Citrus Sinensis ID: 040913

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-----
Protein Sequence
MLDVNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccEEEccccHHHHHHHHHccccccEEEEEEccccccHHHHHHHHHccccccccccccEEEHHHHHHHHcccccccccccccHHHHHHHHHHHccccEEEEEEEccccccccHHHHHHHccccccccEEEEEcccHHHHHHHHHHHccccccHHHHHHcHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHcccccccccHHHHHHHHHHcccccccEEcHHHHHHHHHHccccccccHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccEEcccccHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHccccccccccEEEEEEccHHHHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHccccccHHHcHHHHHHEcHccccHHHHHHEEEEEEcccccEEcHHHHHHHHHHHcHccccHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MLDVNLRLFCERLKRVLageegtltvtdstnltPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKInedvkrpdILKILEDVNQFVHESEEVIDTFFINIMQqqnseeesessTNMALLVGLHSKIIDIRNrmqqlppgdngfdiNEQRDELIHlssegqprldiSEFERAREEWFDLLIEGPIGLSVVAILdssgfdktafaadtynnnhVKFYFDCLAWILDDIirslmppsrvtviigedYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDleevlpdnqngsRVLITVINpslltsfellngekircdyvlvegplirikHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCsvfelplhlKVCCIYLcvfrpgieisSRQLCQLWIAegfipynseeTAELYLKELIHRGFIQ
Flexible Loop (DISEMBL)
MLDVNLRLFCERLKrvlageegtltvtdstnltPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHlssegqprldISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
Low Complexity Region (SEG)
MLDVNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNseeesessTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
Disordered region (IsUnstruct)
***VNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIM***************ALLVGLHSKIIDIRN***********************************EFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGF**
Disordered Region (DISOPRED)
*LDVNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEI*********EADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFI******************ALLVGLHSKIIDIRNRMQQLPPGDN**********************DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLM***************KKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMD*KMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
Disordered Region (DISEMBL)
MLDVNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQ************NMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
Disordered Region (DISPRO)
MLDVNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDI*****************LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLDVNLRLFCERLKRVLAGEEGTLTVTDSTNLTPLLQNLLAESEIIASTLLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTSFELLNGEKIRCDYVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ
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	425	2.2.26 [Sep-21-2011]
P0C8S1	906	Probable disease resistan	yes	no	0.785	0.368	0.232	9e-15
Q8W4J9	908	Disease resistance protei	no	no	0.802	0.375	0.235	3e-13
Q9M667	835	Disease resistance protei	no	no	0.750	0.382	0.247	4e-12
Q9FJK8	908	Probable disease resistan	no	no	0.802	0.375	0.235	6e-12
Q6L3Z7	1317	Putative late blight resi	N/A	no	0.621	0.200	0.269	2e-11
Q9FJB5	901	Disease resistance RPP8-l	no	no	0.790	0.372	0.228	2e-11
Q6L403	1312	Putative late blight resi	N/A	no	0.621	0.201	0.269	2e-11
P59584	910	Disease resistance protei	no	no	0.802	0.374	0.224	3e-11
Q39214	926	Disease resistance protei	no	no	0.536	0.246	0.24	4e-11
Q6L406	1326	Putative late blight resi	N/A	no	0.592	0.190	0.268	4e-11

>sp|P0C8S1|RP8L2_ARATH Probable disease resistance RPP8-like protein 2 OS=Arabidopsis thaliana GN=RPP8L2 PE=1 SV=1

 Score = 81.6 bits (200), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 98/422 (23%), Positives = 184/422 (43%), Gaps = 88/422 (20%)

Query: 83  LEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLV----------GLHSKIID 132
           LEDV   V++++++I++F +N ++ +    + +  T    LV          G+  +I +
Sbjct: 62  LEDVKDIVYDADDIIESFLLNELRGKEKGIKKQVRTLACFLVDRRKFASDIEGITKRISE 121

Query: 133 IRNRMQQLP------PGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDLLIEG 186
           +   MQ L        G     + E++ E+    S      D+   +++ EE  D L+E 
Sbjct: 122 VIVGMQSLGIQHIADGGGRSLSLQERQREIRQTFSRNSES-DLVGLDQSVEELVDHLVEN 180

Query: 187 PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-------DDIIRSLMP--- 236
              + VV++    G  KT  A   ++++ V+ +FD  +W+         D+ + ++    
Sbjct: 181 D-SVQVVSVSGMGGIGKTTLARQVFHHDIVRRHFDGFSWVCVSQQFTRKDVWQRILQDLR 239

Query: 237 PSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLI 296
           P    +I  ++Y L+  +  + L + +Y + LDDV    E WD ++ V P ++ G ++L+
Sbjct: 240 PYDEGIIQMDEYTLQGELF-ELLESGRYLLVLDDVWKE-EDWDRIKAVFP-HKRGWKMLL 296

Query: 297 TVIN---------------PSLLTS------FE-LLNGEKIRCDY--------------- 319
           T  N               P +LT       FE +++  + + ++               
Sbjct: 297 TSRNEGLGLHADPTCFAFRPRILTPEQSWKLFERIVSSRRDKTEFKVDEAMGKEMVTYCG 356

Query: 320 -----VLVEGPLIRIKHSAWQFFVLH-------YGSAALGNYMDEKMVLAVLSRTCSVFE 367
                V V G L+  KH+  ++  +H        G + L +  +   V  VLS   S  +
Sbjct: 357 GLPLAVKVLGGLLAKKHTVLEWKRVHSNIVTHIVGKSGLSDD-NSNSVYRVLS--LSYED 413

Query: 368 LPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFI-PYNS----EETAELYLKELIHRG 422
           LP+ LK C  YL  F    +I  + L   W+AEG I P++     ++T E YL+EL+ R 
Sbjct: 414 LPMQLKHCFFYLAHFPEDYKIDVKILFNYWVAEGIITPFHDGSTIQDTGESYLEELVRRN 473

Query: 423 FI 424
            +
Sbjct: 474 MV 475

Potential disease resistance protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8W4J9|RPP8_ARATH Disease resistance protein RPP8 OS=Arabidopsis thaliana GN=RPP8 PE=1 SV=2

 Score = 76.6 bits (187), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 100/424 (23%), Positives = 177/424 (41%), Gaps = 83/424 (19%)

Query: 79  ILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH---SKIIDIRN 135
           +   LEDV   V ++E++I+++ +N +  +    +         L   H   S I  I  
Sbjct: 58  VRNFLEDVKDLVFDAEDIIESYVLNKLSGKGKGVKKHVRRLACFLTDRHKVASDIEGITK 117

Query: 136 RMQQLPPGDNGFDINEQRDELIHLSSEGQPRL--------------DISEFERAREEWFD 181
           R+ ++      F I +  D    LS + + R+              D+   E++ +E   
Sbjct: 118 RISEVIGEMQSFGIQQIIDGGRSLSLQERQRVQREIRQTYPDSSESDLVGVEQSVKELVG 177

Query: 182 LLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----------ILDDI 230
            L+E  +   VV+I    G  KT  A   ++++ V+ +FD  AW           +   I
Sbjct: 178 HLVENDVH-QVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRI 236

Query: 231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQN 290
           ++ L P     ++  ++Y L++ + +  L   +Y + LDDV    E WD ++ V P  + 
Sbjct: 237 LQELQPHDG-DILQMDEYALQRKLFQ-LLEAGRYLVVLDDVWKK-EDWDVIKAVFP-RKR 292

Query: 291 GSRVLITVIN--------PSLLT-SFELLNGE-----------------KIRCD------ 318
           G ++L+T  N        P+ LT    +LN E                 ++R D      
Sbjct: 293 GWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRLDEEMEAM 352

Query: 319 -------------YVLVEGPLIRIKHSA--WQFFVLHYGSAAL-GNYMDEKMVLAVLS-R 361
                         V   G L+  KH+   W+    + GS  + G+++D+  + +V    
Sbjct: 353 GKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVFDNIGSQIVGGSWLDDNSLNSVYRIL 412

Query: 362 TCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNS-EETAELYLKELIH 420
           + S  +LP HLK C + L  F    EIS+  L   W AEG    ++ E++ E YL+EL+ 
Sbjct: 413 SLSYEDLPTHLKHCFLNLAHFPEDSEISTYSLFYYWAAEGIYDGSTIEDSGEYYLEELVR 472

Query: 421 RGFI 424
           R  +
Sbjct: 473 RNLV 476

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. The interaction with TIP (TCV-interacting protein) may be essential for the recognition of the avirulence proteins, and the triggering of the defense response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M667|RPP13_ARATH Disease resistance protein RPP13 OS=Arabidopsis thaliana GN=RPP13 PE=2 SV=2

 Score = 73.2 bits (178), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 105/425 (24%), Positives = 167/425 (39%), Gaps = 106/425 (24%)

Query: 89  FVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFD 148
           F ++ E+V+DT+ + + ++         +  +   +  +S + DIR   +++       D
Sbjct: 68  FAYDVEDVLDTYHLKLEERSQRRGLRRLTNKIGRKMDAYSIVDDIRILKRRI------LD 121

Query: 149 INEQRDELIHLSSEGQPR-------LDISEFERAR-----------EEWFDLLIEGPIGL 190
           I  +R E   +    +P+       L + +  RAR           E+   +L+E  +  
Sbjct: 122 ITRKR-ETYGIGGLKEPQGGGNTSSLRVRQLRRARSVDQEEVVVGLEDDAKILLEKLLDY 180

Query: 191 S-----VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----------ILDDIIRSL 234
                 +++I    G  KTA A   YN+  VK  F+  AW           IL  IIRSL
Sbjct: 181 EEKNRFIISIFGMGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSL 240

Query: 235 MPPSRVTVIIGEDY-KLKK-------SILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLP 286
              S      GE+  K++K         L   L  KKY + +DD+    E WD L+  LP
Sbjct: 241 GMTS------GEELEKIRKFAEEELEVYLYGLLEGKKYLVVVDDIWER-EAWDSLKRALP 293

Query: 287 DNQNGSRVLITVINPSL---------------LT---SFELLNGEKIR------------ 316
            N  GSRV+IT    ++               LT   S+EL      R            
Sbjct: 294 CNHEGSRVIITTRIKAVAEGVDGRFYAHKLRFLTFEESWELFEQRAFRNIQRKDEDLLKT 353

Query: 317 -------CD-----YVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCS 364
                  C       V++ G L R   S W        ++      D+ + +A +    S
Sbjct: 354 GKEMVQKCRGLPLCIVVLAGLLSRKTPSEWN----DVCNSLWRRLKDDSIHVAPIVFDLS 409

Query: 365 VFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNS----EETAELYLKELIH 420
             EL    K+C +YL +F    EI   +L  L +AEGFI  +     E+ A  Y++ELI 
Sbjct: 410 FKELRHESKLCFLYLSIFPEDYEIDLEKLIHLLVAEGFIQGDEEMMMEDVARYYIEELID 469

Query: 421 RGFIQ 425
           R  ++
Sbjct: 470 RSLLE 474

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJK8|RP8L4_ARATH Probable disease resistance RPP8-like protein 4 OS=Arabidopsis thaliana GN=RPP8L4 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 100/424 (23%), Positives = 170/424 (40%), Gaps = 83/424 (19%)

Query: 79  ILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH---SKIIDIRN 135
           +   LEDV   V ++E++I+++ +N ++ +    +         L   H   S I  I  
Sbjct: 58  VRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKKHVRRLARFLTDRHKVASDIEGITK 117

Query: 136 RMQQLPPGDNGFDINEQRDELIHLSSEGQPRL--------------DISEFERAREEWFD 181
           R+  +      F I +  D +  LS + + R+              D+   E++ EE   
Sbjct: 118 RISDVIGEMQSFGIQQIIDGVRSLSLQERQRVQREIRQTYPDSSESDLVGVEQSVEELVG 177

Query: 182 LLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-----------DDI 230
            L+E  I   VV+I    G  KT  A   ++++ V+ +FD  AW+              I
Sbjct: 178 HLVENDI-YQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTLKHVWQRI 236

Query: 231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQN 290
           ++ L P      I+  D    +  L   L   +Y + LDDV    E WD ++ V P  + 
Sbjct: 237 LQELQPHD--GNILQMDESALQPKLFQLLETGRYLLVLDDVWKK-EDWDRIKAVFP-RKR 292

Query: 291 GSRVLITVIN--------PSLLT-SFELLNGE-----------------KIRCD------ 318
           G ++L+T  N        P+ LT    +LN E                 ++R D      
Sbjct: 293 GWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRLDEEMEAM 352

Query: 319 -------------YVLVEGPLIRIKHSA--WQFFVLHYGSAALGNYMDEKMVLAVLSRTC 363
                         V   G L+  KH+   W+    + GS  +G    +   L  ++R  
Sbjct: 353 GKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVSDNIGSQIVGGSCLDDNSLNSVNRIL 412

Query: 364 SVF--ELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNS-EETAELYLKELIH 420
           S+   +LP HLK   +YL  F    +I ++ L   W AEG    ++ +++ E YL+EL+ 
Sbjct: 413 SLSYEDLPTHLKHRFLYLAHFPEDSKIYTQDLFNYWAAEGIYDGSTIQDSGEYYLEELVR 472

Query: 421 RGFI 424
           R  +
Sbjct: 473 RNLV 476

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L3Z7|R1B14_SOLDE Putative late blight resistance protein homolog R1B-14 OS=Solanum demissum GN=R1B-14 PE=3 SV=1

 Score = 71.2 bits (173), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 138/326 (42%), Gaps = 62/326 (19%)

Query: 156 LIHLSSE--GQPRLD--ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY 211
           + H SS+    PR++  I  F+   E   + L+ G  G  V++I    G  KT  A   Y
Sbjct: 523 ITHTSSQLARTPRMNEEIVGFKDVIENLRNRLLNGTKGQDVISIHGMPGLGKTTLANRLY 582

Query: 212 NNNHVKFYFDCLAWILDDIIRSL--MPPSRVTVIIGEDYKLKK-------SILRDFLTNK 262
           ++  V  +FD  A      + S   +  + +   +G+D   +K         LR  L ++
Sbjct: 583 SDRSVVSHFDICAQCCVSQVYSYKELLLALLCDAVGDDSARRKHNENKLADKLRKTLLSR 642

Query: 263 KYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT----------------- 305
           +Y I +DDV  N   WDDL    PD  N SR+++T  +  +                   
Sbjct: 643 RYLILVDDVWDN-SAWDDLRGCFPDANNRSRIILTTRHHEVAKYASVHSDPLHLRMFDED 701

Query: 306 -SFELLN----GEKIRCDYVLVEGPLIRIKHSAWQF---FVLHYG--------------- 342
            S++LL     GEK RC  +L++   +RI     Q     VL  G               
Sbjct: 702 ESWKLLEKKVFGEK-RCSSLLLKDVGLRIAKMCGQLPLSIVLVAGILSEMEKEVECWEQV 760

Query: 343 SAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGF 402
           +  LG ++      A+++++  V  LP HLK C +Y   F     I   +L +LWI+E F
Sbjct: 761 ANNLGTHIHNDS-RAIVNQSYHV--LPCHLKSCFLYFGAFLEDEVIDISRLIRLWISESF 817

Query: 403 IPYNS----EETAELYLKELIHRGFI 424
           I  +     E+ AE YL+ LI R  +
Sbjct: 818 IKSSEGRRLEDIAEGYLENLIGRNLV 843

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.

