Q psy14272         34 IQSNFMKNLYYTLDNS--KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~   66 (194)
                      +|.+....|..++.++  .++||.||.|+|||...
T Consensus        19 g~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a   53 (224)
T d1sxjb2          19 GNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSV   53 (224)
T ss_dssp             SCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhH
Confidence            4556677888899887  46899999999999654

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=94.92  E-value=0.0081  Score=46.29  Aligned_cols=35  Identities=20%  Similarity=0.198  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHHhc-------CCceeeeCCCCCCchHHHHH
Q psy14272         34 IQSNFMKNLYYTLDN-------SKFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~-------gk~~I~ESPTGTGKTLS~L~   68 (194)
                      +|.+....+..++..       -.++||.+|+|||||...-+
T Consensus        13 Gq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~   54 (239)
T d1ixsb2          13 GQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHV   54 (239)
T ss_dssp             SCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHH
Confidence            566666666666642       25799999999999966544

>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=94.75  E-value=0.013  Score=45.87  Aligned_cols=36  Identities=14%  Similarity=0.057  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      |.|.+.+..      ..+++++.||.|||||.+++.-+...+
T Consensus         4 ~eQ~~av~~------~~~~~lI~g~aGTGKTt~l~~rv~~ll   39 (306)
T d1uaaa1           4 PGQQQAVEF------VTGPCLVLAGAGSGKTRVITNKIAHLI   39 (306)
T ss_dssp             HHHHHHHHC------CSSEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhC------CCCCEEEEeeCCccHHHHHHHHHHHHH
Confidence            678875532      245688889999999988765543333

>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=94.58  E-value=0.014  Score=46.37  Aligned_cols=37  Identities=16%  Similarity=0.113  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         33 DIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +.|.+.++.      .++.++|-||.|||||.+++.-+...+.
T Consensus        14 ~eQ~~~v~~------~~g~~lV~g~aGSGKTt~l~~ri~~ll~   50 (318)
T d1pjra1          14 KEQQEAVRT------TEGPLLIMAGAGSGKTRVLTHRIAYLMA   50 (318)
T ss_dssp             HHHHHHHHC------CSSCEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhC------CCCCEEEEecCCccHHHHHHHHHHHHHH
Confidence            678775543      2467888899999999998776544443

>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=94.54  E-value=0.0057  Score=46.53  Aligned_cols=34  Identities=26%  Similarity=0.395  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHhcC--CceeeeCCCCCCchHHHHHH
Q psy14272         36 SNFMKNLYYTLDNS--KFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        36 ~e~M~~I~~~L~~g--k~~I~ESPTGTGKTLS~L~~   69 (194)
                      ......|..++.++  .+++|.||+|+|||...-+-
T Consensus        18 ~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i   53 (237)
T d1sxjd2          18 DHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILAL   53 (237)
T ss_dssp             CTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHH
Confidence            34455677777776  45899999999998654443

>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=94.07  E-value=0.018  Score=47.38  Aligned_cols=18  Identities=33%  Similarity=0.377  Sum_probs=14.9

Q ss_pred             CCceeeeCCCCCCchHHH
Q psy14272         49 SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~   66 (194)
                      .+.++|.+|||||||+-.
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467889999999999643

>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=93.87  E-value=0.015  Score=48.84  Aligned_cols=38  Identities=21%  Similarity=0.198  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         37 NFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        37 e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +++..+..++..++.++|-+|||||||-. |-+.+.++-
T Consensus       154 ~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i~  191 (323)
T d1g6oa_         154 QAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFIP  191 (323)
T ss_dssp             HHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGSC
T ss_pred             HHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhcc
Confidence            55667778888999999999999999953 444444443

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.59  E-value=0.012  Score=45.09  Aligned_cols=34  Identities=21%  Similarity=0.274  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHhcC---CceeeeCCCCCCchHHHHH
Q psy14272         35 QSNFMKNLYYTLDNS---KFGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        35 Q~e~M~~I~~~L~~g---k~~I~ESPTGTGKTLS~L~   68 (194)
                      |.+....|..++.++   ..+||.||.|||||....+
T Consensus        16 ~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~   52 (252)
T d1sxje2          16 NEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMA   52 (252)
T ss_dssp             CHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHT
T ss_pred             cHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHH
Confidence            455666776777655   3589999999999976543

>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=93.57  E-value=0.026  Score=44.00  Aligned_cols=35  Identities=20%  Similarity=0.205  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHhcCC--c-eeeeCCCCCCchHHHHH
Q psy14272         34 IQSNFMKNLYYTLDNSK--F-GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~gk--~-~I~ESPTGTGKTLS~L~   68 (194)
                      +|.+.+..+..++.+++  + +||.+|+|+|||....+
T Consensus        16 g~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~   53 (239)
T d1njfa_          16 GQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARL   53 (239)
T ss_dssp             SCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHH
T ss_pred             ChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHH
Confidence            36778888888898774  2 78999999999976544

>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=93.55  E-value=0.024  Score=48.53  Aligned_cols=45  Identities=18%  Similarity=0.205  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHHHh-cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         33 DIQSNFMKNLYYTLD-NSKFGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        33 ~iQ~e~M~~I~~~L~-~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      +.|.+.+..+   +. ..+.+||-+|||+|||-+ |.+++.++....+++
T Consensus       144 ~~~~~~l~~l---~~~~~GliLvtGpTGSGKSTT-l~~~l~~~~~~~~~i  189 (401)
T d1p9ra_         144 AHNHDNFRRL---IKRPHGIILVTGPTGSGKSTT-LYAGLQELNSSERNI  189 (401)
T ss_dssp             HHHHHHHHHH---HTSSSEEEEEECSTTSCHHHH-HHHHHHHHCCTTSCE
T ss_pred             HHHHHHHHHH---HhhhhceEEEEcCCCCCccHH-HHHHhhhhcCCCceE
Confidence            5666654443   43 357899999999999976 555688886554443

>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=93.38  E-value=0.057  Score=43.33  Aligned_cols=44  Identities=25%  Similarity=0.154  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHHHHhc-----CCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         31 AYDIQSNFMKNLYYTLDN-----SKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~-----gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      -||.|.+-++.+++++..     +.-+|+--..|+|||+..|+-+...+
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            689999999999888753     34578888999999998776543333