Solanum demissum (taxid: 50514)

>sp|Q9FJB5|RP8L3_ARATH Disease resistance RPP8-like protein 3 OS=Arabidopsis thaliana GN=RPP8L3 PE=2 SV=1

 Score = 70.9 bits (172), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 95/415 (22%), Positives = 170/415 (40%), Gaps = 79/415 (19%)

Query: 83  LEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH---SKIIDIRNRM-- 137
           LEDV   V ++E++I+++ +N ++ +    ++        L   H   S I  I  R+  
Sbjct: 62  LEDVKDLVFDAEDIIESYVLNKLRGEGKGVKNHVRRLACFLTDRHKVASDIEGITKRISK 121

Query: 138 -----------QQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDLLIEG 186
                      QQ+  G     + + + E I  +       D+   E++ EE    ++E 
Sbjct: 122 VIGEMQSLGIQQQIIDGGRSLSLQDIQRE-IRQTFPNSSESDLVGVEQSVEELVGPMVEI 180

Query: 187 PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----------ILDDIIRSLM 235
              + VV+I    G  KT  A   ++++ V+ +FD  AW           +   I++ L 
Sbjct: 181 D-NIQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELR 239

Query: 236 PPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVL 295
           P     ++  ++Y ++  + +  L   +Y + LDDV    E WD ++EV P  + G ++L
Sbjct: 240 PHDG-EILQMDEYTIQGKLFQ-LLETGRYLVVLDDVWKE-EDWDRIKEVFP-RKRGWKML 295

Query: 296 ITVIN--------PSLLTS-------------FELLNGEKIRCDY--------------- 319
           +T  N        P+ L+              FE +   +   +Y               
Sbjct: 296 LTSRNEGVGLHADPTCLSFRARILNPKESWKLFERIVPRRNETEYEEMEAIGKEMVTYCG 355

Query: 320 -----VLVEGPLIRIKHSA--WQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVF--ELPL 370
                V V G L+  KH+A  W+    + G+  +G    +   L  + R  S+   +LP 
Sbjct: 356 GLPLAVKVLGGLLANKHTASEWKRVSENIGAQIVGKSCLDDNSLNSVYRILSLSYEDLPT 415

Query: 371 HLKVCCIYLCVFRPGIEISSRQLCQLWIAEG-FIPYNSEETAELYLKELIHRGFI 424
            LK C +YL  F    +I +R L   W AEG +      ++ E YL+EL+ R  +
Sbjct: 416 DLKHCFLYLAHFPEDYKIKTRTLYSYWAAEGIYDGLTILDSGEDYLEELVRRNLV 470

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L403|R1B17_SOLDE Putative late blight resistance protein homolog R1B-17 OS=Solanum demissum GN=R1B-17 PE=3 SV=1

 Score = 70.5 bits (171), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 88/326 (26%), Positives = 138/326 (42%), Gaps = 62/326 (19%)

Query: 156 LIHLSSE--GQPRLD--ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY 211
           + H SS+    PR++  I  F+   E   + L+ G  G  V++I    G  KT  A   Y
Sbjct: 523 ITHTSSQLARTPRMNEEIVGFKDVIENLRNRLLNGTKGQDVISIHGMPGLGKTTLANRLY 582

Query: 212 NNNHVKFYFDCLAWILDDIIRSL--MPPSRVTVIIGEDYKLKK-------SILRDFLTNK 262
           ++  V  +FD  A      + S   +  + +   +G+D   +K         LR  L ++
Sbjct: 583 SDRSVVSHFDICAQCCVSQVYSYKELLLALLCDAVGDDSARRKHNENKLADKLRKTLLSR 642

Query: 263 KYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT----------------- 305
           +Y I +DDV  N   WDDL    PD  N SR+++T  +  +                   
Sbjct: 643 RYLILVDDVWDN-SAWDDLRGCFPDANNRSRIILTTRHHEVAKYASVHSDPLHLRMFDED 701

Query: 306 -SFELLN----GEKIRCDYVLVEGPLIRIKHSAWQF---FVLHYG--------------- 342
            S++LL     GEK RC  +L++   +RI     Q     VL  G               
Sbjct: 702 ESWKLLEKKVFGEK-RCSSLLLKDVGLRIAKMCEQLPLSIVLVAGILSEMEKEVECWEQV 760

Query: 343 SAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGF 402
           +  LG ++      A+++++  V  LP HLK C +Y   F     I   +L +LWI+E F
Sbjct: 761 ANNLGTHIHNDS-RAIVNQSYHV--LPCHLKSCFLYFGAFLEDEVIDISRLIRLWISESF 817

Query: 403 IPYNS----EETAELYLKELIHRGFI 424
           I  +     E+ AE YL+ LI R  +
Sbjct: 818 IKSSEGRRLEDIAEGYLENLIGRNLV 843

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.

Solanum demissum (taxid: 50514)

>sp|P59584|RP8HA_ARATH Disease resistance protein RPH8A OS=Arabidopsis thaliana GN=RPH8A PE=3 SV=1

 Score = 70.5 bits (171), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 95/424 (22%), Positives = 173/424 (40%), Gaps = 83/424 (19%)

Query: 79  ILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH---SKIIDIRN 135
           +   LEDV   V ++E++I+++ +N ++ +    +         L   H   S I  I  
Sbjct: 58  VRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKKHVRRLARFLTDRHKVASDIEGITK 117

Query: 136 RMQQLPPGDNGFDINEQRDELIHLSSEGQPRL--------------DISEFERAREEWFD 181
           R+ ++      F I +  D    LS + + R+              D+   E++  E   
Sbjct: 118 RISEVIGEMQSFGIQQIIDGGRSLSLQERQRVQREIRQTYPDSSESDLVGVEQSVTELVC 177

Query: 182 LLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-----------DDI 230
            L+E  +   VV+I    G  KT  A   ++++ V+ +FD  AW+              I
Sbjct: 178 HLVENDVH-QVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRI 236

Query: 231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQN 290
           ++ L P     ++  ++Y ++  + +  L   +Y + LDDV    E WD ++ V P  + 
Sbjct: 237 LQELQPHDG-EILQMDEYTIQGKLFQ-LLETGRYLVVLDDVWKK-EDWDRIKAVFP-RKR 292

Query: 291 GSRVLITVIN--------PSLLT-SFELLNGE-----------------KIRCD------ 318
           G ++L+T  N        P+ LT    +LN E                 ++R D      
Sbjct: 293 GWKMLLTSRNEGVGIHADPTCLTFRASILNPEESWKLCERIVFPRRDETEVRLDEEMEAM 352

Query: 319 -------------YVLVEGPLIRIKHSA--WQFFVLHYGSAALGNYMDEKMVLAVLSRTC 363
                         V   G L+  KH+   W+    + GS  +G    +   L  + R  
Sbjct: 353 GKEMVTHCGGLPLAVKALGGLLANKHTVPEWKRVSDNIGSQIVGGSCLDDNSLNSVYRIL 412

Query: 364 SVF--ELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNS-EETAELYLKELIH 420
           S+   +LP HLK C ++L  +    +I ++ L   W AEG    ++ +++ E YL+EL+ 
Sbjct: 413 SLSYEDLPTHLKHCFLHLAHYPEDSKIYTQDLFNYWAAEGIYDGSTIQDSGEYYLEELVR 472

Query: 421 RGFI 424
           R  +
Sbjct: 473 RNLV 476

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to RPP8, it does not specifically recognize the Emco5 avirulence protein from Hyaloperonospora parasitica.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score = 69.7 bits (169), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 129/300 (43%), Gaps = 72/300 (24%)

Query: 192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-------ILDDIIRSLMP---PSRVT 241
           VVA++   G  KT  +A+ + +  V+ +F+  AW       +++D+ R+++        T
Sbjct: 195 VVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADT 254

Query: 242 VIIGEDYKLKK----SILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLIT 297
            I  E Y L        L ++L +K+Y + LDDV     +W ++   LPD   GSRV++T
Sbjct: 255 QIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVW-TTGLWREISIALPDGIYGSRVMMT 313

Query: 298 VIN----------------------------------PSLLTSFELLNGEKI------RC 317
             +                                  P+ L      N E I      RC
Sbjct: 314 TRDMNVASFPYGIGSTKHEIELLKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVERC 373

Query: 318 DYVLVE----GPLIRIK--HSAWQ--FFVLHYGSAALGNYMDEKMVLAVLSRTCSVFELP 369
             + +     G ++  K   S W+  +  L++    L N  + K+V +++    S  +LP
Sbjct: 374 QGLPLAIASLGSMMSTKKFESEWKKVYSTLNW---ELNNNHELKIVRSIM--FLSFNDLP 428

Query: 370 LHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIP----YNSEETAELYLKELIHRGFIQ 425
             LK C +Y  +F     +  ++L ++W+A+ F+       +EE A+ YL EL++R  +Q
Sbjct: 429 YPLKRCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKAEEVADSYLNELVYRNMLQ 488

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q6L406|R1B19_SOLDE Putative late blight resistance protein homolog R1B-19 OS=Solanum demissum GN=R1B-19 PE=5 SV=2

 Score = 69.7 bits (169), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 85/317 (26%), Positives = 131/317 (41%), Gaps = 65/317 (20%)

Query: 165 PRL--DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDC 222
           PR+  +I  FE   E     L+ G  G  V++I    G  KT  A   Y++  V   FD 
Sbjct: 536 PRMKEEIVGFEDIIENLRKKLLNGTKGQDVISIHGMPGLGKTTLANRLYSDRSVVSQFDI 595

Query: 223 LA-------WILDDIIRSLMPPSRVTVIIGEDYKLKK-------SILRDFLTNKKYFIAL 268
            A       +   D++ SL+  +     IGE+ + ++        +LR  L  ++Y I +
Sbjct: 596 CAQCCVSQVYSYKDLLLSLLCDT-----IGEESERRELPDNELADMLRKTLLPRRYLILV 650

Query: 269 DDVCHNIEIWDDLEEVLPDNQNGSRVLITV------------INPSLLTSFELLNGEKIR 316
           DDV  N  +WDDL    PD  N SR+++T             I+P  L  F+     K  
Sbjct: 651 DDVWEN-SVWDDLRGCFPDTNNRSRIILTTRHHEVAKYASVHIDPLHLRMFDENESWKFL 709

Query: 317 CDYVLVE---GPLI-----RIKHSAWQFFVLHYGSAALGNYMDEKM-------------- 354
              V  E    PL+     RI     Q        A + + M++++              
Sbjct: 710 EKNVFGEESCSPLLRDVGQRIAKMCGQLPFSIVLVAGIPSEMEKEVECWEQVANNLGTRI 769

Query: 355 ---VLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNS---- 407
                A++ ++  V  LP HLK C +Y   F   + I   +L +LWI+E FI  +     
Sbjct: 770 HNDSRAIVDQSYHV--LPCHLKSCFLYFAAFLEDVVIYISRLLRLWISEAFIKSSEGRSL 827

Query: 408 EETAELYLKELIHRGFI 424
           E+ AE YL+ LI R  +
Sbjct: 828 EDIAEGYLENLIGRNLV 844

Confers resistance to late blight (Phytophthora infestans) races carrying the avirulence gene Avr1. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth.

Solanum demissum (taxid: 50514)

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	425
297744819	597	unnamed protein product [Vitis vinifera]	0.821	0.584	0.290	7e-25
359489158	531	PREDICTED: putative disease resistance p	0.821	0.657	0.290	8e-25
359489156	899	PREDICTED: probable disease resistance p	0.821	0.388	0.290	9e-25
147780806	597	hypothetical protein VITISV_008412 [Viti	0.821	0.584	0.288	3e-24
351721361	934	NBS-LRR type disease resistance protein	0.804	0.366	0.266	1e-23
359489148	897	PREDICTED: probable disease resistance R	0.868	0.411	0.290	2e-23
297745275	1136	unnamed protein product [Vitis vinifera]	0.781	0.292	0.270	3e-21
359489796	795	PREDICTED: disease susceptibility protei	0.816	0.436	0.265	5e-21
297745279	920	unnamed protein product [Vitis vinifera]	0.816	0.377	0.265	6e-21
359491404	922	PREDICTED: probable disease resistance R	0.769	0.354	0.266	3e-20

>gi|297744819|emb|CBI38087.3| unnamed protein product [Vitis vinifera]

 Score =  121 bits (303), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 124/427 (29%), Positives = 190/427 (44%), Gaps = 78/427 (18%)

Query: 71  NEDVKR---PDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH 127
           + D KR   P I   +  +    +++E+VID F   +  QQ    +      + L+  L 
Sbjct: 47  DADAKRRYDPRIKLWVSQIRDVTYDAEDVIDRFMFEMNHQQQGSLKCLKFLKLRLVHKLE 106

Query: 128 SKIIDIRNRMQQLPPGDNGFDIN-----EQRDELIHLSSEGQP---RLDISEFERAREEW 179
           S+I +I  +++++    + F +         +E++       P    +++   +   +  
Sbjct: 107 SRIREINTKIEKIKAAKSTFVVETLPAASSPNEVVPHRERRAPIVEEVNVVGIQEDAKSV 166

Query: 180 FDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL---DDIIRSLMP 236
              L+ G +  +VV+I+   G  KT  A   YN+N V+  FDC AWI    +  IR L+ 
Sbjct: 167 KQKLLNGEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELLL 226

Query: 237 PSRVTV-IIGEDYKLK------KSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQ 289
              V V I+ E+ + K       + LRD+LT KKY I +DD+  N E WD L    PD+ 
Sbjct: 227 GIAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRN-EAWDRLGLYFPDSV 285

Query: 290 NGSRVLITVINP---------------SLLT---SFELL--------------------N 311
           NGSRVLIT  N                S LT   S+EL                      
Sbjct: 286 NGSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 312 GEKIRCD------YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNYMDEKMVLAVLSRT 362
           G+KI  +       ++V G L+  K     +WQ  VL   +  L    D    L VL+  
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQ-KVLDSLTWHLNQGPDS--CLGVLA-- 400

Query: 363 CSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE----TAELYLKEL 418
            S  ++P +LK C +Y  +F    EI + +L +LW+AEGFI    EE     AE +L+EL
Sbjct: 401 LSYNDMPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIGEDVAEDHLQEL 460

Query: 419 IHRGFIQ 425
           +HR  IQ
Sbjct: 461 VHRSMIQ 467

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489158|ref|XP_003633890.1| PREDICTED: putative disease resistance protein At1g50180-like [Vitis vinifera]

 Score =  121 bits (303), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 124/427 (29%), Positives = 190/427 (44%), Gaps = 78/427 (18%)

Query: 71  NEDVKR---PDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH 127
           + D KR   P I   +  +    +++E+VID F   +  QQ    +      + L+  L 
Sbjct: 47  DADAKRRYDPRIKLWVSQIRDVTYDAEDVIDRFMFEMNHQQQGSLKCLKFLKLRLVHKLE 106

Query: 128 SKIIDIRNRMQQLPPGDNGFDIN-----EQRDELIHLSSEGQP---RLDISEFERAREEW 179
           S+I +I  +++++    + F +         +E++       P    +++   +   +  
Sbjct: 107 SRIREINTKIEKIKAAKSTFVVETLPAASSPNEVVPHRERRAPIVEEVNVVGIQEDAKSV 166

Query: 180 FDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL---DDIIRSLMP 236
              L+ G +  +VV+I+   G  KT  A   YN+N V+  FDC AWI    +  IR L+ 
Sbjct: 167 KQKLLNGEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELLL 226

Query: 237 PSRVTV-IIGEDYKLK------KSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQ 289
              V V I+ E+ + K       + LRD+LT KKY I +DD+  N E WD L    PD+ 
Sbjct: 227 GIAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRN-EAWDRLGLYFPDSV 285

Query: 290 NGSRVLITVINP---------------SLLT---SFELL--------------------N 311
           NGSRVLIT  N                S LT   S+EL                      
Sbjct: 286 NGSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 312 GEKIRCD------YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNYMDEKMVLAVLSRT 362
           G+KI  +       ++V G L+  K     +WQ  VL   +  L    D    L VL+  
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQ-KVLDSLTWHLNQGPDS--CLGVLA-- 400

Query: 363 CSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE----TAELYLKEL 418
            S  ++P +LK C +Y  +F    EI + +L +LW+AEGFI    EE     AE +L+EL
Sbjct: 401 LSYNDMPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIGEDVAEDHLQEL 460

Query: 419 IHRGFIQ 425
           +HR  IQ
Sbjct: 461 VHRSMIQ 467

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489156|ref|XP_003633889.1| PREDICTED: probable disease resistance protein RDL6/RF9-like [Vitis vinifera]

 Score =  120 bits (302), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 124/427 (29%), Positives = 190/427 (44%), Gaps = 78/427 (18%)

Query: 71  NEDVKR---PDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH 127
           + D KR   P I   +  +    +++E+VID F   +  QQ    +      + L+  L 
Sbjct: 47  DADAKRRYDPRIKLWVSQIRDVTYDAEDVIDRFMFEMNHQQQGSLKCLKFLKLRLVHKLE 106

Query: 128 SKIIDIRNRMQQLPPGDNGFDIN-----EQRDELIHLSSEGQP---RLDISEFERAREEW 179
           S+I +I  +++++    + F +         +E++       P    +++   +   +  
Sbjct: 107 SRIREINTKIEKIKAAKSTFIVETLPAASWPNEVVPHRERRAPIVEEVNVVGIQEDAKSV 166

Query: 180 FDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL---DDIIRSLMP 236
              L+ G +  +VV+I+   G  KT  A   YN+N V+  FDC AWI    +  IR L+ 
Sbjct: 167 KQKLLNGEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELLL 226

Query: 237 PSRVTV-IIGEDYKLK------KSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQ 289
              V V I+ E+ + K       + LRD+LT KKY I +DD+  N E WD L    PD+ 
Sbjct: 227 GVAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRN-EAWDRLGLYFPDSV 285

Query: 290 NGSRVLITVINP---------------SLLT---SFELL--------------------N 311
           NGSRVLIT  N                S LT   S+EL                      
Sbjct: 286 NGSRVLITSRNKQIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 312 GEKIRCD------YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNYMDEKMVLAVLSRT 362
           G+KI  +       ++V G L+  K     +WQ  VL   +  L    D    L VL+  
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQ-KVLDSLTWHLNQGPDS--CLGVLA-- 400

Query: 363 CSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE----TAELYLKEL 418
            S  ++P +LK C +Y  +F    EI + +L +LW+AEGFI    EE     AE +L+EL
Sbjct: 401 LSYNDMPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIAEDVAEDHLQEL 460

Query: 419 IHRGFIQ 425
           +HR  IQ
Sbjct: 461 VHRSMIQ 467

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147780806|emb|CAN70484.1| hypothetical protein VITISV_008412 [Vitis vinifera]

 Score =  119 bits (298), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 123/427 (28%), Positives = 189/427 (44%), Gaps = 78/427 (18%)

Query: 71  NEDVKR---PDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLH 127
           + D KR   P I   +  +    +++E+VID F   +  QQ    +      + L+  L 
Sbjct: 47  DADAKRRYDPRIKLWVSQIRDVTYDAEDVIDRFMFEMNHQQQGSLKCLKFLKLRLVHKLE 106

Query: 128 SKIIDIRNRMQQLPPGDNGFDIN-----EQRDELIHLSSEGQP---RLDISEFERAREEW 179
           S+I +I  +++++    + F +         +E++       P    +++   +   +  
Sbjct: 107 SRIREINTKIEKIKAAKSTFVVETLPAASSPNEVVPHRERRAPIVEEVNVVGIQEDAKSV 166

Query: 180 FDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL---DDIIRSLMP 236
              L+ G +  +VV+I+   G  KT  A   YN+N V+  FDC AWI    +  IR L+ 
Sbjct: 167 KQKLLNGEMRRAVVSIVGMGGLGKTTLAKKVYNDNDVQQCFDCHAWIYVSQEYTIRELLL 226

Query: 237 PSRVTV-IIGEDYKLK------KSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQ 289
              V V I+ E+ + K       + LRD+LT KKY I +DD+    E WD L    PD+ 
Sbjct: 227 GXAVRVGILSEEERSKMNESDLGNSLRDYLTTKKYLIVMDDMWRX-EAWDRLGLYFPDSV 285

Query: 290 NGSRVLITVINP---------------SLLT---SFELL--------------------N 311
           NGSRVLIT  N                S LT   S+EL                      
Sbjct: 286 NGSRVLITSRNKEIGLYADPQTIPHELSFLTEEESWELFLKKIFLAGSANAVCPRELEEL 345

Query: 312 GEKIRCD------YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNYMDEKMVLAVLSRT 362
           G+KI  +       ++V G L+  K     +WQ  VL   +  L    D    L VL+  
Sbjct: 346 GKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQ-KVLDSLTWHLNQGPDS--CLGVLA-- 400

Query: 363 CSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE----TAELYLKEL 418
            S  ++P +LK C +Y  +F    EI + +L +LW+AEGFI    EE     AE +L+EL
Sbjct: 401 LSYNDMPYYLKSCFLYCGLFPEDSEIRTDKLIRLWVAEGFIQRRGEEIGEDVAEDHLQEL 460

Query: 419 IHRGFIQ 425
           +HR  IQ
Sbjct: 461 VHRSMIQ 467

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721361|ref|NP_001235671.1| NBS-LRR type disease resistance protein [Glycine max] gi|223452621|gb|ACM89637.1| NBS-LRR type disease resistance protein [Glycine max]

 Score =  117 bits (293), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 113/424 (26%), Positives = 180/424 (42%), Gaps = 82/424 (19%)

Query: 75  KRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVGLHSKIIDIR 134
           K P++   ++ V    H+ E+ ID F + ++ Q      S    N  +   + S I +I+
Sbjct: 54  KDPELKAWVKRVRDVAHDMEDAIDEFSLRLVDQHGQGNSSSFHVNFFIRHRIASNIQNIK 113

Query: 135 NRMQQLPPG-DNGFDINEQRDELIHLSSEGQPRL----DISEFERAREEWFDLLIEGPIG 189
           +R+  +  G  N   I     + + L S+G   L    D+   ++ + +  DLL     G
Sbjct: 114 SRVDIISQGRPNIAGIGSGSSQRLRLDSQGDALLLEEADLVGIDKPKRQLSDLLFNEEAG 173

Query: 190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------LDDIIRSLM--- 235
            +V+ I    G  KT  A   Y++  VK  F   AWI           L D+++ L    
Sbjct: 174 RAVIPIYGMGGLGKTTLAKQVYDDPKVKKRFRIHAWINVSQSFQLEVLLKDLVQQLHNVI 233

Query: 236 -PPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRV 294
             PS   V   +  +LK+ ++++ L   +Y I LDDV H +++WD ++  LP+N  GSRV
Sbjct: 234 GKPSPEAVGQMKSDQLKE-LIKNLLQQSRYLIVLDDVWH-VKVWDSVKLALPNNNRGSRV 291

Query: 295 LITVINP--SLLTSFELLNGEKIRCDYVLVE----------------------------- 323
           ++T      +L +  EL  G+    +++  E                             
Sbjct: 292 MLTTRKKDIALYSCAEL--GKDFNLEFLPEEESWYLFCKKTFQGNPCPPYLEAVCRNILK 349

Query: 324 ------------GPLIRIKHSA----WQFFVLHYGSAALGN--YMDEKMVLAVLSRTCSV 365
                       G  +  K+ A    WQ     +GS   GN    D K VL++     S 
Sbjct: 350 MCGGLPLAIVAIGGALATKNRANIEEWQMVYRSFGSEIEGNDKLEDMKKVLSL-----SF 404

Query: 366 FELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNS----EETAELYLKELIHR 421
            ELP +LK C +YL +F     I   +L +LWIAEGF+        EE A+ YLKEL+ R
Sbjct: 405 NELPYYLKSCLLYLSIFPEFHAIEHMRLIRLWIAEGFVNGEDGKTLEEVADSYLKELLDR 464

Query: 422 GFIQ 425
             +Q
Sbjct: 465 SLLQ 468

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489148|ref|XP_003633887.1| PREDICTED: probable disease resistance RPP8-like protein 4-like [Vitis vinifera]

 Score =  117 bits (292), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 131/451 (29%), Positives = 203/451 (45%), Gaps = 82/451 (18%)

Query: 50  LLANYEADMALLLFQLLRKKI---NEDVKR---PDILKILEDVNQFVHESEEVIDTFFIN 103
           LL+  E  + LL  +L   ++   + D KR   P I   +  +    +++E+VID F   
Sbjct: 23  LLSRVEEQVKLLSSELEWMRLFLKDADAKRRYDPRIKLWVSQIRDVTYDAEDVIDRFMFE 82

Query: 104 IMQQQNSEEESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDIN-----EQRDELIH 158
           +  QQ    +      +  +  L S+I +I  +++++    + + +         +E + 
Sbjct: 83  MNHQQQGSLKCLQFLKLRFVHKLESRIREINIKIEKIMANKSRYGVETLPAASSSNEAVP 142

Query: 159 LSSEGQPRLDISEF---ERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNH 215
              +  P ++++     E A+    +LL  G +  +VV+I+   G  KT  A   YN+N 
Sbjct: 143 HKEKRAPIVEVNVVGIQEDAKSVKQNLL-NGEMRRAVVSIVGMGGLGKTTLAKKVYNDND 201

Query: 216 VKFYFDCLAWIL---DDIIRSLMPPSRVTV-IIGEDYKLK------KSILRDFLTNKKYF 265
           V+  FDC AWI    +  IR L+    V V I+ E+ + K         LRD+LT KKY 
Sbjct: 202 VRQCFDCHAWIYVSQEYTIRELLLGVAVCVRILSEEERSKMDESELGDRLRDYLTTKKYL 261

Query: 266 IALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINP---------------SLLT---SF 307
           I LDD+  N E WD L    PD+ NGSRVLIT  N                S LT   S+
Sbjct: 262 IVLDDMWRN-EAWDRLGLYFPDSVNGSRVLITSRNKEIGFYADPQAIPHELSFLTEEESW 320

Query: 308 ELL--------------------NGEKIRCD------YVLVEGPLIRIKHS---AWQFFV 338
           EL                      G+KI  +       ++V G L+  K     +WQ  V
Sbjct: 321 ELFLKKIFLAGSANAVCPRELEELGKKIVANCGGLPLAIVVLGGLLSRKEKTPLSWQ-KV 379

Query: 339 LHYGSAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWI 398
           L   +  L    D    L VL+   S  ++P +LK C +Y  +F    EI + +L +LW+
Sbjct: 380 LDSLTWHLNQGPDS--CLGVLA--LSYNDMPYYLKSCFLYCGLFPEDSEIWTDKLIRLWV 435

Query: 399 AEGFIPYN----SEETAELYLKELIHRGFIQ 425
           AEGFI       +E+ AE +L+EL+HR  IQ
Sbjct: 436 AEGFIQRRGVEIAEDVAEDHLQELVHRSMIQ 466

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745275|emb|CBI40355.3| unnamed protein product [Vitis vinifera]

 Score =  109 bits (272), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 115/425 (27%), Positives = 179/425 (42%), Gaps = 93/425 (21%)

Query: 86  VNQF---VHESEEVIDTFFINIMQQQNSEEESESSTNMALLVG----------LHSKIID 132
           VNQ     H++E+VID F +N+  +Q      +    +   VG          L S++ D
Sbjct: 62  VNQIRNATHDAEDVIDEFILNMDHRQRRLNTLKFLKCLPACVGFADKLPFIHELDSRVKD 121

Query: 133 IRNRMQQLPPGDNGFDINE------QRDELIHLSSEGQPRL----DISEFERAREEWFDL 182
           I   +  +    + + + +         + +    E +P +    D+   E   EE   +
Sbjct: 122 INVMIGAIMANRSKYGLGDLVASSSSTTDQVAAHKEKRPPVVEESDVVGIEDGIEEVKQM 181

Query: 183 LIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----------ILDDII 231
           L++     SVV+I+   G  KT FA   YN   V+ +FDC AW           IL DI 
Sbjct: 182 LMKEETRRSVVSIVGMGGLGKTTFAKKVYNQRDVQQHFDCKAWVYVSQEFRAREILLDIA 241

Query: 232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNG 291
              M  S     + E    +K  L ++L  KKY I +DDV  + E+W  L   LP+ ++G
Sbjct: 242 NHFMSLSEKEKEMRESELGEK--LCEYLKEKKYLIVMDDVWSS-EVWSRLRSHLPEAKDG 298

Query: 292 SRVLITVINP---------SLLTSFELLN-----------------------------GE 313
           S+VLIT  N          + +    L+N                             G+
Sbjct: 299 SKVLITTRNKEIALQATSQAFIYELRLMNDDESWQLFLKKTFQGTSTPHTLSRELEEPGK 358

Query: 314 KI--RCD----YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNYMDEKMVLAVLSRTCS 364
           KI  +C      V+V G L+  K     +W+  +     A++  Y+D+     +     S
Sbjct: 359 KIVAKCKGLPLAVVVLGGLLSTKEKTKPSWEKVL-----ASIEWYLDQGPESCMGILALS 413

Query: 365 VFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEET----AELYLKELIH 420
             +LP +LK C +Y  +F    EI + +L +LW+AEGFI    +ET    AE Y+ ELIH
Sbjct: 414 YNDLPYYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKETLEDIAEDYMHELIH 473

Query: 421 RGFIQ 425
           R  IQ
Sbjct: 474 RSLIQ 478

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489796|ref|XP_003633980.1| PREDICTED: disease susceptibility protein LOV1-like [Vitis vinifera]

 Score =  108 bits (270), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 117/440 (26%), Positives = 184/440 (41%), Gaps = 93/440 (21%)

Query: 71  NEDVKRPDILKILEDVNQF---VHESEEVIDTFFINIMQQQNSEEESESSTNMALLVG-- 125
           + D KR    +I   VNQ     H++E+VID F +N+  +Q      +    +   VG  
Sbjct: 47  DADSKRIHDERIKLWVNQIRNATHDAEDVIDEFIVNMDHRQRRLNTLKLLKCLPTCVGFA 106

Query: 126 --------LHSKIIDIRNRMQQLPPGDNGFDINE------QRDELIHLSSEGQPRL---- 167
                   L S++ DI   +  +    + + + +         + +    E +P +    
Sbjct: 107 DKLPFIHELDSRVKDINVMIGAIMANRSKYGLGDLVASSSSTTDQVAAHKEKRPPVVEES 166

Query: 168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-- 225
           D+   E   EE   +L++     SVV+I+   G  KT  A   YN   V+ +FDC AW  
Sbjct: 167 DVVGIEDGTEEVKQMLMKEETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQQHFDCKAWVY 226

Query: 226 ---------ILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIE 276
                    IL DI    M  S     + E    +K  L ++L  KKY + +DDV  + E
Sbjct: 227 VSQEFRAREILLDIANRFMSLSEKEKEMRESELGEK--LCEYLKEKKYLVVMDDVWSS-E 283

Query: 277 IWDDLEEVLPDNQNGSRVLITVINP---------SLLTSFELLN---------------- 311
           +W  L   LP+ ++GS+VLIT  N          + +    L+N                
Sbjct: 284 VWSRLRSHLPEAKDGSKVLITTRNKEIALHATSQAFIYELRLMNDDESWQLFLKKTFQGT 343

Query: 312 -------------GEKI--RCD----YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNY 349
                        G+KI  +C      V+V G L+  K     +W+  +     A++  Y
Sbjct: 344 STPHTLIRELEEPGKKIVAKCKGLPLAVVVLGGLLSTKEKTKPSWEKVL-----ASIEWY 398