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=93.32  E-value=0.015  Score=41.22  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=16.6

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      +.++|.||+|||||-  ||-+|+
T Consensus         8 K~I~i~G~~GsGKTT--la~~La   28 (192)
T d1lw7a2           8 KTVAILGGESSGKSV--LVNKLA   28 (192)
T ss_dssp             EEEEEECCTTSHHHH--HHHHHH
T ss_pred             eEEEEECCCCCCHHH--HHHHHH
Confidence            678999999999984  555554

>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=93.32  E-value=0.03  Score=42.86  Aligned_cols=17  Identities=24%  Similarity=0.524  Sum_probs=14.5

Q ss_pred             CceeeeCCCCCCchHHH
Q psy14272         50 KFGIFESPTGTGKSLSL   66 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~   66 (194)
                      .+++|-||+|||||...
T Consensus        53 ~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          53 RAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999653

>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=92.90  E-value=0.03  Score=39.70  Aligned_cols=30  Identities=23%  Similarity=0.298  Sum_probs=24.1

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      +++|-++.||||| ++++..+.++...+.++
T Consensus         4 vi~itG~~GSGKT-TL~~~L~~~l~~~g~~v   33 (170)
T d1np6a_           4 LLAFAAWSGTGKT-TLLKKLIPALCARGIRP   33 (170)
T ss_dssp             EEEEECCTTSCHH-HHHHHHHHHHHHTTCCE
T ss_pred             EEEEEcCCCCCHH-HHHHHHHHHHHHCCCeE
Confidence            6788999999999 67888888887766553

>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=92.77  E-value=0.018  Score=41.04  Aligned_cols=21  Identities=14%  Similarity=0.241  Sum_probs=16.5

Q ss_pred             CCceeeeCCCCCCchHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGIL   71 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al   71 (194)
                      +++++|+||+|+|||-  +|..|
T Consensus         1 ~kiI~i~G~~GsGKsT--~~~~L   21 (190)
T d1khta_           1 NKVVVVTGVPGVGSTT--SSQLA   21 (190)
T ss_dssp             CCEEEEECCTTSCHHH--HHHHH
T ss_pred             CCEEEEECCCCCCHHH--HHHHH
Confidence            4789999999999984  45544

>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=92.74  E-value=0.029  Score=40.18  Aligned_cols=26  Identities=27%  Similarity=0.434  Sum_probs=17.3

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +++||+++.|+|||- .+--+..+|..
T Consensus         2 kiivi~G~~GsGKTT-~~~~La~~L~~   27 (194)
T d1nksa_           2 KIGIVTGIPGVGKST-VLAKVKEILDN   27 (194)
T ss_dssp             EEEEEEECTTSCHHH-HHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHH-HHHHHHHHHHH
Confidence            478999999999993 23333345543

>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=92.54  E-value=0.022  Score=39.33  Aligned_cols=16  Identities=31%  Similarity=0.451  Sum_probs=13.7

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      .++++|.||.|||||-
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            4678899999999983

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=92.53  E-value=0.026  Score=44.17  Aligned_cols=36  Identities=19%  Similarity=0.150  Sum_probs=26.1

Q ss_pred             HHhcCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         45 TLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        45 ~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      -|..|..+||-|+||+|||.-.+--++.|+..++.+
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~   66 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKK   66 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCC
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccc
Confidence            355678999999999999965555556666555443

>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=92.42  E-value=0.021  Score=49.94  Aligned_cols=23  Identities=35%  Similarity=0.357  Sum_probs=18.0

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .+++++-+|||||||+  |+=.|+-
T Consensus        49 ksNILliGPTGvGKTl--LAr~LAk   71 (443)
T d1g41a_          49 PKNILMIGPTGVGKTE--IARRLAK   71 (443)
T ss_dssp             CCCEEEECCTTSSHHH--HHHHHHH
T ss_pred             cccEEEECCCCCCHHH--HHHHHHH
Confidence            3689999999999995  5555553

>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=92.13  E-value=0.023  Score=46.32  Aligned_cols=40  Identities=30%  Similarity=0.238  Sum_probs=26.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHh--cCCceeeeCCCCCCchHH
Q psy14272         26 PFPFDAYDIQSNFMKNLYYTLD--NSKFGIFESPTGTGKSLS   65 (194)
Q Consensus        26 ~fPy~py~iQ~e~M~~I~~~L~--~gk~~I~ESPTGTGKTLS   65 (194)
                      .|||.-=-+|..+-++|.-++-  .+.+++|++|+|||||..
T Consensus         3 ~~~f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~l   44 (333)
T d1g8pa_           3 VFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTA   44 (333)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHH
T ss_pred             CCChhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHH
Confidence            3566533466555555443332  456799999999999964

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=91.93  E-value=0.036  Score=47.10  Aligned_cols=21  Identities=33%  Similarity=0.532  Sum_probs=16.4

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ++++|-+|||+|||.  |+=+|+
T Consensus        69 ~niLfiGPTGvGKTE--lAk~LA   89 (364)
T d1um8a_          69 SNILLIGPTGSGKTL--MAQTLA   89 (364)
T ss_dssp             CCEEEECCTTSSHHH--HHHHHH
T ss_pred             cceeeeCCCCccHHH--HHHHHH
Confidence            568999999999994  444554

>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=91.87  E-value=0.1  Score=44.01  Aligned_cols=38  Identities=21%  Similarity=0.367  Sum_probs=27.2

Q ss_pred             CCCCC-CCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHH
Q psy14272         26 PFPFD-AYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        26 ~fPy~-py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L   67 (194)
                      .||-. .-+.|..   ++..++. +++.|+.+|.|||||..+.
T Consensus       143 ~~~~~~~~~~Q~~---A~~~al~-~~~~vI~G~pGTGKTt~i~  181 (359)
T d1w36d1         143 LFPVSDEINWQKV---AAAVALT-RRISVISGGPGTGKTTTVA  181 (359)
T ss_dssp             TCCCTTSCCHHHH---HHHHHHT-BSEEEEECCTTSTHHHHHH
T ss_pred             hccCcccccHHHH---HHHHHHc-CCeEEEEcCCCCCceehHH
Confidence            35533 3467888   5555554 5799999999999998753