Query: 350 MDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE 409
           +D+     +     S  +LP +LK C +Y  +F    EI + +L +LW+AEGFI    +E
Sbjct: 399 LDQGPESCMGILALSYNDLPYYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKE 458

Query: 410 T----AELYLKELIHRGFIQ 425
           T    AE Y+ ELIHR  IQ
Sbjct: 459 TLEDIAEDYMHELIHRSLIQ 478

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745279|emb|CBI40359.3| unnamed protein product [Vitis vinifera]

 Score =  108 bits (269), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 117/440 (26%), Positives = 184/440 (41%), Gaps = 93/440 (21%)

Query: 71  NEDVKRPDILKILEDVNQF---VHESEEVIDTFFINIMQQQNSEEESESSTNMALLVG-- 125
           + D KR    +I   VNQ     H++E+VID F +N+  +Q      +    +   VG  
Sbjct: 47  DADSKRIHDERIKLWVNQIRNATHDAEDVIDEFIVNMDHRQRRLNTLKLLKCLPTCVGFA 106

Query: 126 --------LHSKIIDIRNRMQQLPPGDNGFDINE------QRDELIHLSSEGQPRL---- 167
                   L S++ DI   +  +    + + + +         + +    E +P +    
Sbjct: 107 DKLPFIHELDSRVKDINVMIGAIMANRSKYGLGDLVASSSSTTDQVAAHKEKRPPVVEES 166

Query: 168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-- 225
           D+   E   EE   +L++     SVV+I+   G  KT  A   YN   V+ +FDC AW  
Sbjct: 167 DVVGIEDGTEEVKQMLMKEETRRSVVSIVGMGGLGKTTLAKKVYNQRDVQQHFDCKAWVY 226

Query: 226 ---------ILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIE 276
                    IL DI    M  S     + E    +K  L ++L  KKY + +DDV  + E
Sbjct: 227 VSQEFRAREILLDIANRFMSLSEKEKEMRESELGEK--LCEYLKEKKYLVVMDDVWSS-E 283

Query: 277 IWDDLEEVLPDNQNGSRVLITVINP---------SLLTSFELLN---------------- 311
           +W  L   LP+ ++GS+VLIT  N          + +    L+N                
Sbjct: 284 VWSRLRSHLPEAKDGSKVLITTRNKEIALHATSQAFIYELRLMNDDESWQLFLKKTFQGT 343

Query: 312 -------------GEKI--RCD----YVLVEGPLIRIKHS---AWQFFVLHYGSAALGNY 349
                        G+KI  +C      V+V G L+  K     +W+  +     A++  Y
Sbjct: 344 STPHTLIRELEEPGKKIVAKCKGLPLAVVVLGGLLSTKEKTKPSWEKVL-----ASIEWY 398

Query: 350 MDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE 409
           +D+     +     S  +LP +LK C +Y  +F    EI + +L +LW+AEGFI    +E
Sbjct: 399 LDQGPESCMGILALSYNDLPYYLKSCFLYCGIFPEDSEIKASKLIRLWLAEGFIQRRGKE 458

Query: 410 T----AELYLKELIHRGFIQ 425
           T    AE Y+ ELIHR  IQ
Sbjct: 459 TLEDIAEDYMHELIHRSLIQ 478

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359491404|ref|XP_002274414.2| PREDICTED: probable disease resistance RPP8-like protein 2-like [Vitis vinifera]

 Score =  105 bits (263), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 114/427 (26%), Positives = 180/427 (42%), Gaps = 100/427 (23%)

Query: 85  DVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVG-------LHSKIIDIRNRM 137
           D+    ++ ++VIDTF     QQ+  E     S   A ++        +  KI  I  ++
Sbjct: 80  DIRDVAYDIDDVIDTFLCKTAQQRK-EGFFRLSGRYAFVLSDPVAHWKISKKINRIMEKI 138

Query: 138 QQLPPGDNGFDI----------------NEQRDELIHLSSEG--QPRLDISEFERAREEW 179
            ++    + + I                 E+R    H   E    P  DI    R  E W
Sbjct: 139 HEITDSRSTYGIENIGRGGGRSFATDRLQEKRRSSSHACEEDVVGPLQDI----RTLESW 194

Query: 180 FDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------LD 228
              LI G   L +++I+  +G  KT  A   Y++N VK  FD   W+           L 
Sbjct: 195 ---LIHGETRLCILSIVGMAGLGKTTLAKKLYHSNDVKKNFDFCGWVYVSQEYRPKDTLQ 251

Query: 229 DIIRSL--MPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLP 286
           ++++ +  +P + +  +  ED +     L  FL  KKYFI LDD+    E+WDDL+   P
Sbjct: 252 NLVKRVTGLPRAELEKMDKEDLE---EALSKFLEEKKYFIVLDDIWKK-EVWDDLKAAFP 307

Query: 287 DNQNGSRVLIT---------------VINPSLLT---SFELLN----------------- 311
           D +NGSR++ T               +  P LL+    +ELL+                 
Sbjct: 308 DRKNGSRIIFTTRFKDVALHADPRSPLHEPCLLSDEDGWELLSRKVCLEWNAKTSLPPWS 367

Query: 312 ---GEKI--RCD----YVLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKMVLAVLSRT 362
              G +I  RC      ++V G L+  K + +  ++    S       D      +L+ +
Sbjct: 368 KELGIQIVKRCGGLPLAIVVMGGLLSRKDATFNEWLKVLQSVHWQLAQDPTQCAEILALS 427

Query: 363 CSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE----TAELYLKEL 418
            S  +LP +LK C +Y  +F    EIS+R+L  LW+AEGF+    +E     AE YL+EL
Sbjct: 428 YS--DLPYYLKSCFLYFGLFPEDYEISARRLILLWVAEGFVQPRGQEPLEDVAEDYLEEL 485

Query: 419 IHRGFIQ 425
           + R  IQ
Sbjct: 486 VGRSMIQ 492

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

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	425
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.510	0.238	0.232	4.4e-13
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.508	0.239	0.224	9.5e-12
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.52	0.260	0.264	1.1e-11
TAIR|locus:2152536	908	AT5G48620 [Arabidopsis thalian	0.510	0.238	0.236	1.5e-11
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.247	0.113	0.291	5.7e-11
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.505	0.237	0.25	6.2e-11
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.247	0.125	0.352	6.5e-11
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.522	0.244	0.203	6.8e-11
UNIPROTKB|Q84UB1	928	Pi-ta "Pi-ta protein" [Oryza s	0.331	0.151	0.313	1.9e-10
UNIPROTKB|Q9AY26	928	Pi-ta "Pi-ta protein" [Oryza s	0.331	0.151	0.313	1.9e-10

TAIR|locus:2176486 RPP8 "RECOGNITION OF PERONOSPORA PARASITICA 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 4.4e-13, Sum P(2) = 4.4e-13
 Identities = 58/250 (23%), Positives = 106/250 (42%)

Query:    79 ILKILEDVNQFVHESEEVIDTFFINIMQQQNXXXXXXXXTNMALLVGLH---SKIIDIRN 135
             +   LEDV   V ++E++I+++ +N +  +              L   H   S I  I  
Sbjct:    58 VRNFLEDVKDLVFDAEDIIESYVLNKLSGKGKGVKKHVRRLACFLTDRHKVASDIEGITK 117

Query:   136 RM------------QQLPPGDNGFDINE-QRDEL-IHLSSEGQPRLDISEFERAREEWFD 181
             R+            QQ+  G     + E QR +  I  +       D+   E++ +E   
Sbjct:   118 RISEVIGEMQSFGIQQIIDGGRSLSLQERQRVQREIRQTYPDSSESDLVGVEQSVKELVG 177

Query:   182 LLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-----------DDI 230
              L+E  +   VV+I    G  KT  A   ++++ V+ +FD  AW+              I
Sbjct:   178 HLVENDVH-QVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRI 236

Query:   231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQN 290
             ++ L P     ++  ++Y L++ + +  L   +Y + LDDV    E WD ++ V P  + 
Sbjct:   237 LQELQPHDG-DILQMDEYALQRKLFQ-LLEAGRYLVVLDDVWKK-EDWDVIKAVFP-RKR 292

Query:   291 GSRVLITVIN 300
             G ++L+T  N
Sbjct:   293 GWKMLLTSRN 302

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0051707 "response to other organism" evidence=IMP

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 9.5e-12, Sum P(2) = 9.5e-12
 Identities = 56/249 (22%), Positives = 106/249 (42%)

Query:    79 ILKILEDVNQFVHESEEVIDTFFINIMQQQNXXXXXXXXTNMALLVGLH---SKIIDIRN 135
             +   LEDV   V ++E++I+++ +N ++ +              L   H   S I  I  
Sbjct:    58 VRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKNHVRRLACFLTDRHKVASDIEGITK 117

Query:   136 RM-------------QQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFERAREEWFDL 182
             R+             QQ+  G     + + + E I  +       D+   E++ EE    
Sbjct:   118 RISKVIGEMQSLGIQQQIIDGGRSLSLQDIQRE-IRQTFPNSSESDLVGVEQSVEELVGP 176

Query:   183 LIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-----------DDII 231
             ++E    + VV+I    G  KT  A   ++++ V+ +FD  AW+              I+
Sbjct:   177 MVEID-NIQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRIL 235

Query:   232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNG 291
             + L P     ++  ++Y ++  + +  L   +Y + LDDV    E WD ++EV P  + G
Sbjct:   236 QELRPHDG-EILQMDEYTIQGKLFQ-LLETGRYLVVLDDVWKE-EDWDRIKEVFP-RKRG 291

Query:   292 SRVLITVIN 300
              ++L+T  N
Sbjct:   292 WKMLLTSRN 300

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:504956483 AT3G46730 [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 1.1e-11, Sum P(2) = 1.1e-11
 Identities = 68/257 (26%), Positives = 110/257 (42%)

Query:    72 EDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNXXXXXXXXTNMALLVGLHSKII 131
             ED    +  K++ D+    ++ E+V+DT+F+ + ++            +      ++ + 
Sbjct:    54 EDEVSKEWTKLVLDI---AYDIEDVLDTYFLKLEERSLRRGLLRLTNKIGKKRDAYNIVE 110

Query:   132 DIRN---RMQQLPPGDNGFDI---NEQRDELIHLSSEGQ----PRLDISEFERAREEWFD 181
             DIR    R+  +      F I   NE R E I      Q    P +D  E     E+   
Sbjct:   111 DIRTLKRRILDITRKRETFGIGSFNEPRGENITNVRVRQLRRAPPVDQEELVVGLEDDVK 170

Query:   182 LLIEGPIGLS------VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW---------- 225
             +L+   +  +      +++I    G  KTA A   YN+  VK  FDC AW          
Sbjct:   171 ILLVKLLSDNEKDKSYIISIFGMGGLGKTALARKLYNSGDVKRRFDCRAWTYVSQEYKTR 230

Query:   226 -ILDDIIRSLMPPSRVTV----IIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDD 280
              IL  IIRSL   S   +    +  ED +L+   L   L  K Y + +DDV  + + W+ 
Sbjct:   231 DILIRIIRSLGIVSAEEMEKIKMFEEDEELEV-YLYGLLEGKNYMVVVDDVW-DPDAWES 288

Query:   281 LEEVLPDNQNGSRVLIT 297
             L+  LP +  GS+V+IT
Sbjct:   289 LKRALPCDHRGSKVIIT 305

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2152536 AT5G48620 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 1.5e-11, Sum P(2) = 1.5e-11
 Identities = 59/250 (23%), Positives = 108/250 (43%)

Query:    79 ILKILEDVNQFVHESEEVIDTFFINIMQQQNXXXXXXXXTNMALLVGLHSKIIDIRNRMQ 138
             +   LEDV   V ++E++I+++ +N ++ +              L   H    DI    +
Sbjct:    58 VRNFLEDVKDLVFDAEDIIESYVLNKLRGEGKGVKKHVRRLARFLTDRHKVASDIEGITK 117

Query:   139 QLPP--GD-NGFDINEQRDELIHLSSEGQPRL---------DISE-----FERAREEWFD 181
             ++    G+   F I +  D +  LS + + R+         D SE      E++ EE   
Sbjct:   118 RISDVIGEMQSFGIQQIIDGVRSLSLQERQRVQREIRQTYPDSSESDLVGVEQSVEELVG 177

Query:   182 LLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-----------DDI 230
              L+E  I   VV+I    G  KT  A   ++++ V+ +FD  AW+              I
Sbjct:   178 HLVENDI-YQVVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTLKHVWQRI 236

Query:   231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQN 290
             ++ L P     ++  ++  L+  + +  L   +Y + LDDV    E WD ++ V P  + 
Sbjct:   237 LQELQPHDG-NILQMDESALQPKLFQ-LLETGRYLLVLDDVWKK-EDWDRIKAVFP-RKR 292

Query:   291 GSRVLITVIN 300
             G ++L+T  N
Sbjct:   293 GWKMLLTSRN 302

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 128 (50.1 bits), Expect = 5.7e-11, Sum P(2) = 5.7e-11
 Identities = 35/120 (29%), Positives = 64/120 (53%)

Query:   192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-------LDDIIRSLMPP---SRVT 241
             VVA++   G  KT  +A+ + +  V+ +F+  AW+       ++D+ R+++        T
Sbjct:   195 VVAVVGMGGSGKTTLSANIFKSQSVRRHFESYAWVTISKSYVIEDVFRTMIKEFYKEADT 254

Query:   242 VIIGEDYKL--KKSI--LRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLIT 297
              I  E Y L  ++ +  L ++L +K+Y + LDDV     +W ++   LPD   GSRV++T
Sbjct:   255 QIPAELYSLGYRELVEKLVEYLQSKRYIVVLDDVW-TTGLWREISIALPDGIYGSRVMMT 313

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009626 "plant-type hypersensitive response" evidence=IDA

TAIR|locus:2025916 AT1G59780 "AT1G59780" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 6.2e-11, Sum P(2) = 6.2e-11
 Identities = 60/240 (25%), Positives = 109/240 (45%)

Query:    83 LEDVNQFVHESEEVIDTFFIN-IMQQQNXXXXXXXXTNMAL-LVGLHSKIIDIRNRMQQL 140
             LE++ +  +++E++I+ F +   +  ++          +AL +  +  +I  +   MQ L
Sbjct:    67 LEEIKEITYDAEDIIEIFLLKGSVNMRSLACFPGGRREIALQITSISKRISKVIQVMQNL 126

Query:   141 P-PGD--NGFDIN---EQRDELIH-LSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVV 193
                 D  +G D +   E++ EL H  SSE +  L     E+  E+  + L+ G      V
Sbjct:   127 GIKSDIMDGVDSHAQLERKRELRHTFSSESESNL--VGLEKNVEKLVEELV-GNDSSHGV 183

Query:   194 AILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-------DDIIRSLM---PPSRVTVI 243
             +I    G  KT  A   ++++ VK +FD LAW+         D+ ++++    P      
Sbjct:   184 SITGLGGLGKTTLARQIFDHDKVKSHFDGLAWVCVSQEFTRKDVWKTILGNLSPKYKDSD 243

Query:   244 IGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSL 303
             + ED   KK  L   L  KK  I  DD+    E W  +  + P+ + G +VL+T  N ++
Sbjct:   244 LPEDDIQKK--LFQLLETKKALIVFDDLWKR-EDWYRIAPMFPERKAGWKVLLTSRNDAI 300

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2075170 RPP13 "RECOGNITION OF PERONOSPORA PARASITICA 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 6.5e-11, Sum P(2) = 6.5e-11
 Identities = 42/119 (35%), Positives = 56/119 (47%)