>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=91.77  E-value=0.05  Score=43.08  Aligned_cols=32  Identities=13%  Similarity=0.184  Sum_probs=22.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      ++++++|-+|||+|||-+..=-+ .|+..++++
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA-~~~~~~g~k   36 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLG-RYYQNLGKK   36 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHH-HHHHTTTCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH-HHHHHCCCc
Confidence            35788889999999997744333 455555544

>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=91.75  E-value=0.022  Score=40.65  Aligned_cols=17  Identities=24%  Similarity=0.421  Sum_probs=15.2

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .|++++|.+|+|||||-
T Consensus         3 ~g~iI~l~G~~GsGKST   19 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKST   19 (176)
T ss_dssp             TTEEEEEEECTTSCHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            47889999999999995

>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=91.74  E-value=0.037  Score=39.25  Aligned_cols=26  Identities=12%  Similarity=-0.068  Sum_probs=19.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      .|.+.+|-+|+|+|||.-.+.-+..+
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45799999999999996544444433

>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=91.42  E-value=0.028  Score=39.56  Aligned_cols=16  Identities=31%  Similarity=0.291  Sum_probs=13.6

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      .+++|+.+|+|+|||-
T Consensus         2 kklIii~G~pGsGKTT   17 (152)
T d1ly1a_           2 KKIILTIGCPGSGKST   17 (152)
T ss_dssp             CEEEEEECCTTSSHHH
T ss_pred             CEEEEEECCCCCCHHH
Confidence            3578899999999984

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=91.18  E-value=0.029  Score=39.37  Aligned_cols=15  Identities=47%  Similarity=0.711  Sum_probs=13.3

Q ss_pred             CceeeeCCCCCCchH
Q psy14272         50 KFGIFESPTGTGKSL   64 (194)
Q Consensus        50 k~~I~ESPTGTGKTL   64 (194)
                      +++++.||+|||||-
T Consensus         3 klI~i~G~~GsGKTT   17 (176)
T d2bdta1           3 KLYIITGPAGVGKST   17 (176)
T ss_dssp             EEEEEECSTTSSHHH
T ss_pred             eEEEEECCCCCCHHH
Confidence            578899999999994

>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=90.98  E-value=0.12  Score=41.18  Aligned_cols=34  Identities=24%  Similarity=0.263  Sum_probs=23.8

Q ss_pred             CHHHHHHHHHHHHHHhc-------C----CceeeeCCCCCCchHH
Q psy14272         32 YDIQSNFMKNLYYTLDN-------S----KFGIFESPTGTGKSLS   65 (194)
Q Consensus        32 y~iQ~e~M~~I~~~L~~-------g----k~~I~ESPTGTGKTLS   65 (194)
                      .+.+++.++.+...+..       |    +.++|.+|.|||||+.
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            56666666666555532       1    4589999999999964

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=90.68  E-value=0.057  Score=39.80  Aligned_cols=32  Identities=22%  Similarity=0.226  Sum_probs=21.6

Q ss_pred             HhcCCceeeeCCCCCCchHHHHHHHHHHHhhh
Q psy14272         46 LDNSKFGIFESPTGTGKSLSLICGILKWYYDH   77 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~~   77 (194)
                      |..|.+.+|.+|+|+|||.-.+--+..++...
T Consensus        23 i~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~   54 (242)
T d1tf7a1          23 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF   54 (242)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHHH
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence            34578999999999999954333334444443

>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=90.66  E-value=0.1  Score=44.14  Aligned_cols=15  Identities=27%  Similarity=0.751  Sum_probs=13.6

Q ss_pred             CceeeeCCCCCCchH
Q psy14272         50 KFGIFESPTGTGKSL   64 (194)
Q Consensus        50 k~~I~ESPTGTGKTL   64 (194)
                      ..++|-+|+|||||+
T Consensus       155 ~~~~~~g~~~~gk~~  169 (362)
T d1svma_         155 RYWLFKGPIDSGKTT  169 (362)
T ss_dssp             CEEEEECSTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            579999999999996

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=90.62  E-value=0.037  Score=39.45  Aligned_cols=17  Identities=24%  Similarity=0.427  Sum_probs=14.5

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .++++||.+|.|||||-
T Consensus         5 ~~~iivl~G~~GsGKsT   21 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSA   21 (171)
T ss_dssp             TSEEEEEECSTTSCHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            45789999999999984

>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=90.53  E-value=0.052  Score=44.99  Aligned_cols=32  Identities=22%  Similarity=0.259  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHHhc--------C---CceeeeCCCCCCchHH
Q psy14272         34 IQSNFMKNLYYTLDN--------S---KFGIFESPTGTGKSLS   65 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~--------g---k~~I~ESPTGTGKTLS   65 (194)
                      +|-+.+..|+.++..        .   .+.+|-+|||+|||..
T Consensus        27 GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~l   69 (315)
T d1qvra3          27 GQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTEL   69 (315)
T ss_dssp             SCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHH
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHH
Confidence            577777777766642        1   2568999999999964

>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=90.48  E-value=0.07  Score=43.94  Aligned_cols=37  Identities=24%  Similarity=0.266  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHhc--------C---CceeeeCCCCCCchHHHHHHHHH
Q psy14272         34 IQSNFMKNLYYTLDN--------S---KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        34 iQ~e~M~~I~~~L~~--------g---k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      +|.+....|..++..        .   .+.+|-+|||+|||.  |+-+|+
T Consensus        26 GQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~--lak~la   73 (315)
T d1r6bx3          26 GQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTE--VTVQLS   73 (315)
T ss_dssp             SCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHH--HHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHH--HHHHHH
Confidence            466666666666531        1   257899999999995  444444

>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=90.45  E-value=0.037  Score=40.88  Aligned_cols=29  Identities=14%  Similarity=0.185  Sum_probs=21.3

Q ss_pred             hcCCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         47 DNSKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        47 ~~gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      -.|.+++|.+|+|+|||.-.+--+...+.
T Consensus        32 ~~G~l~~i~G~~G~GKT~~~l~~a~~~~~   60 (258)
T d2i1qa2          32 ESQSVTEFAGVFGSGKTQIMHQSCVNLQN   60 (258)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHTTC
T ss_pred             cCCeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            34689999999999999755555544443

>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=90.36  E-value=0.11  Score=41.12  Aligned_cols=35  Identities=20%  Similarity=0.086  Sum_probs=22.7

Q ss_pred             CCHHHHHHHHHHHHHHhcC-----CceeeeCCCCCCchHH
Q psy14272         31 AYDIQSNFMKNLYYTLDNS-----KFGIFESPTGTGKSLS   65 (194)
Q Consensus        31 py~iQ~e~M~~I~~~L~~g-----k~~I~ESPTGTGKTLS   65 (194)
                      ++..-.+-...+.+.+.+.     ..++|-+|+|||||+.
T Consensus        17 ~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~l   56 (246)
T d1d2na_          17 PVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTAL   56 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHH
T ss_pred             HHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHH
Confidence            4444455555555555543     2388999999999964

>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=89.89  E-value=0.12  Score=41.11  Aligned_cols=33  Identities=9%  Similarity=0.212  Sum_probs=22.3

Q ss_pred             HHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         38 FMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        38 ~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      +...+..+...+..+++.+|+||||++  +.-+|.
T Consensus        12 ~~~~~~~~a~~~~pvlI~Ge~GtGK~~--~A~~ih   44 (247)
T d1ny5a2          12 ILEKIKKISCAECPVLITGESGVGKEV--VARLIH   44 (247)
T ss_dssp             HHHHHHHHTTCCSCEEEECSTTSSHHH--HHHHHH
T ss_pred             HHHHHHHHhCCCCCEEEECCCCcCHHH--HHHHHH
Confidence            334444444557889999999999985  444444

>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=89.76  E-value=0.087  Score=41.82  Aligned_cols=30  Identities=23%  Similarity=0.074  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .+++|-+|||+|||-++.=-+ .|+..++.+
T Consensus        12 ~vi~lvGptGvGKTTTiAKLA-a~~~~~~~k   41 (213)
T d1vmaa2          12 FVIMVVGVNGTGKTTSCGKLA-KMFVDEGKS   41 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHH-HHHHHTTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HHHHHCCCc
Confidence            378889999999997754333 345554444

>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=89.67  E-value=0.17  Score=36.35  Aligned_cols=15  Identities=13%  Similarity=0.439  Sum_probs=12.1

Q ss_pred             CCcee-eeCCCCCCch
Q psy14272         49 SKFGI-FESPTGTGKS   63 (194)
Q Consensus        49 gk~~I-~ESPTGTGKT   63 (194)
                      +..+| |.||+|||||
T Consensus        21 ~~~iIgI~G~~GSGKS   36 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKT   36 (198)
T ss_dssp             SSEEEEEEECTTSSHH
T ss_pred             CCEEEEEECCCCCCHH
Confidence            34455 8999999999

>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=89.57  E-value=0.062  Score=37.88  Aligned_cols=16  Identities=25%  Similarity=0.459  Sum_probs=14.3

Q ss_pred             cCCceeeeCCCCCCch
Q psy14272         48 NSKFGIFESPTGTGKS   63 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKT   63 (194)
                      ..++++|.+|.|+|||
T Consensus         2 ~~kiI~l~G~~GsGKs   17 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKS   17 (178)
T ss_dssp             CCCEEEEECCTTSSHH
T ss_pred             CCeEEEEECCCCCCHH
Confidence            3578999999999999

>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=89.41  E-value=0.059  Score=40.44  Aligned_cols=17  Identities=24%  Similarity=0.200  Sum_probs=14.7

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      .+.++++-||.|+|||-
T Consensus        28 ~~~~i~i~G~~G~GKTs   44 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSS   44 (283)
T ss_dssp             CSSEEEEEESTTSSHHH
T ss_pred             cCCEEEEEcCCCCcHHH
Confidence            45788899999999994

>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=89.32  E-value=0.092  Score=41.61  Aligned_cols=30  Identities=17%  Similarity=0.088  Sum_probs=16.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .+++|-+|||+|||-++.=-+ .|+...+.+
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA-~~~~~~g~k   42 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLA-YFYKKKGFK   42 (211)
T ss_dssp             EEEEEECSCCC----HHHHHH-HHHHHTTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HHHHHCCCc
Confidence            467789999999997743333 355544443

>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=89.24  E-value=0.09  Score=41.39  Aligned_cols=32  Identities=13%  Similarity=0.132  Sum_probs=20.5

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      +.++++|-+|||+|||-+..=-+ .|+...+.+
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA-~~~~~~g~k   40 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLA-LYYKGKGRR   40 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHH-HHHHHTTCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH-HHHHHCCCc
Confidence            45678889999999976533322 344444444

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=89.23  E-value=0.12  Score=37.45  Aligned_cols=30  Identities=10%  Similarity=-0.112  Sum_probs=23.6

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHhhhhhhh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYYDHKIVG   81 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~~~~~~~   81 (194)
                      ++-|-++.||||| ++|.-.+.+|...+.++
T Consensus         3 ii~I~G~~gSGKT-Tli~~l~~~L~~~g~~v   32 (165)
T d1xjca_           3 VWQVVGYKHSGKT-TLMEKWVAAAVREGWRV   32 (165)
T ss_dssp             EEEEECCTTSSHH-HHHHHHHHHHHHTTCCE
T ss_pred             EEEEEeCCCCCHH-HHHHHHHHHHHhCCCeE
Confidence            4568899999999 57778888888776554

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.23  E-value=0.082  Score=39.02  Aligned_cols=16  Identities=25%  Similarity=0.540  Sum_probs=14.6

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      |+++||-+|+|+|||-
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            7889999999999984

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=87.84  E-value=0.089  Score=39.12  Aligned_cols=19  Identities=32%  Similarity=0.392  Sum_probs=16.6