Query:   192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----------ILDDIIRSL-MPPSR 239
             +++I    G  KTA A   YN+  VK  F+  AW           IL  IIRSL M    
Sbjct:   187 IISIFGMGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGE 246

Query:   240 VTVIIGEDYKLKKSI-LRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLIT 297
                 I +  + +  + L   L  KKY + +DD+    E WD L+  LP N  GSRV+IT
Sbjct:   247 ELEKIRKFAEEELEVYLYGLLEGKKYLVVVDDIWER-EAWDSLKRALPCNHEGSRVIIT 304

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

GO:0009814 "defense response, incompatible interaction" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 129 (50.5 bits), Expect = 6.8e-11, Sum P(2) = 6.8e-11
 Identities = 51/251 (20%), Positives = 111/251 (44%)

Query:    79 ILKILEDVNQFVHESEEVIDTFFINIMQQQNXXXXXXXXTNMALLVGLHSKIID---IRN 135
             +  ++E++ + V+++E++I+T+ +     +          +  ++       +D   IR 
Sbjct:    58 VRNVVEEIKEIVYDAEDIIETYLLKEKLWKTSGIKMRIRRHACIISDRRRNALDVGGIRT 117

Query:   136 RMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISE-FERAREEWF---DLLIEGPIG-- 189
             R+  +      F + +   +  ++  +G  + ++ + F +  E  F   ++ ++  +G  
Sbjct:   118 RISDVIRDMQSFGVQQAIVDGGYMQPQGDRQREMRQTFSKDYESDFVGLEVNVKKLVGYL 177

Query:   190 -----LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDD-----------IIRS 233
                  + VV+I    G  KT  A   +N+  VK  FD LAW+              I+++
Sbjct:   178 VDEENVQVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQN 237

Query:   234 LMPPSRVTVIIG-EDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGS 292
             L    +   I+  E+ +L   + +  L   K  I  DD+  + E WD ++ + P N+ G 
Sbjct:   238 LTSREKKDEILQMEEAELHDKLFQ-LLETSKSLIVFDDIWKD-EDWDLIKPIFPPNK-GW 294

Query:   293 RVLITVINPSL 303
             +VL+T  N S+
Sbjct:   295 KVLLTSQNESV 305

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

UNIPROTKB|Q84UB1 Pi-ta "Pi-ta protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 129 (50.5 bits), Expect = 1.9e-10, Sum P(2) = 1.9e-10
 Identities = 52/166 (31%), Positives = 80/166 (48%)

Query:   154 DELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY-- 211
             D  +H    G+   DIS  +  R  W   L +G   L V +I+ S G  KT  A + Y  
Sbjct:   201 DAAVHGQLVGR---DISMQKLVR--W---LADGEPKLKVASIVGSGGVGKTTLATEFYRL 252

Query:   212 NNNHVKFYFDCLAW-----------ILDDIIRSLMPPSR-VTVIIGEDYKLKKSILRDFL 259
             +   +   FDC A+           IL D++  L P  +  +  + E  +L ++I R  L
Sbjct:   253 HGRRLDAPFDCRAFVRTPRKPDMTKILTDMLSQLRPQHQHQSSDVWEVDRLLETI-RTHL 311

Query:   260 TNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITV-INPSLL 304
              +K+YFI ++D+  +  +WD +   LPDN + SR+LIT  I P  L
Sbjct:   312 QDKRYFIIIEDLWAS-SMWDIVSRGLPDNNSCSRILITTEIEPVAL 356

GO:0006952 "defense response" evidence=IMP

UNIPROTKB|Q9AY26 Pi-ta "Pi-ta protein" [Oryza sativa (taxid:4530)]

 Score = 129 (50.5 bits), Expect = 1.9e-10, Sum P(2) = 1.9e-10
 Identities = 52/166 (31%), Positives = 80/166 (48%)

Query:   154 DELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY-- 211
             D  +H    G+   DIS  +  R  W   L +G   L V +I+ S G  KT  A + Y  
Sbjct:   201 DAAVHGQLVGR---DISMQKLVR--W---LADGEPKLKVASIVGSGGVGKTTLATEFYRL 252

Query:   212 NNNHVKFYFDCLAW-----------ILDDIIRSLMPPSR-VTVIIGEDYKLKKSILRDFL 259
             +   +   FDC A+           IL D++  L P  +  +  + E  +L ++I R  L
Sbjct:   253 HGRRLDAPFDCRAFVRTPRKPDMTKILTDMLSQLRPQHQHQSSDVWEVDRLLETI-RTHL 311

Query:   260 TNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITV-INPSLL 304
              +K+YFI ++D+  +  +WD +   LPDN + SR+LIT  I P  L
Sbjct:   312 QDKRYFIIIEDLWAS-SMWDIVSRGLPDNNSCSRILITTEIEPVAL 356

GO:0006952 "defense response" evidence=IMP

---

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 Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	425
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	3e-13

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 69.3 bits (170), Expect = 3e-13
 Identities = 75/276 (27%), Positives = 113/276 (40%), Gaps = 60/276 (21%)

Query: 183 LIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----------ILDDII 231
           L+E    L VV I+   G  KT  A   YN++ V  +FD +AW           +  DI+
Sbjct: 12  LLEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDIL 71

Query: 232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNG 291
           + L       V   E     K  +++ L  K++ + LDDV    + WD +    PD +NG
Sbjct: 72  QELGLDDSDWVEKNESELAVK--IKEALLRKRFLLVLDDVWEKND-WDKIGVPFPDGENG 128

Query: 292 SRVLIT---------------VINPSLLT---SFELLN-----------------GEKI- 315
           SRV++T                     L    S+EL +                  ++I 
Sbjct: 129 SRVIVTTRSESVAGRMGGTSKPHEVESLEPEESWELFSNKVFEKELPPCPELEEVAKEIV 188

Query: 316 -RCD----YVLVEGPLIRIKH--SAWQFFVLHYGSAALGNYMDEKMVLAVLSRTCSVFEL 368
            +C      + V G L+  K     W+  +    +   G     + VL++LS   S   L
Sbjct: 189 EKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQLNNELAGRDGLNE-VLSILS--LSYDNL 245

Query: 369 PLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIP 404
           P+HLK C +YL +F     I   QL +LWIAEGF+ 
Sbjct: 246 PMHLKRCFLYLALFPEDYNIRKEQLIKLWIAEGFVI 281

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	425
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.97
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.58
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.33
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	98.32
PF13173	128	AAA_14: AAA domain	98.31
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.31
PF05729	166	NACHT: NACHT domain	98.3
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.28
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.27
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.21
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.21
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.04
PTZ00202	550	tuzin; Provisional	98.03
PRK13342	413	recombination factor protein RarA; Reviewed	98.02
cd01128	249	rho_factor Transcription termination factor rho is	98.02
PRK04841	903	transcriptional regulator MalT; Provisional	97.94
PRK09376	416	rho transcription termination factor Rho; Provisio	97.91
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.88
PRK13341	725	recombination factor protein RarA/unknown domain f	97.79
PRK06893	229	DNA replication initiation factor; Validated	97.78
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.77
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.76
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.71
PHA02544	316	44 clamp loader, small subunit; Provisional	97.7
PRK12402	337	replication factor C small subunit 2; Reviewed	97.7
PRK04195	482	replication factor C large subunit; Provisional	97.65
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.64
COG2256	436	MGS1 ATPase related to the helicase subunit of the	97.63
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.62
TIGR00767	415	rho transcription termination factor Rho. Members	97.62
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.61
PRK08727	233	hypothetical protein; Validated	97.6
PRK08116	268	hypothetical protein; Validated	97.57
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.55
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.54
PLN03025	319	replication factor C subunit; Provisional	97.53
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.53
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.51
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.5
PF00004	132	AAA: ATPase family associated with various cellula	97.48
PRK09087	226	hypothetical protein; Validated	97.47
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.47
PRK10536	262	hypothetical protein; Provisional	97.46
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.46
PRK08118	167	topology modulation protein; Reviewed	97.45
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.43
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.41
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.4
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.39
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.38
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.37
KOG2028	554	consensus ATPase related to the helicase subunit o	97.34
PRK06526	254	transposase; Provisional	97.32
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.32
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.31
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.29
PRK08181	269	transposase; Validated	97.28
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.26
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.25
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.25
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.25
PHA00729	226	NTP-binding motif containing protein	97.25
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.24
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.23
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.22
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.22
CHL00095	821	clpC Clp protease ATP binding subunit	97.2
smart00382	148	AAA ATPases associated with a variety of cellular	97.2
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.2
PRK08084	235	DNA replication initiation factor; Provisional	97.19
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.19
PRK10865	857	protein disaggregation chaperone; Provisional	97.19
CHL00181	287	cbbX CbbX; Provisional	97.18
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.18
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.17
PRK12377	248	putative replication protein; Provisional	97.15
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.15
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.14
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.14
PRK07261	171	topology modulation protein; Provisional	97.13
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.12
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.12
PRK05642	234	DNA replication initiation factor; Validated	97.12
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.09
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.09
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.08
PRK06620	214	hypothetical protein; Validated	97.08
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.07
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.07
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.06
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.04
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.03
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.01
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.95
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.92
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.91
PRK09183	259	transposase/IS protein; Provisional	96.9
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	96.9
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.88
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	96.86
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.86
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.84
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.84
PRK06696	223	uridine kinase; Validated	96.83
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	96.82
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.81
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	96.8
PRK10865	857	protein disaggregation chaperone; Provisional	96.8
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.79
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.79
PRK14086	617	dnaA chromosomal replication initiation protein; P	96.79
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.78
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.77
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.77
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.75
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	96.74
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.74
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.73
PRK07667	193	uridine kinase; Provisional	96.72
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.71
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	96.71
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	96.69
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	96.69
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.69
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.68
COG3899	849	Predicted ATPase [General function prediction only	96.68
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.67
PRK05541	176	adenylylsulfate kinase; Provisional	96.66
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	96.65
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	96.63
PRK06921	266	hypothetical protein; Provisional	96.62
PRK08939	306	primosomal protein DnaI; Reviewed	96.61
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	96.59
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	96.59
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.58
CHL00176	638	ftsH cell division protein; Validated	96.55
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	96.52
PRK06835	329	DNA replication protein DnaC; Validated	96.52
PRK12422	445	chromosomal replication initiation protein; Provis	96.5
CHL00095	821	clpC Clp protease ATP binding subunit	96.48
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.47
PRK15455	644	PrkA family serine protein kinase; Provisional	96.46
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.43
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.38
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.36
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.34
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	96.33
PRK07952	244	DNA replication protein DnaC; Validated	96.32
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	96.29
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	96.28
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.28
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.26
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.26
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.25
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.21
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.2
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	96.2
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.19
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.18
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.18
PRK05480	209	uridine/cytidine kinase; Provisional	96.14
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.13
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.13
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	96.12
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.11
PRK08233	182	hypothetical protein; Provisional	96.1
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	96.1
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.1
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.06
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.04
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.03
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.01
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.99
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	95.98
PTZ00301	210	uridine kinase; Provisional	95.98
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	95.97
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.97
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	95.96
PRK06547	172	hypothetical protein; Provisional	95.96
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	95.94
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	95.93
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.92
PRK13531	498	regulatory ATPase RavA; Provisional	95.91
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.89
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	95.88
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	95.88
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	95.85
PRK06762	166	hypothetical protein; Provisional	95.8
PRK12608	380	transcription termination factor Rho; Provisional	95.79
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	95.76
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.73
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	95.73
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	95.73
PRK08058	329	DNA polymerase III subunit delta'; Validated	95.69
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	95.67
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	95.67
cd03115	173	SRP The signal recognition particle (SRP) mediates	95.65
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	95.65
PRK05707	328	DNA polymerase III subunit delta'; Validated	95.64
PRK05022	509	anaerobic nitric oxide reductase transcription reg	95.64
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	95.64
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	95.63
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.6
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	95.58
PRK03839	180	putative kinase; Provisional	95.58
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.58
cd03246	173	ABCC_Protease_Secretion This family represents the	95.57
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	95.57
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.57
PRK14527	191	adenylate kinase; Provisional	95.56
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.56
PRK04296	190	thymidine kinase; Provisional	95.55
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	95.55
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.54
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	95.54
cd03216	163	ABC_Carb_Monos_I This family represents the domain	95.5
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	95.49
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.47
cd00983	325	recA RecA is a bacterial enzyme which has roles in	95.42
PRK04040	188	adenylate kinase; Provisional	95.41
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	95.41
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.41
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	95.41
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	95.4
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	95.4
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	95.4
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	95.39
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	95.38
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.38
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.38
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	95.37
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	95.36
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	95.35
CHL00195	489	ycf46 Ycf46; Provisional	95.35
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	95.35
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	95.34
PRK14738	206	gmk guanylate kinase; Provisional	95.3
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	95.3
PF03205	140	MobB: Molybdopterin guanine dinucleotide synthesis	95.28
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.28
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	95.28
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.26
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	95.26
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	95.26
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	95.26
PLN02318	656	phosphoribulokinase/uridine kinase	95.24
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.23
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	95.22
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	95.22
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	95.2
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	95.2
PRK10751	173	molybdopterin-guanine dinucleotide biosynthesis pr	95.18
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	95.18
PRK09354	349	recA recombinase A; Provisional	95.17
COG0488	530	Uup ATPase components of ABC transporters with dup	95.17
PRK10867	433	signal recognition particle protein; Provisional	95.17
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	95.16
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	95.15
PRK00131	175	aroK shikimate kinase; Reviewed	95.14
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	95.14
PRK00625	173	shikimate kinase; Provisional	95.13
cd01394	218	radB RadB. The archaeal protein radB shares simila	95.11
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.11
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.1
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	95.07
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.07
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	95.04
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	95.04
PRK06217	183	hypothetical protein; Validated	95.02
PRK00889	175	adenylylsulfate kinase; Provisional	95.01
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	95.01
cd03300	232	ABC_PotA_N PotA is an ABC-type transporter and the	95.0
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.0
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	94.99
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	94.97
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	94.96
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	94.95
PRK13947	171	shikimate kinase; Provisional	94.93
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	94.91
PRK05439	311	pantothenate kinase; Provisional	94.9
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	94.88
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	94.87
PRK14974	336	cell division protein FtsY; Provisional	94.87
PRK00300	205	gmk guanylate kinase; Provisional	94.86
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.83
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	94.82
TIGR00959	428	ffh signal recognition particle protein. This mode	94.81
PRK07594	433	type III secretion system ATPase SsaN; Validated	94.81
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	94.8
PRK03846	198	adenylylsulfate kinase; Provisional	94.79
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.78
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	94.77
PRK13537	306	nodulation ABC transporter NodI; Provisional	94.75
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	94.74
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	94.73
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	94.72
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	94.71
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	94.7
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	94.68
PRK13949	169	shikimate kinase; Provisional	94.67
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	94.65
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	94.64
PRK08149	428	ATP synthase SpaL; Validated	94.63
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	94.63
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	94.62
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	94.62
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	94.61
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	94.61
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	94.61
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	94.6
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.59
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	94.59
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	94.59
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	94.58
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	94.58
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	94.58
PRK00279	215	adk adenylate kinase; Reviewed	94.57
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	94.54
PRK14530	215	adenylate kinase; Provisional	94.5
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	94.49
COG1428	216	Deoxynucleoside kinases [Nucleotide transport and	94.46
PRK14528	186	adenylate kinase; Provisional	94.45
PRK07399	314	DNA polymerase III subunit delta'; Validated	94.44
PF00005	137	ABC_tran: ABC transporter This structure is on hol	94.43
TIGR01846	694	type_I_sec_HlyB type I secretion system ABC transp	94.43
cd00820	107	PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPC	94.43
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	94.42
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	94.4
TIGR00073	207	hypB hydrogenase accessory protein HypB. HypB is i	94.39
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	94.38
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.38
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	94.37
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	94.37
TIGR00176	155	mobB molybdopterin-guanine dinucleotide biosynthes	94.37
PRK09435	332	membrane ATPase/protein kinase; Provisional	94.36
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	94.36
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	94.35
PRK13975	196	thymidylate kinase; Provisional	94.33
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.32
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	94.31
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	94.31
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	94.31
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	94.29
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.25
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	94.25
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	94.22
PRK05057	172	aroK shikimate kinase I; Reviewed	94.22
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	94.2
PRK12678	672	transcription termination factor Rho; Provisional	94.18
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	94.17
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	94.17
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	94.14
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	94.13
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	94.13
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	94.13
COG3903	414	Predicted ATPase [General function prediction only	94.11
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.1
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	94.09
PRK14737	186	gmk guanylate kinase; Provisional	94.09
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	94.05
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	94.05
PRK13948	182	shikimate kinase; Provisional	94.05
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	94.04
PRK06936	439	type III secretion system ATPase; Provisional	94.02
COG2019	189	AdkA Archaeal adenylate kinase [Nucleotide transpo	94.01
COG1763	161	MobB Molybdopterin-guanine dinucleotide biosynthes	94.01
PF07726	131	AAA_3: ATPase family associated with various cellu	94.0
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	94.0
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	93.98
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	93.97
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	93.94
PRK00409	782	recombination and DNA strand exchange inhibitor pr	93.93
PHA02774	613	E1; Provisional	93.93
PRK13946	184	shikimate kinase; Provisional	93.93
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	93.91
PRK12339	197	2-phosphoglycerate kinase; Provisional	93.9
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	93.89
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	93.88
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	93.87
PLN02348	395	phosphoribulokinase	93.87
COG1100	219	GTPase SAR1 and related small G proteins [General	93.87
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	93.85
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	93.85
PRK04182	180	cytidylate kinase; Provisional	93.85
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	93.84
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.83
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	93.82
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	93.81
KOG0066	807	consensus eIF2-interacting protein ABC50 (ABC supe	93.81
KOG1969	877	consensus DNA replication checkpoint protein CHL12	93.8
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	93.79
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	93.79
cd04163	168	Era Era subfamily. Era (E. coli Ras-like protein)	93.78
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	93.76
cd03116	159	MobB Molybdenum is an essential trace element in t	93.76
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	93.75
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	93.73
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	93.72
PRK14493	274	putative bifunctional molybdopterin-guanine dinucl	93.72
PRK09825	176	idnK D-gluconate kinase; Provisional	93.71
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	93.71
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	93.7
COG0237	201	CoaE Dephospho-CoA kinase [Coenzyme metabolism]	93.69
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	93.69
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	93.69
KOG0927	614	consensus Predicted transporter (ABC superfamily)	93.68
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	93.68
PLN02200	234	adenylate kinase family protein	93.67
TIGR01842	544	type_I_sec_PrtD type I secretion system ABC transp	93.66
PRK04301	317	radA DNA repair and recombination protein RadA; Va	93.66
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	93.61
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	93.61
PLN02796	347	D-glycerate 3-kinase	93.61
PF00154	322	RecA: recA bacterial DNA recombination protein; In	93.61
TIGR00064	272	ftsY signal recognition particle-docking protein F	93.6
KOG0927	614	consensus Predicted transporter (ABC superfamily)	93.56
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	93.54
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	93.54
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	93.53
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	93.53
cd01862	172	Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase th	93.52
smart00173	164	RAS Ras subfamily of RAS small GTPases. Similar in	93.51
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	93.49
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	93.48
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	93.46
PRK08356	195	hypothetical protein; Provisional	93.46
TIGR00231	161	small_GTP small GTP-binding protein domain. This m	93.45
cd04119	168	RJL RJL (RabJ-Like) subfamily. RJLs are found in m	93.45
PRK10463	290	hydrogenase nickel incorporation protein HypB; Pro	93.44
PRK10789	569	putative multidrug transporter membrane\ATP-bindin	93.43
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	93.43
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	93.42
cd04155	173	Arl3 Arl3 subfamily. Arl3 (Arf-like 3) is an Arf f	93.4
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	93.39
PRK01184	184	hypothetical protein; Provisional	93.39
COG3840	231	ThiQ ABC-type thiamine transport system, ATPase co	93.39
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	93.38
COG0410	237	LivF ABC-type branched-chain amino acid transport	93.38
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	93.37
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	93.37
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	93.37
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	93.36
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	93.34
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	93.34
cd04113	161	Rab4 Rab4 subfamily. Rab4 has been implicated in n	93.32
TIGR03258	362	PhnT 2-aminoethylphosphonate ABC transport system,	93.3
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	93.29
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	93.27
PRK03731	171	aroL shikimate kinase II; Reviewed	93.26
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	93.24
PRK13695	174	putative NTPase; Provisional	93.24
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	93.24
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	93.23
COG1135	339	AbcC ABC-type metal ion transport system, ATPase c	93.23
PRK14532	188	adenylate kinase; Provisional	93.22
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	93.22
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	93.19
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	93.19
PRK05922	434	type III secretion system ATPase; Validated	93.19
smart00175	164	RAB Rab subfamily of small GTPases. Rab GTPases ar	93.19
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.18
cd04138	162	H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras,	93.18
cd03269	210	ABC_putative_ATPase This subfamily is involved in	93.15
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	93.14
PRK10416	318	signal recognition particle-docking protein FtsY;	93.12
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	93.12
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	93.09
PRK08099	399	bifunctional DNA-binding transcriptional repressor	93.09
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	93.09
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	93.09
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	93.08
COG4133	209	CcmA ABC-type transport system involved in cytochr	93.08
PRK08769	319	DNA polymerase III subunit delta'; Validated	93.08
cd00876	160	Ras Ras family. The Ras family of the Ras superfam	93.08
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	93.06
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	93.06
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	93.04
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	93.03
cd00154	159	Rab Rab family. Rab GTPases form the largest famil	93.03
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	93.02
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	93.02
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	93.01
cd00879	190	Sar1 Sar1 subfamily. Sar1 is an essential componen	93.0
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	93.0
PRK06964	342	DNA polymerase III subunit delta'; Validated	92.99
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	92.99
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	92.98
PRK15453	290	phosphoribulokinase; Provisional	92.98
COG4107	258	PhnK ABC-type phosphonate transport system, ATPase	92.97
cd02026	273	PRK Phosphoribulokinase (PRK) is an enzyme involve	92.97
PRK06761	282	hypothetical protein; Provisional	92.96
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	92.96
cd04124	161	RabL2 RabL2 subfamily. RabL2 (Rab-like2) subfamily	92.95
PRK13768	253	GTPase; Provisional	92.94
PRK06820	440	type III secretion system ATPase; Validated	92.94
cd01864	165	Rab19 Rab19 subfamily. Rab19 proteins are associat	92.92
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	92.91
PF00071	162	Ras: Ras family; InterPro: IPR001806 Small GTPases	92.91

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=2.6e-56  Score=476.23  Aligned_cols=366  Identities=21%  Similarity=0.340  Sum_probs=292.9

Q ss_pred             HHHhHHHHHHHHHHHHHHHhhhhccCChhHHHHHHHHHHHhhhhHHHHHHHHHHHhhhcCCCcc----------ccccc-
Q 040913           50 LLANYEADMALLLFQLLRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEE----------SESST-  118 (425)
Q Consensus        50 ~l~~l~~d~~~l~~~~l~~a~~~~~~~~~v~~Wl~~lr~layd~eD~lD~~~~~~~~~~~~~~~----------~~~~~-  118 (425)
                      .+.++++++..++ .++++++.++.....+..|...+++++|++||+++.|.......+..+..          ++..+ 
T Consensus        29 ~i~~Lk~~L~~l~-~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~~c~~~~~  107 (889)
T KOG4658|consen   29 YILELKENLKALQ-SALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKANDLLSTRSVERQRLCLCGFC  107 (889)
T ss_pred             HHHHHHHHHHHHH-HHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHHHhhhhhH
Confidence            5666676766665 68999999999999999999999999999999999999887665332210          11111 


Q ss_pred             --chhhhhHHHHHHHHHHHHHhccCCCCCCCCccCC--CcccccCCCCCCCCCCcccchhhHHHHHHHHhcCCCCcEEEE
Q 040913          119 --NMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQ--RDELIHLSSEGQPRLDISEFERAREEWFDLLIEGPIGLSVVA  194 (425)
Q Consensus       119 --~~~~r~~i~~~i~~i~~~l~~i~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~  194 (425)
                        .....+.+++++-.+...++.+..+.. +.....  .+....++.|..+..+ ||.+..++++.+.|..++.  .+++
T Consensus       108 ~~~~~~~~~~~~rv~~~l~~ve~l~~~~~-~~~~~~~~~~~~~~e~~~~~~~~~-VG~e~~~~kl~~~L~~d~~--~iv~  183 (889)
T KOG4658|consen  108 SKNVSDSYKYGKRVSKVLREVESLGSKGV-FEVVGESLDPREKVETRPIQSESD-VGLETMLEKLWNRLMEDDV--GIVG  183 (889)
T ss_pred             hHhhhhhHhHHHHHHHHHHHHHHhccccc-eecccccccchhhcccCCCCcccc-ccHHHHHHHHHHHhccCCC--CEEE
Confidence              333334455555555555554442211 111110  0111122445555555 9999999999999999874  8999


Q ss_pred             EEecCCCchHHHHHHhhcCcc-ccccccchHHH-----------HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCC
Q 040913          195 ILDSSGFDKTAFAADTYNNNH-VKFYFDCLAWI-----------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNK  262 (425)
Q Consensus       195 IvG~gGvGKTtLa~~v~~~~~-~~~~F~~~~wv-----------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~k  262 (425)
                      |+||||+||||||+.++|+.. ++.+||..+||           .++|+..++....  .....+..+++..|.+.|++|
T Consensus       184 i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~--~~~~~~~~~~~~~i~~~L~~k  261 (889)
T KOG4658|consen  184 IYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDE--EWEDKEEDELASKLLNLLEGK  261 (889)
T ss_pred             EECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCc--ccchhhHHHHHHHHHHHhccC
Confidence            999999999999999999988 99999999999           5666666665433  233334479999999999999


Q ss_pred             eEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH------------------hcCcC-------------
Q 040913          263 KYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS------------------FELLN-------------  311 (425)
Q Consensus       263 r~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~------------------~~Lf~-------------  311 (425)
                      |||||||||| +..+|+.++.++|...+||||++|||++.||..                  |.||.             
T Consensus       262 rfllvLDDIW-~~~dw~~I~~~~p~~~~g~KvvlTTRs~~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~~~~~~  340 (889)
T KOG4658|consen  262 RFLLVLDDIW-EEVDWDKIGVPFPSRENGSKVVLTTRSEEVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTLGSHPD  340 (889)
T ss_pred             ceEEEEeccc-ccccHHhcCCCCCCccCCeEEEEEeccHhhhhccccCCccccccccCccccHHHHHHhhcccccccccc
Confidence            9999999999 999999999999999889999999999999987                  99994             


Q ss_pred             ----CCCc--ccc-----chhhhccccCCChH-HHHHHHHHhchhc-cCCCCchHHHHHHhchhhcccCCChhhHHHHhh
Q 040913          312 ----GEKI--RCD-----YVLVEGPLIRIKHS-AWQFFVLHYGSAA-LGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIY  378 (425)
Q Consensus       312 ----~~~I--kC~-----i~~~g~~L~~~~~~-~w~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~sy~~Lp~~lk~cfly  378 (425)
                          |++|  +|+     ++++|+.|+.|+.. +|+++.+.+.+.. .+.+.+++.++++|+  +||++||+++|.||+|
T Consensus       341 i~~lak~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~~~~~~~i~~iLk--lSyd~L~~~lK~CFLy  418 (889)
T KOG4658|consen  341 IEELAKEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADFSGMEESILPILK--LSYDNLPEELKSCFLY  418 (889)
T ss_pred             HHHHHHHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCCCchhhhhHHhhh--ccHhhhhHHHHHHHHh
Confidence                5666  887     99999999999999 9999999998773 333333448999999  9999999999999999


Q ss_pred             hhccCCCCcccHHHHHHHHHHcCCCC-----CCHHHHHHHHHHHHHHCcCCC
Q 040913          379 LCVFRPGIEISSRQLCQLWIAEGFIP-----YNSEETAELYLKELIHRGFIQ  425 (425)
Q Consensus       379 ~sifP~~~~i~~~~Li~~Wiaeg~i~-----~~~e~~a~~~~~eLv~r~llq  425 (425)
                      ||+||+||+|+++.||.+|+||||+.     .++++.|..|+++||++||++
T Consensus       419 calFPED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~  470 (889)
T KOG4658|consen  419 CALFPEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLI  470 (889)
T ss_pred             hccCCcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHh
Confidence            99999999999999999999999997     578899999999999999974

>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=100.00  E-value=1.7e-40  Score=318.37  Aligned_cols=229  Identities=30%  Similarity=0.505  Sum_probs=186.1

Q ss_pred             chhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-----------HHHHHHHhCCCCCC
Q 040913          172 FERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------LDDIIRSLMPPSRV  240 (425)
Q Consensus       172 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-----------~~~il~~l~~~~~~  240 (425)
                      ||.++++|.+.|.....+.++|+|+||||+||||||..++++..++.+|+.++|+           +..|+.++......
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~   80 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSS   80 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-ST
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccc
Confidence            6889999999999966789999999999999999999999977799999999999           77888888877441


Q ss_pred             CccCCCCHHHHHHHHHHHhcCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH--------------
Q 040913          241 TVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS--------------  306 (425)
Q Consensus       241 ~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~--------------  306 (425)
                       .....+.+.+...+.+.|+++++|||||||| +...|+.+...++....||+||||||+..++..              
T Consensus        81 -~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~-~~~~~~~l~~~~~~~~~~~kilvTTR~~~v~~~~~~~~~~~~l~~L~  158 (287)
T PF00931_consen   81 -ISDPKDIEELQDQLRELLKDKRCLLVLDDVW-DEEDLEELREPLPSFSSGSKILVTTRDRSVAGSLGGTDKVIELEPLS  158 (287)
T ss_dssp             -SSCCSSHHHHHHHHHHHHCCTSEEEEEEEE--SHHHH-------HCHHSS-EEEEEESCGGGGTTHHSCEEEEECSS--
T ss_pred             -cccccccccccccchhhhccccceeeeeeec-ccccccccccccccccccccccccccccccccccccccccccccccc
Confidence             1145678889999999999999999999999 999999999888887789999999999998764              


Q ss_pred             ----hcCcC-----------------CCCc--ccc-----chhhhccccCCChH-HHHHHHHHhchhccCCCCchHHHHH
Q 040913          307 ----FELLN-----------------GEKI--RCD-----YVLVEGPLIRIKHS-AWQFFVLHYGSAALGNYMDEKMVLA  357 (425)
Q Consensus       307 ----~~Lf~-----------------~~~I--kC~-----i~~~g~~L~~~~~~-~w~~~~~~~~~~~~~~~~~~~~~~~  357 (425)
                          ++||.                 +++|  +|+     ++++|+.|+.++.. +|+++++++.............+..
T Consensus       159 ~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPLal~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~~~~~~~~~~  238 (287)
T PF00931_consen  159 EEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPLALKLIASYLRSKSTVDEWEEALEELENSLRESRDYDRSVFS  238 (287)
T ss_dssp             HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HHHHHHHHHHHHHHHSSSSHHHHHHHHHHCHTCSSGSCHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence                55663                 2344  787     99999999776644 9999999887766433221228999


Q ss_pred             HhchhhcccCCChhhHHHHhhhhccCCCCcccHHHHHHHHHHcCCCC
Q 040913          358 VLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIP  404 (425)
Q Consensus       358 ~l~~~~sy~~Lp~~lk~cfly~sifP~~~~i~~~~Li~~Wiaeg~i~  404 (425)
                      ++.  +||+.||+++|.||+|||+||+++.|+++.|+++|+|||||+
T Consensus       239 ~l~--~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~lW~~e~~i~  283 (287)
T PF00931_consen  239 ALE--LSYDSLPDELRRCFLYLSIFPEGVPIPRERLIRLWVAEGFIS  283 (287)
T ss_dssp             HHH--HHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHHHHTT-HHTC
T ss_pred             cce--echhcCCccHHHHHhhCcCCCCCceECHHHHHHHHHHCCCCc
Confidence            999  999999999999999999999999999999999999999995

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.