Q ss_pred             HhcCCceeeeCCCCCCchH
Q psy14272         46 LDNSKFGIFESPTGTGKSL   64 (194)
Q Consensus        46 L~~gk~~I~ESPTGTGKTL   64 (194)
                      +..+++++|.+|+|||||-
T Consensus         5 ~~~~~iI~l~G~pGSGKsT   23 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGT   23 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHH
T ss_pred             ccCCcEEEEECCCCCCHHH
Confidence            5677899999999999984

>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=87.79  E-value=0.11  Score=42.87  Aligned_cols=45  Identities=22%  Similarity=0.245  Sum_probs=30.6

Q ss_pred             ccCCC--CCCCHHHHHHHHHH-----HHHHhcCCc--eeeeCCCCCCchHHHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNL-----YYTLDNSKF--GIFESPTGTGKSLSLIC   68 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I-----~~~L~~gk~--~I~ESPTGTGKTLS~L~   68 (194)
                      .|.|.  |.|-..|.++-..+     .+++.+|.+  ++.-++||||||.+++.
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            44454  56777888877653     245656744  45579999999999743

>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=87.64  E-value=0.14  Score=40.55  Aligned_cols=30  Identities=10%  Similarity=0.031  Sum_probs=20.2

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHhhhhhh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYYDHKIV   80 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~~~~~~   80 (194)
                      .+++|-+|||+|||-++.=-+ .|+...+++
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA-~~~~~~g~k   39 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLA-RQFEQQGKS   39 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHH-HHHHTTTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HHHHHCCCc
Confidence            357789999999997744333 455554444

>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=87.60  E-value=0.31  Score=40.48  Aligned_cols=44  Identities=20%  Similarity=0.216  Sum_probs=31.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHhcCCceeeeCCCCCCchHHHHHHHHHHHhh
Q psy14272         27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYD   76 (194)
Q Consensus        27 fPy~py~iQ~e~M~~I~~~L~~gk~~I~ESPTGTGKTLS~L~~al~wl~~   76 (194)
                      +...||++|.-  -.+  +|..|  -|.|..||=||||+.-+|+......
T Consensus        77 lG~RhyDVQLi--Ggi--~L~~G--~iaem~TGEGKTL~a~l~a~l~al~  120 (273)
T d1tf5a3          77 TGMFPFKVQLM--GGV--ALHDG--NIAEMKTGEGKTLTSTLPVYLNALT  120 (273)
T ss_dssp             HSCCCCHHHHH--HHH--HHHTT--SEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             hceEEehhHHH--HHH--HHHhh--hheeecCCCcchhHHHHHHHHHHhc
Confidence            45678888865  333  24566  5889999999999988886655544

>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=87.16  E-value=0.1  Score=40.36  Aligned_cols=17  Identities=35%  Similarity=0.604  Sum_probs=15.3

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      +|+++||-||+|+|||-
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            58899999999999984

>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=87.02  E-value=0.11  Score=36.86  Aligned_cols=22  Identities=18%  Similarity=0.311  Sum_probs=16.7

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHH
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      +.+++|.||.|+|||-  +|-.|.
T Consensus         5 ~~~I~i~G~~GsGKTT--~~~~La   26 (174)
T d1y63a_           5 GINILITGTPGTGKTS--MAEMIA   26 (174)
T ss_dssp             SCEEEEECSTTSSHHH--HHHHHH
T ss_pred             CCEEEEEeCCCCCHHH--HHHHHH
Confidence            3568899999999994  555554

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=86.66  E-value=0.16  Score=42.55  Aligned_cols=44  Identities=20%  Similarity=0.175  Sum_probs=28.3

Q ss_pred             cCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHHHH
Q psy14272         25 FPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLIC   68 (194)
Q Consensus        25 ~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~L~   68 (194)
                      |.|.  |.|-..|.++...+    .+.+-+|.  .++.-++||||||.+.+.
T Consensus        82 f~FD~vf~~~~~Q~~Vy~~~~~plv~~~l~G~n~tifaYGqTGSGKTyTm~G  133 (362)
T d1v8ka_          82 FCFDFAFDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGG  133 (362)
T ss_dssp             EECSEEECTTCCHHHHHHHTTHHHHHHHHTTCEEEEEEEESTTSSHHHHHHC
T ss_pred             EeCCeecCCCCCHHHHHHHHHHHHHHHHHhccCceEEeeccCCCCCceeeee
Confidence            4444  55777788766553    33333453  344569999999999754

>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=86.52  E-value=0.11  Score=36.43  Aligned_cols=14  Identities=21%  Similarity=0.342  Sum_probs=12.1

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      .+++.||.|||||-
T Consensus         6 ~I~i~G~pGsGKTT   19 (173)
T d1rkba_           6 NILLTGTPGVGKTT   19 (173)
T ss_dssp             CEEEECSTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            57789999999993

>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=86.39  E-value=0.1  Score=42.88  Aligned_cols=46  Identities=13%  Similarity=0.152  Sum_probs=31.2

Q ss_pred             CCccCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHHH
Q psy14272         22 PSEFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        22 ~~~~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      ...|.|.  |.|-..|.++...+    .+.+-+|.  .++.-++||||||.+++
T Consensus        41 ~~~f~FD~vf~~~~~q~~vf~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          41 SKPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             TEEEECSEEECTTCCHHHHHHHHTHHHHHHHHTTCCEEEEEECSTTSSHHHHHT
T ss_pred             CceeECCEEECCCCCHHHHHHHHHHHHHHHHHcCCCcceeeecccCCCCceecc
Confidence            3456666  56777788776654    33334563  46679999999999974

>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=86.37  E-value=0.082  Score=44.51  Aligned_cols=44  Identities=20%  Similarity=0.261  Sum_probs=29.0

Q ss_pred             ccCCC--CCCCHHHHHHHHHHHHHH---hcC--CceeeeCCCCCCchHHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNLYYTL---DNS--KFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I~~~L---~~g--k~~I~ESPTGTGKTLS~L   67 (194)
                      .|.|.  |.|-..|.++...|...+   -+|  ..++.-++||||||+++.
T Consensus        93 ~F~FD~vf~~~~~Q~~Vy~~v~plv~~vl~G~n~ti~aYGqtGSGKT~Tm~  143 (368)
T d2ncda_          93 IFSFDQVFHPLSSQSDIFEMVSPLIQSALDGYNICIFAYGQTGSGKTYTMD  143 (368)
T ss_dssp             EEECSEEECTTCCHHHHHTTTHHHHHHHHTTCEEEEEEECSTTSSHHHHHT
T ss_pred             eeECCeEECCCCCccchHHHHHHHHHHHhcccceeEEeeccCCCccceEec
Confidence            45555  556667888765543332   345  346778999999999863