>PLN03210 Resistant to P

Probab=99.97  E-value=4.9e-31  Score=294.86  Aligned_cols=235  Identities=17%  Similarity=0.212  Sum_probs=184.5

Q ss_pred             CCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-----------------
Q 040913          164 QPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------------  226 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-----------------  226 (425)
                      .+..++||++..++++..+|.-+....++|+||||||+||||||+++|+  ++..+|+..+|+                 
T Consensus       181 ~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~~~~~~~~~  258 (1153)
T PLN03210        181 NDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSMEIYSSANP  258 (1153)
T ss_pred             cccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccchhhcccccc
Confidence            3456799999999999999876666799999999999999999999999  777788766543                 


Q ss_pred             ---------HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEe
Q 040913          227 ---------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLIT  297 (425)
Q Consensus       227 ---------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivT  297 (425)
                               ...++.++.....   .....    ...+++.|++||+|||||||| +...|+.+.......++||+||||
T Consensus       259 ~~~~~~~~l~~~~l~~il~~~~---~~~~~----~~~~~~~L~~krvLLVLDdv~-~~~~l~~L~~~~~~~~~GsrIIiT  330 (1153)
T PLN03210        259 DDYNMKLHLQRAFLSEILDKKD---IKIYH----LGAMEERLKHRKVLIFIDDLD-DQDVLDALAGQTQWFGSGSRIIVI  330 (1153)
T ss_pred             cccchhHHHHHHHHHHHhCCCC---cccCC----HHHHHHHHhCCeEEEEEeCCC-CHHHHHHHHhhCccCCCCcEEEEE
Confidence                     1122223222211   00011    145778899999999999999 999999998776666789999999


Q ss_pred             cCChhHHHH-----------------hcCcC----------------CCCc--ccc-----chhhhccccCCChHHHHHH
Q 040913          298 VINPSLLTS-----------------FELLN----------------GEKI--RCD-----YVLVEGPLIRIKHSAWQFF  337 (425)
Q Consensus       298 TR~~~va~~-----------------~~Lf~----------------~~~I--kC~-----i~~~g~~L~~~~~~~w~~~  337 (425)
                      ||+.+++..                 |+||.                +++|  +|+     ++++|+.|+.++..+|+.+
T Consensus       331 Trd~~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~~~~~~~l~~~iv~~c~GLPLAl~vlgs~L~~k~~~~W~~~  410 (1153)
T PLN03210        331 TKDKHFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSPPDGFMELASEVALRAGNLPLGLNVLGSYLRGRDKEDWMDM  410 (1153)
T ss_pred             eCcHHHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhCCCcHHHHHHHHHHcCCCHHHHHHH
Confidence            999998853                 77773                3445  787     9999999999876699999


Q ss_pred             HHHhchhccCCCCchHHHHHHhchhhcccCCChh-hHHHHhhhhccCCCCcccHHHHHHHHHHcCCCCCCHHHHHHHHHH
Q 040913          338 VLHYGSAALGNYMDEKMVLAVLSRTCSVFELPLH-LKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLK  416 (425)
Q Consensus       338 ~~~~~~~~~~~~~~~~~~~~~l~~~~sy~~Lp~~-lk~cfly~sifP~~~~i~~~~Li~~Wiaeg~i~~~~e~~a~~~~~  416 (425)
                      ++++.....   .   .+..+|+  +||++||++ .|.||++||.||.+..++   .+..|+|++...      ++.-++
T Consensus       411 l~~L~~~~~---~---~I~~~L~--~SYd~L~~~~~k~~Fl~ia~ff~~~~~~---~v~~~l~~~~~~------~~~~l~  473 (1153)
T PLN03210        411 LPRLRNGLD---G---KIEKTLR--VSYDGLNNKKDKAIFRHIACLFNGEKVN---DIKLLLANSDLD------VNIGLK  473 (1153)
T ss_pred             HHHHHhCcc---H---HHHHHHH--HhhhccCccchhhhhheehhhcCCCCHH---HHHHHHHhcCCC------chhChH
Confidence            999876432   1   8999999  999999875 999999999999997654   578888887662      233488


Q ss_pred             HHHHCcCCC
Q 040913          417 ELIHRGFIQ  425 (425)
Q Consensus       417 eLv~r~llq  425 (425)
                      .|+++||++
T Consensus       474 ~L~~ksLi~  482 (1153)
T PLN03210        474 NLVDKSLIH  482 (1153)
T ss_pred             HHHhcCCEE
Confidence            999999974

syringae 6; Provisional

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.58  E-value=3e-07  Score=92.27  Aligned_cols=108  Identities=18%  Similarity=0.155  Sum_probs=72.1

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-----------HHH
Q 040913          163 GQPRLDISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------LDD  229 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-----------~~~  229 (425)
                      ...+..++||+++.++|...|...  ......+.|+|++|+|||++++.++++.......-..+++           +..
T Consensus        26 ~~~P~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~  105 (394)
T PRK00411         26 DYVPENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSE  105 (394)
T ss_pred             CCcCCCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHH
Confidence            335567999999999999988543  2234557799999999999999999843211100011111           567


Q ss_pred             HHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccC
Q 040913          230 IIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVC  272 (425)
Q Consensus       230 il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw  272 (425)
                      |+.++.....  .....+..++...+.+.+.  ++..+||||+++
T Consensus       106 i~~~l~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d  148 (394)
T PRK00411        106 IARQLFGHPP--PSSGLSFDELFDKIAEYLDERDRVLIVALDDIN  148 (394)
T ss_pred             HHHHhcCCCC--CCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHh
Confidence            7777765211  1123456777778887775  456899999997

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

Probab=98.33  E-value=4.8e-06  Score=78.88  Aligned_cols=88  Identities=17%  Similarity=0.228  Sum_probs=52.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH----------HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHH-
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI----------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDF-  258 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv----------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~-  258 (425)
                      .+++.|+|++|+|||||++.+++...... + ..+|+          +..|...++.+..     ..+...+...+... 
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~-~-~~~~~~~~~~~~~~~l~~i~~~lG~~~~-----~~~~~~~~~~l~~~l  115 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQER-V-VAAKLVNTRVDAEDLLRMVAADFGLETE-----GRDKAALLRELEDFL  115 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCC-e-EEeeeeCCCCCHHHHHHHHHHHcCCCCC-----CCCHHHHHHHHHHHH
Confidence            56789999999999999999998533211 1 11121          4455555544322     12223333333332 


Q ss_pred             ---h-cCCeEEEEecccCC-ChhhHHHHHhh
Q 040913          259 ---L-TNKKYFIALDDVCH-NIEIWDDLEEV  284 (425)
Q Consensus       259 ---l-~~kr~LlVLDdvw~-~~~~~~~l~~~  284 (425)
                         . .+++++||+||++. +...++.+...
T Consensus       116 ~~~~~~~~~~vliiDe~~~l~~~~~~~l~~l  146 (269)
T TIGR03015       116 IEQFAAGKRALLVVDEAQNLTPELLEELRML  146 (269)
T ss_pred             HHHHhCCCCeEEEEECcccCCHHHHHHHHHH
Confidence               2 67889999999983 23466666543

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=98.32  E-value=1.5e-06  Score=86.16  Aligned_cols=107  Identities=20%  Similarity=0.075  Sum_probs=69.0

Q ss_pred             CCCCcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCcccc-cc----c-----cch-----HHHH
Q 040913          165 PRLDISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHVK-FY----F-----DCL-----AWIL  227 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~-~~----F-----~~~-----~wv~  227 (425)
                      .+..++||+.++++|...|...  ......+.|+|++|+|||++++.+++.-.-. ..    |     +|.     .-++
T Consensus        13 ~p~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~   92 (365)
T TIGR02928        13 VPDRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVL   92 (365)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHH
Confidence            3457999999999999998752  2234568899999999999999998732100 00    1     110     1116


Q ss_pred             HHHHHHhCC-CCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccC
Q 040913          228 DDIIRSLMP-PSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVC  272 (425)
Q Consensus       228 ~~il~~l~~-~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw  272 (425)
                      ..|+.++.. .... .....+..++...+.+.+.  +++++||||+++
T Consensus        93 ~~i~~~l~~~~~~~-~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d  139 (365)
T TIGR02928        93 VELANQLRGSGEEV-PTTGLSTSEVFRRLYKELNERGDSLIIVLDEID  139 (365)
T ss_pred             HHHHHHHhhcCCCC-CCCCCCHHHHHHHHHHHHHhcCCeEEEEECchh
Confidence            777777742 1000 1122345566666666664  568899999997

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.

>PF13173 AAA_14: AAA domain

Probab=98.31  E-value=1.1e-06  Score=73.54  Aligned_cols=96  Identities=17%  Similarity=0.249  Sum_probs=62.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHH-----HHHHHHHHHhcCCeE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYK-----LKKSILRDFLTNKKY  264 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~-----~l~~~l~~~l~~kr~  264 (425)
                      .+++.|.|+.|+|||||+++++++..   .....+++               ..+.....     ++.+.+.+....+..
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYI---------------NFDDPRDRRLADPDLLEYFLELIKPGKK   63 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceee---------------ccCCHHHHHHhhhhhHHHHHHhhccCCc
Confidence            46889999999999999999887422   01111111               00000000     033444444445788


Q ss_pred             EEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHH
Q 040913          265 FIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       265 LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va  304 (425)
                      +|+||++. ....|......+-+..+..+|++|+.+....
T Consensus        64 ~i~iDEiq-~~~~~~~~lk~l~d~~~~~~ii~tgS~~~~l  102 (128)
T PF13173_consen   64 YIFIDEIQ-YLPDWEDALKFLVDNGPNIKIILTGSSSSLL  102 (128)
T ss_pred             EEEEehhh-hhccHHHHHHHHHHhccCceEEEEccchHHH
Confidence            99999998 7778888777776666678999999886655

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.31  E-value=8.9e-06  Score=78.65  Aligned_cols=47  Identities=17%  Similarity=0.201  Sum_probs=38.4

Q ss_pred             CCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+|+|++..++.|..++...   ......+.++|++|+|||+||+.+.+.
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~   53 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANE   53 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            46899999999998888642   223556779999999999999999883

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.

>PF05729 NACHT: NACHT domain

Probab=98.30  E-value=9.9e-07  Score=76.72  Aligned_cols=107  Identities=19%  Similarity=0.229  Sum_probs=59.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCcccccc----ccchHHH----------HHHHHHHhCCCCCCCccCCCCHHHHHHHHH
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFY----FDCLAWI----------LDDIIRSLMPPSRVTVIIGEDYKLKKSILR  256 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv----------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~  256 (425)
                      +++.|+|.+|+||||+++.+...-.....    +...+|.          ...+...+......      ........+.
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~~~~~   74 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPE------SIAPIEELLQ   74 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhcc------chhhhHHHHH
Confidence            47889999999999999998874322221    2223333          11233333222211      0111111222


Q ss_pred             HHh-cCCeEEEEecccCCChh---------hHHH-HHhhCCC-CCCCcEEEEecCChhHH
Q 040913          257 DFL-TNKKYFIALDDVCHNIE---------IWDD-LEEVLPD-NQNGSRVLITVINPSLL  304 (425)
Q Consensus       257 ~~l-~~kr~LlVLDdvw~~~~---------~~~~-l~~~l~~-~~~gskIivTTR~~~va  304 (425)
                      ..+ +.++++||+|++. +..         .+.. +...++. ..++++++||||.....
T Consensus        75 ~~~~~~~~~llilDglD-E~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~  133 (166)
T PF05729_consen   75 ELLEKNKRVLLILDGLD-ELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFP  133 (166)
T ss_pred             HHHHcCCceEEEEechH-hcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHH
Confidence            222 5789999999996 321         1222 3333443 35689999999987753

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.28  E-value=3.4e-05  Score=75.45  Aligned_cols=49  Identities=18%  Similarity=0.148  Sum_probs=39.6

Q ss_pred             CCCCcccchhhHHHHHHHHhc---CCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          165 PRLDISEFERAREEWFDLLIE---GPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~---~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-.+++|++..++.+..++..   .......+.++|++|+||||||+.+.+.
T Consensus        23 ~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~   74 (328)
T PRK00080         23 SLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANE   74 (328)
T ss_pred             CHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHH
Confidence            345699999999998877764   2334567789999999999999999883

>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=98.27  E-value=4.5e-06  Score=76.79  Aligned_cols=43  Identities=23%  Similarity=0.298  Sum_probs=35.4

Q ss_pred             cccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          169 ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |+||+.+.++|.+++..+.  .+.+.|+|+.|+|||+|++.+.+.
T Consensus         1 F~gR~~el~~l~~~l~~~~--~~~~~l~G~rg~GKTsLl~~~~~~   43 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGP--SQHILLYGPRGSGKTSLLKEFINE   43 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhc--CcEEEEEcCCcCCHHHHHHHHHHH
Confidence            6899999999999998754  567889999999999999999883

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>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=98.21  E-value=4e-06  Score=70.72  Aligned_cols=42  Identities=24%  Similarity=0.172  Sum_probs=34.6

Q ss_pred             ccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          170 SEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .|++...+.+...+....  .+.+.|+|.+|+|||||++.+++.
T Consensus         1 ~~~~~~~~~i~~~~~~~~--~~~v~i~G~~G~GKT~l~~~i~~~   42 (151)
T cd00009           1 VGQEEAIEALREALELPP--PKNLLLYGPPGTGKTTLARAIANE   42 (151)
T ss_pred             CchHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHH
Confidence            367788888888876643  567889999999999999999984

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.