>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=86.35  E-value=0.16  Score=38.23  Aligned_cols=25  Identities=24%  Similarity=0.235  Sum_probs=18.4

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|.+.+|.+|+|+|||.-.+--+..
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~   49 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVEN   49 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            5689999999999999644333333

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=86.32  E-value=0.22  Score=38.35  Aligned_cols=27  Identities=26%  Similarity=0.311  Sum_probs=20.9

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWY   74 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl   74 (194)
                      .|.+++|-||+|+|||.-.+--++.++
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            478999999999999976655555443

>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=86.02  E-value=0.24  Score=40.33  Aligned_cols=27  Identities=22%  Similarity=0.384  Sum_probs=21.5

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .++.||+|+-|||||.++..=++..+.
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            467999999999999987776665553

>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=85.85  E-value=0.21  Score=41.02  Aligned_cols=18  Identities=39%  Similarity=0.564  Sum_probs=15.5

Q ss_pred             CCceeeeCCCCCCchHHH
Q psy14272         49 SKFGIFESPTGTGKSLSL   66 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~   66 (194)
                      ..+++|-++||+|||.++
T Consensus        50 ~~H~~I~G~tGsGKT~~l   67 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLL   67 (433)
T ss_dssp             GGCEEEEECTTSSHHHHH
T ss_pred             cceEEEEeCCCCcHHHHH
Confidence            467999999999999764

>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=85.82  E-value=0.14  Score=40.52  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=16.7

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKW   73 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~w   73 (194)
                      +-++|.+|.|||||+  |+-++++
T Consensus        39 ~giLL~GppGtGKT~--l~~ala~   60 (258)
T d1e32a2          39 RGILLYGPPGTGKTL--IARAVAN   60 (258)
T ss_dssp             CEEEEECCTTSSHHH--HHHHHHH
T ss_pred             ceeEEecCCCCCchH--HHHHHHH
Confidence            458899999999996  4555554

>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=85.48  E-value=0.21  Score=40.02  Aligned_cols=25  Identities=28%  Similarity=0.498  Sum_probs=18.6

Q ss_pred             CCceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         49 SKFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        49 gk~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +++-+|-||||+|||-  |+-||.|+.
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            4567888999999995  455677753

>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=85.46  E-value=0.13  Score=38.54  Aligned_cols=22  Identities=14%  Similarity=-0.016  Sum_probs=17.2

Q ss_pred             cCCceeeeCCCCCCchHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      .|.+++|-+|+|||||.-.+-.
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            3578999999999999644433

>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=85.19  E-value=0.3  Score=42.20  Aligned_cols=42  Identities=24%  Similarity=0.362  Sum_probs=36.1

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHhcC-CceeeeCCCCCCchHH
Q psy14272         24 EFPFPFDAYDIQSNFMKNLYYTLDNS-KFGIFESPTGTGKSLS   65 (194)
Q Consensus        24 ~~~fPy~py~iQ~e~M~~I~~~L~~g-k~~I~ESPTGTGKTLS   65 (194)
                      ..+-||.|--=|=+.++.|.+.|..| +..++.+-||||||+.
T Consensus         5 ~~~~~~~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~   47 (413)
T d1t5la1           5 QLVAPYEPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFT   47 (413)
T ss_dssp             CCCCSSCCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHH
T ss_pred             EEecCCCCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHH
Confidence            35568999989999999999999887 6688899999999964

>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=85.07  E-value=0.14  Score=36.53  Aligned_cols=23  Identities=26%  Similarity=0.315  Sum_probs=15.6

Q ss_pred             eeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         52 GIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        52 ~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +++.+|+|+|||- ++-.++..+.
T Consensus         3 i~I~G~~G~GKST-Ll~~i~~~l~   25 (178)
T d1ye8a1           3 IIITGEPGVGKTT-LVKKIVERLG   25 (178)
T ss_dssp             EEEECCTTSSHHH-HHHHHHHHHG
T ss_pred             EEEECCCCcHHHH-HHHHHHhcCC
Confidence            6889999999995 3333344443

>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=85.01  E-value=0.26  Score=37.74  Aligned_cols=31  Identities=13%  Similarity=0.086  Sum_probs=21.0

Q ss_pred             cCCceeeeCCCCCCchHHHHHHHHHHHhhhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGILKWYYDHKI   79 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~al~wl~~~~~   79 (194)
                      .|..++||+|-|+|||-- +-....||...+.
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            477899999999999842 2223446665543

>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=84.53  E-value=0.15  Score=38.26  Aligned_cols=29  Identities=21%  Similarity=0.282  Sum_probs=20.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHHH-HHHHhhhh
Q psy14272         48 NSKFGIFESPTGTGKSLSLICGI-LKWYYDHK   78 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~a-l~wl~~~~   78 (194)
                      .|+.++||++-|+|||-  +|-. ..+|...+
T Consensus         1 rgkfIviEG~dGsGKsT--~~~~L~~~L~~~g   30 (210)
T d4tmka_           1 RSKYIVIEGLEGAGKTT--ARNVVVETLEQLG   30 (210)
T ss_dssp             CCCEEEEEECTTSCHHH--HHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHH--HHHHHHHHHHhCC
Confidence            37889999999999984  3333 33555443

>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=84.53  E-value=0.43  Score=36.79  Aligned_cols=21  Identities=19%  Similarity=0.134  Sum_probs=15.5

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      ..+++-||+|||||.  |+-++.
T Consensus        37 n~l~l~G~~G~GKTH--Ll~A~~   57 (213)
T d1l8qa2          37 NPIFIYGSVGTGKTH--LLQAAG   57 (213)
T ss_dssp             SSEEEECSSSSSHHH--HHHHHH
T ss_pred             CcEEEECCCCCcHHH--HHHHHH
Confidence            348899999999995  444444

>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=84.43  E-value=0.17  Score=37.73  Aligned_cols=15  Identities=40%  Similarity=0.623  Sum_probs=13.1

Q ss_pred             CceeeeCCCCCCchH
Q psy14272         50 KFGIFESPTGTGKSL   64 (194)
Q Consensus        50 k~~I~ESPTGTGKTL   64 (194)
                      +.+||.||+|+|||-
T Consensus         2 rpIvl~GpsG~GK~t   16 (186)
T d1gkya_           2 RPIVISGPSGTGKST   16 (186)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            468999999999984

>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=84.29  E-value=0.16  Score=37.47  Aligned_cols=20  Identities=20%  Similarity=0.004  Sum_probs=16.4

Q ss_pred             cCCceeeeCCCCCCchHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLI   67 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L   67 (194)
                      .|.+++|-+|+|||||.-.+
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            45799999999999996433

>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=83.96  E-value=0.085  Score=37.00  Aligned_cols=24  Identities=17%  Similarity=0.120  Sum_probs=17.8

Q ss_pred             CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         50 KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      .+.||-+|+|+|||-  |+-||.|+.
T Consensus        25 ~~tvi~G~NGsGKSt--il~Ai~~~L   48 (222)
T d1qhla_          25 LVTTLSGGNGAGKST--TMAAFVTAL   48 (222)
T ss_dssp             HHHHHHSCCSHHHHH--HHHHHHHHH
T ss_pred             CeEEEECCCCCCHHH--HHHHHHHHh
Confidence            367788999999994  455566664

>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=83.89  E-value=0.2  Score=40.17  Aligned_cols=21  Identities=33%  Similarity=0.455  Sum_probs=16.1

Q ss_pred             CceeeeCCCCCCchHHHHHHHHH
Q psy14272         50 KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        50 k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      +.++|.+|+|||||+.  +-+++
T Consensus        46 ~~iLL~GppGtGKT~l--a~~iA   66 (256)
T d1lv7a_          46 KGVLMVGPPGTGKTLL--AKAIA   66 (256)
T ss_dssp             CEEEEECCTTSCHHHH--HHHHH
T ss_pred             CeEEeeCCCCCCccHH--HHHHH
Confidence            4589999999999964  44444

>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=83.55  E-value=0.24  Score=40.86  Aligned_cols=44  Identities=25%  Similarity=0.439  Sum_probs=30.4

Q ss_pred             ccCCC--CCCCHHHHHHHHHHHHHHh---cCC--ceeeeCCCCCCchHHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNLYYTLD---NSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I~~~L~---~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      .|.|.  |.|-..|.++.+.|...+.   +|.  -++.-++||||||.+++
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            34444  5566779888887655443   343  35568999999999984

>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=83.53  E-value=0.15  Score=42.77  Aligned_cols=43  Identities=19%  Similarity=0.353  Sum_probs=28.4

Q ss_pred             ccCCC--CCCCHHHHHHHHHHHH---HHhcCC--ceeeeCCCCCCchHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNLYY---TLDNSK--FGIFESPTGTGKSLSL   66 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I~~---~L~~gk--~~I~ESPTGTGKTLS~   66 (194)
                      .|.|.  |.|-..|.++.+.|..   .+-+|.  .++.-++||||||.++
T Consensus        43 ~f~FD~vf~~~~~q~~vy~~v~~lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          43 QHMYDRVFDGNATQDDVFEDTKYLVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             EEECSEEECTTCCHHHHHHTTTHHHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             EEECCeecCCCCCHHHHHHHHHHHHHHHhcCCceeeeccccCCCCccccc
Confidence            45555  5566778877766532   223453  3566799999999997

>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=83.42  E-value=0.18  Score=37.79  Aligned_cols=16  Identities=31%  Similarity=0.150  Sum_probs=14.0

Q ss_pred             CCceeeeCCCCCCchH
Q psy14272         49 SKFGIFESPTGTGKSL   64 (194)
Q Consensus        49 gk~~I~ESPTGTGKTL   64 (194)
                      .+.++||||-|+|||-
T Consensus         2 ~k~I~ieG~dGsGKST   17 (241)
T d1p5zb_           2 IKKISIEGNIAAGKST   17 (241)
T ss_dssp             CEEEEEECSTTSSHHH
T ss_pred             CCEEEEECCCCCCHHH
Confidence            4678999999999984

>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=83.18  E-value=0.24  Score=40.80  Aligned_cols=44  Identities=20%  Similarity=0.248  Sum_probs=28.9

Q ss_pred             ccCCC--CCCCHHHHHHHHHH----HHHHhcCC--ceeeeCCCCCCchHHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNSK--FGIFESPTGTGKSLSLI   67 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I----~~~L~~gk--~~I~ESPTGTGKTLS~L   67 (194)
                      .|.|.  |.+-..|.++...+    .+.+-+|.  .++.-++||||||.+++
T Consensus        48 ~f~FD~vf~~~~~q~~vy~~~~~~lv~~~l~G~n~~i~aYGqtgSGKTyTm~   99 (345)
T d1x88a1          48 TYTFDMVFGASTKQIDVYRSVVCPILDEVIMGYNCTIFAYGQTGTGKTFTME   99 (345)
T ss_dssp             EEECSEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEECTTSSHHHHHT
T ss_pred             eEecCEEeCCCCCHHHHHHHHHHHhHHHHhccCCceEEeeeeccccceEEee
Confidence            35555  55666787766543    34444563  36678999999998864

>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=83.05  E-value=0.19  Score=35.11  Aligned_cols=17  Identities=12%  Similarity=0.036  Sum_probs=14.4

Q ss_pred             cCCceeeeCCCCCCchH
Q psy14272         48 NSKFGIFESPTGTGKSL   64 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTL   64 (194)
                      +|.+++|-++.|+|||-
T Consensus         5 ~g~~I~l~G~~GsGKTT   21 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDA   21 (183)
T ss_dssp             CCEEEEEECSTTSSHHH
T ss_pred             CCeEEEEECCCCCCHHH
Confidence            46678899999999993

>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=82.88  E-value=0.18  Score=37.06  Aligned_cols=14  Identities=14%  Similarity=0.211  Sum_probs=11.9

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      .++|.||.|||||-
T Consensus         5 ~I~i~GppGsGKsT   18 (189)
T d1zaka1           5 KVMISGAPASGKGT   18 (189)
T ss_dssp             CEEEEESTTSSHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            47899999999963

>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=82.76  E-value=0.37  Score=35.75  Aligned_cols=24  Identities=21%  Similarity=0.407  Sum_probs=17.2

Q ss_pred             ceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         51 FGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        51 ~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      +++|-+|.|+||| +||-..+.|+.
T Consensus         2 vi~v~G~~GsGKT-TLl~~ll~~~~   25 (244)
T d1yrba1           2 IVVFVGTAGSGKT-TLTGEFGRYLE   25 (244)
T ss_dssp             EEEEECSTTSSHH-HHHHHHHHHHT
T ss_pred             EEEEEcCCCCcHH-HHHHHHHHHHh
Confidence            5788999999998 34445555554

>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=82.53  E-value=0.2  Score=36.66  Aligned_cols=14  Identities=29%  Similarity=0.451  Sum_probs=12.6

Q ss_pred             ceeeeCCCCCCchH
Q psy14272         51 FGIFESPTGTGKSL   64 (194)
Q Consensus        51 ~~I~ESPTGTGKTL   64 (194)
                      +++|||+.|+|||-
T Consensus        11 ~I~ieG~~GsGKTT   24 (197)
T d2vp4a1          11 TVLIEGNIGSGKTT   24 (197)
T ss_dssp             EEEEECSTTSCHHH
T ss_pred             EEEEECCCCCCHHH
Confidence            68899999999994

>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=82.35  E-value=0.24  Score=41.07  Aligned_cols=44  Identities=27%  Similarity=0.287  Sum_probs=28.4

Q ss_pred             ccCCC--CCCCHHHHHHHHHH----HHHHhcCCc--eeeeCCCCCCchHHHH
Q psy14272         24 EFPFP--FDAYDIQSNFMKNL----YYTLDNSKF--GIFESPTGTGKSLSLI   67 (194)
Q Consensus        24 ~~~fP--y~py~iQ~e~M~~I----~~~L~~gk~--~I~ESPTGTGKTLS~L   67 (194)
                      .|.|.  |.+-..|.++.+.+    .+.+-+|..  ++.-++||||||.+++
T Consensus        47 ~f~FD~vf~~~~~q~~vy~~~~~plv~~~l~G~n~ti~aYG~tgSGKT~Tm~   98 (354)
T d1goja_          47 SFTFDRVFDMSCKQSDIFDFSIKPTVDDILNGYNGTVFAYGQTGAGKSYTMM   98 (354)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHHHTTTCCEEEEEECSTTSSHHHHHT
T ss_pred             eEECCeEcCCCCCHHHHHHHHHHHHHHHhhccCceeEEecccCCCCcceeee
Confidence            35555  44666787766544    333345643  6668999999999864

>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=81.32  E-value=0.74  Score=36.56  Aligned_cols=34  Identities=26%  Similarity=0.324  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHhcC---CceeeeCCCCCCchHHHHHHHHH
Q psy14272         37 NFMKNLYYTLDNS---KFGIFESPTGTGKSLSLICGILK   72 (194)
Q Consensus        37 e~M~~I~~~L~~g---k~~I~ESPTGTGKTLS~L~~al~   72 (194)
                      .|+..++..|...   .-++|-+|.+||||+  +|.+|.
T Consensus        38 ~Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~--f~~sl~   74 (205)
T d1tuea_          38 TFLGALKSFLKGTPKKNCLVFCGPANTGKSY--FGMSFI   74 (205)
T ss_dssp             HHHHHHHHHHHTCTTCSEEEEESCGGGCHHH--HHHHHH
T ss_pred             HHHHHHHHHHcCCCCceEEEEECCCCccHHH--HHHHHH
Confidence            6788888888543   458899999999996  454333

>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=81.03  E-value=0.27  Score=36.80  Aligned_cols=15  Identities=33%  Similarity=0.629  Sum_probs=12.9

Q ss_pred             CceeeeCCCCCCchH
Q psy14272         50 KFGIFESPTGTGKSL   64 (194)
Q Consensus        50 k~~I~ESPTGTGKTL   64 (194)
                      +.+||.+|+|+|||-
T Consensus         1 rpIvl~GPsGsGK~t   15 (190)
T d1lvga_           1 RPVVLSGPSGAGKST   15 (190)
T ss_dssp             CCEEEECCTTSSHHH
T ss_pred             CeEEEECCCCCCHHH
Confidence            358899999999984

>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=80.77  E-value=0.97  Score=36.30  Aligned_cols=38  Identities=13%  Similarity=-0.014  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHhcC----CceeeeCCCCCCchHHHHHHHHHHHh
Q psy14272         36 SNFMKNLYYTLDNS----KFGIFESPTGTGKSLSLICGILKWYY   75 (194)
Q Consensus        36 ~e~M~~I~~~L~~g----k~~I~ESPTGTGKTLS~L~~al~wl~   75 (194)
                      ..||..++.+|..+    ..++|-+|.+||||.  ++-+|..+.
T Consensus        87 ~~f~~~l~~~L~~~~~k~n~~~l~G~~~tGKS~--f~~~i~~~l  128 (267)
T d1u0ja_          87 QYAASVFLGWATKKFGKRNTIWLFGPATTGKTN--IAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHH--HHHHHHHHS
T ss_pred             HHHHHHHHHHHcCCCCccEEEEEEcCCCCCHHH--HHHHHHHHh
Confidence            35778888888643    346788999999995  555555443

>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=80.60  E-value=0.44  Score=35.22  Aligned_cols=22  Identities=14%  Similarity=-0.183  Sum_probs=17.1

Q ss_pred             cCCceeeeCCCCCCchHHHHHH
Q psy14272         48 NSKFGIFESPTGTGKSLSLICG   69 (194)
Q Consensus        48 ~gk~~I~ESPTGTGKTLS~L~~   69 (194)
                      .|.+++|-+|+|+|||.-.+.-
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            3578999999999999654433