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

Probab=98.21  E-value=1.4e-06  Score=77.46  Aligned_cols=46  Identities=20%  Similarity=0.107  Sum_probs=31.4

Q ss_pred             CcccchhhHHHHHHHHhc-CCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          168 DISEFERAREEWFDLLIE-GPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .|+||+++.+++...|.. .....+.+.|+|.+|+|||+|.+.++..
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~   47 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDR   47 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            389999999999999952 2345789999999999999999988773

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

Probab=98.04  E-value=9.9e-06  Score=67.71  Aligned_cols=103  Identities=16%  Similarity=0.255  Sum_probs=63.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcccc----ccccchHHH-----------HHHHHHHhCCCCCCCccCCCCHHHHHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVK----FYFDCLAWI-----------LDDIIRSLMPPSRVTVIIGEDYKLKKSI  254 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv-----------~~~il~~l~~~~~~~~~~~~~~~~l~~~  254 (425)
                      .+++.|+|.+|+|||++++.+.++..-.    .+ ...+|+           ...|+.++......    ..+...+.+.
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~----~~~~~~l~~~   78 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNH-PDVIYVNCPSSRTPRDFAQEILEALGLPLKS----RQTSDELRSL   78 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCC-EEEEEEEHHHHSSHHHHHHHHHHHHT-SSSS----TS-HHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCC-CcEEEEEeCCCCCHHHHHHHHHHHhCccccc----cCCHHHHHHH
Confidence            5688999999999999999998842100    01 111132           67777777776541    3467778888


Q ss_pred             HHHHhcCCe-EEEEecccCCCh---hhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          255 LRDFLTNKK-YFIALDDVCHNI---EIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       255 l~~~l~~kr-~LlVLDdvw~~~---~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      +.+.+...+ .+||+|++. .-   ..++.++....  ..+.++|+..+.
T Consensus        79 ~~~~l~~~~~~~lviDe~~-~l~~~~~l~~l~~l~~--~~~~~vvl~G~~  125 (131)
T PF13401_consen   79 LIDALDRRRVVLLVIDEAD-HLFSDEFLEFLRSLLN--ESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHHHCTEEEEEEETTH-HHHTHHHHHHHHHHTC--SCBEEEEEEESS
T ss_pred             HHHHHHhcCCeEEEEeChH-hcCCHHHHHHHHHHHh--CCCCeEEEEECh
Confidence            888887654 599999996 33   34444544433  556677766544

>PTZ00202 tuzin; Provisional

Probab=98.03  E-value=5.1e-05  Score=75.03  Aligned_cols=137  Identities=14%  Similarity=0.065  Sum_probs=84.2

Q ss_pred             CCCCCCCCCcccchhhHHHHHHHHhcCC-CCcEEEEEEecCCCchHHHHHHhhcCccccccc-c--chHHHHHHHHHHhC
Q 040913          160 SSEGQPRLDISEFERAREEWFDLLIEGP-IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-D--CLAWILDDIIRSLM  235 (425)
Q Consensus       160 ~~~~~~~~~~vGr~~~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~--~~~wv~~~il~~l~  235 (425)
                      .+.+.+...|+||+.+...+...|...+ ...+++.|.|++|+|||||++.+......-..| +  ...+++..|+.+++
T Consensus       255 ~~lPa~~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNprg~eElLr~LL~ALG  334 (550)
T PTZ00202        255 QSAPAVIRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVRGTEDTLRSVVKALG  334 (550)
T ss_pred             cCCCCCccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCCCHHHHHHHHHHHcC
Confidence            3445567789999999999999987543 335689999999999999999988743321111 1  12344888899988


Q ss_pred             CCCCCCccCCCCHHHHHHHHHHHh-----c-CCeEEEEecccCCChhhHHHHH---hhCCCCCCCcEEEEecCChhHH
Q 040913          236 PPSRVTVIIGEDYKLKKSILRDFL-----T-NKKYFIALDDVCHNIEIWDDLE---EVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~l-----~-~kr~LlVLDdvw~~~~~~~~l~---~~l~~~~~gskIivTTR~~~va  304 (425)
                      .+..      ....++...|.+.+     . |++.+||+- +. +.+.+..+-   ..|.....-|.|++---.+++.
T Consensus       335 V~p~------~~k~dLLrqIqeaLl~~~~e~GrtPVLII~-lr-eg~~l~rvyne~v~la~drr~ch~v~evpleslt  404 (550)
T PTZ00202        335 VPNV------EACGDLLDFISEACRRAKKMNGETPLLVLK-LR-EGSSLQRVYNEVVALACDRRLCHVVIEVPLESLT  404 (550)
T ss_pred             CCCc------ccHHHHHHHHHHHHHHHHHhCCCCEEEEEE-ec-CCCcHHHHHHHHHHHHccchhheeeeeehHhhcc
Confidence            6432      22344555555544     2 567777765 33 333332221   1233334456777665554443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.02  E-value=1.2e-05  Score=81.23  Aligned_cols=108  Identities=19%  Similarity=0.157  Sum_probs=63.0

Q ss_pred             CCcccchhhHHH---HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCcc
Q 040913          167 LDISEFERAREE---WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVI  243 (425)
Q Consensus       167 ~~~vGr~~~~~~---l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~  243 (425)
                      .+++|.+..+..   +..++..+.  ...+.++|++|+||||||+.+.+  .....|...--           .    ..
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~~~--~~~ilL~GppGtGKTtLA~~ia~--~~~~~~~~l~a-----------~----~~   72 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEAGR--LSSMILWGPPGTGKTTLARIIAG--ATDAPFEALSA-----------V----TS   72 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHcCC--CceEEEECCCCCCHHHHHHHHHH--HhCCCEEEEec-----------c----cc
Confidence            458888877555   777776554  55677899999999999999988  33333421000           0    00


Q ss_pred             CCCCHHHHHHHHHHHh-cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEE
Q 040913          244 IGEDYKLKKSILRDFL-TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLI  296 (425)
Q Consensus       244 ~~~~~~~l~~~l~~~l-~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIiv  296 (425)
                      ...+...+........ .+++.+|++|+++. +....+.+...+..   |+.+++
T Consensus        73 ~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~LL~~le~---~~iilI  124 (413)
T PRK13342         73 GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED---GTITLI  124 (413)
T ss_pred             cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCHHHHHHHHHHhhc---CcEEEE
Confidence            0111222333322222 45888999999973 33455556555533   454444

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.02  E-value=4.9e-06  Score=77.64  Aligned_cols=82  Identities=13%  Similarity=0.028  Sum_probs=52.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---------HHHHHHHh-----CCCCCCCccC-CCCHHHHHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------LDDIIRSL-----MPPSRVTVII-GEDYKLKKSI  254 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------~~~il~~l-----~~~~~~~~~~-~~~~~~l~~~  254 (425)
                      -..++|+|++|+|||||++.+|++.... +|+..+|+         ..++++++     ......+... ..-.......
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~   94 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEK   94 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHH
Confidence            3568899999999999999999965544 89998887         66777777     3322211000 0000112222


Q ss_pred             HHHH-hcCCeEEEEecccC
Q 040913          255 LRDF-LTNKKYFIALDDVC  272 (425)
Q Consensus       255 l~~~-l~~kr~LlVLDdvw  272 (425)
                      ...+ -.|++.++++|++-
T Consensus        95 a~~~~~~G~~vll~iDei~  113 (249)
T cd01128          95 AKRLVEHGKDVVILLDSIT  113 (249)
T ss_pred             HHHHHHCCCCEEEEEECHH
Confidence            2222 24899999999995

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.94  E-value=3.4e-05  Score=85.69  Aligned_cols=125  Identities=15%  Similarity=0.147  Sum_probs=71.8

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------------HHHHHHH
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------------LDDIIRS  233 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------------~~~il~~  233 (425)
                      .+.++-|+.    |.+.|... ...+++.|.|++|.||||++......      ++.++|+            ...++..
T Consensus        13 ~~~~~~R~r----l~~~l~~~-~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~   81 (903)
T PRK04841         13 LHNTVVRER----LLAKLSGA-NNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAA   81 (903)
T ss_pred             ccccCcchH----HHHHHhcc-cCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHH
Confidence            345555554    44444432 35789999999999999999987752      2235565            3444444


Q ss_pred             hCCCCCC--C-------ccCCCCHHHHHHHHHHHhc--CCeEEEEecccCC-C-hhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          234 LMPPSRV--T-------VIIGEDYKLKKSILRDFLT--NKKYFIALDDVCH-N-IEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       234 l~~~~~~--~-------~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~-~-~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      +......  +       .....+...+...+...+.  +.+++|||||+.. + ....+.+...++....+.++|||||.
T Consensus        82 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~  161 (903)
T PRK04841         82 LQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRN  161 (903)
T ss_pred             HHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCC
Confidence            4321110  0       0111233334444444443  6889999999952 2 22233444444455557789899998


Q ss_pred             h
Q 040913          301 P  301 (425)
Q Consensus       301 ~  301 (425)
                      .
T Consensus       162 ~  162 (903)
T PRK04841        162 L  162 (903)
T ss_pred             C
Confidence            4

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.91  E-value=9.5e-06  Score=79.43  Aligned_cols=93  Identities=14%  Similarity=0.014  Sum_probs=56.6

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---------HHHHHHHhCCCCCCCccCCCCH
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------LDDIIRSLMPPSRVTVIIGEDY  248 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------~~~il~~l~~~~~~~~~~~~~~  248 (425)
                      ++++++..=.. -.-..|+|++|+||||||+.+|++.... ||++++||         ..++.+++....-....+....
T Consensus       158 rvID~l~PIGk-GQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~  235 (416)
T PRK09376        158 RIIDLIAPIGK-GQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAE  235 (416)
T ss_pred             eeeeeeccccc-CceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHH
Confidence            45555544221 2346899999999999999999965544 89999998         6677777753111001111111


Q ss_pred             HH-----HHHHHHHH--hcCCeEEEEecccC
Q 040913          249 KL-----KKSILRDF--LTNKKYFIALDDVC  272 (425)
Q Consensus       249 ~~-----l~~~l~~~--l~~kr~LlVLDdvw  272 (425)
                      ..     ..-...+.  -.|++.+|++|++-
T Consensus       236 ~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsIt  266 (416)
T PRK09376        236 RHVQVAEMVIEKAKRLVEHGKDVVILLDSIT  266 (416)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEEChH
Confidence            11     11111122  25799999999994

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.88  E-value=8.6e-05  Score=72.12  Aligned_cols=122  Identities=12%  Similarity=0.134  Sum_probs=78.7

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc----cccccccchHHHHHHHHHHhCCCCCCCc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN----HVKFYFDCLAWILDDIIRSLMPPSRVTV  242 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~----~~~~~F~~~~wv~~~il~~l~~~~~~~~  242 (425)
                      .+++|.+..++.+.+++..+. -.+...++|+.|+||||+|+.+++.-    ....|.|...|.         . ..   
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~-~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~---------~-~~---   69 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR-FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFK---------P-IN---   69 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC-CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEec---------c-cc---
Confidence            467898999999999987654 35677899999999999998887621    123454543331         0 00   


Q ss_pred             cCCCCHHHHHHHHHH----HhcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          243 IIGEDYKLKKSILRD----FLTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       243 ~~~~~~~~l~~~l~~----~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ......+++.+.+..    -..+++-++|+|++.. +.+.++.+...+.....++.+|++|.+.+
T Consensus        70 ~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~  134 (313)
T PRK05564         70 KKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLE  134 (313)
T ss_pred             CCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChH
Confidence            011233443333321    1234555666666532 67889999999988778899888886654

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.79  E-value=8.6e-05  Score=79.40  Aligned_cols=109  Identities=18%  Similarity=0.215  Sum_probs=62.6

Q ss_pred             CCcccchhhHH---HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCcc
Q 040913          167 LDISEFERARE---EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVI  243 (425)
Q Consensus       167 ~~~vGr~~~~~---~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~  243 (425)
                      .+++|.+....   .+.+.+..+.  ...+.++|++|+||||||+.+++  ....+|..    +....    .       
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~~~--~~slLL~GPpGtGKTTLA~aIA~--~~~~~f~~----lna~~----~-------   88 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKADR--VGSLILYGPPGVGKTTLARIIAN--HTRAHFSS----LNAVL----A-------   88 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHH--HhcCccee----ehhhh----h-------
Confidence            45889887764   4555555443  55677999999999999999998  44444421    00000    0       


Q ss_pred             CCCCHHHHHHHHHHHh--cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEe
Q 040913          244 IGEDYKLKKSILRDFL--TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLIT  297 (425)
Q Consensus       244 ~~~~~~~l~~~l~~~l--~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivT  297 (425)
                      ...+...........+  .+++.+|+|||++. +...++.+...+.   .|+.++++
T Consensus        89 ~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL~~lE---~g~IiLI~  142 (725)
T PRK13341         89 GVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALLPWVE---NGTITLIG  142 (725)
T ss_pred             hhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHHHHhc---CceEEEEE
Confidence            0011122222232222  24678999999962 4455666655443   35555553

>PRK06893 DNA replication initiation factor; Validated

Probab=97.78  E-value=4.4e-05  Score=70.69  Aligned_cols=24  Identities=13%  Similarity=0.079  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.+-++|++|+|||+|++.+.+.
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~   62 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNH   62 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            456889999999999999999983

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.77  E-value=0.0001  Score=73.22  Aligned_cols=57  Identities=18%  Similarity=0.071  Sum_probs=43.1

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhcC--C---------CCcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          162 EGQPRLDISEFERAREEWFDLLIEG--P---------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~~--~---------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      +.....++.|++..+++|.+.+...  .         ...+-+.++|++|+|||+||+.+++  ....+|
T Consensus       117 p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~--~l~~~~  184 (364)
T TIGR01242       117 PNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH--ETNATF  184 (364)
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH--hCCCCE
Confidence            4445567899999999998877532  1         2345688999999999999999998  454454

Many proteins may score above the trusted cutoff because an internal

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.76  E-value=0.00012  Score=77.48  Aligned_cols=133  Identities=15%  Similarity=0.094  Sum_probs=81.0

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccccc---chHHH----------HHHHH--
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFD---CLAWI----------LDDII--  231 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~---~~~wv----------~~~il--  231 (425)
                      ++++|.+..+..+.+.+....  ...+.|+|++|+||||||+.+++.......+.   ...|+          ...+.  
T Consensus       154 ~~iiGqs~~~~~l~~~ia~~~--~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~d~~~i~~~  231 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVASPF--PQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNP  231 (615)
T ss_pred             HhceeCcHHHHHHHHHHhcCC--CCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccCCHHHHhHH
Confidence            468999999999888875443  45689999999999999999987432211110   01111          11111  


Q ss_pred             -----------------HHhCCC---------CCCC-----ccCCCCHHHHHHHHHHHhcCCeEEEEecccCC-ChhhHH
Q 040913          232 -----------------RSLMPP---------SRVT-----VIIGEDYKLKKSILRDFLTNKKYFIALDDVCH-NIEIWD  279 (425)
Q Consensus       232 -----------------~~l~~~---------~~~~-----~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~  279 (425)
                                       ...+..         ....     +....+ ...+..+...+++++++++.|+.|. +...|+
T Consensus       232 llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld-~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~  310 (615)
T TIGR02903       232 LLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELD-PLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPK  310 (615)
T ss_pred             hcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCC-HHHHHHHHHHHhhCeEEeecceeccCCcccch
Confidence                             111100         0000     112222 3457788889999999999887772 235788


Q ss_pred             HHHhhCCCCCCCcEEEE--ecCChh
Q 040913          280 DLEEVLPDNQNGSRVLI--TVINPS  302 (425)
Q Consensus       280 ~l~~~l~~~~~gskIiv--TTR~~~  302 (425)
                      .++..+....+...|++  ||++..
T Consensus       311 ~ik~~~~~~~~~~~VLI~aTt~~~~  335 (615)
T TIGR02903       311 YIKKLFEEGAPADFVLIGATTRDPE  335 (615)
T ss_pred             hhhhhcccCccceEEEEEecccccc
Confidence            88877776665555555  566543

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.71  E-value=0.0013  Score=69.69  Aligned_cols=124  Identities=19%  Similarity=0.205  Sum_probs=75.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------------HHHHHHHhCCCCCCC--
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------------LDDIIRSLMPPSRVT--  241 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------------~~~il~~l~~~~~~~--  241 (425)
                      +.++++.|.... ..+.+.|..++|.|||||+-+...  +... =..++|.            ...++..|....+..  
T Consensus        24 R~rL~~~L~~~~-~~RL~li~APAGfGKttl~aq~~~--~~~~-~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~   99 (894)
T COG2909          24 RPRLLDRLRRAN-DYRLILISAPAGFGKTTLLAQWRE--LAAD-GAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGD   99 (894)
T ss_pred             cHHHHHHHhcCC-CceEEEEeCCCCCcHHHHHHHHHH--hcCc-ccceeEeecCCccCCHHHHHHHHHHHHHHhCccccH
Confidence            456666666552 489999999999999999988753  1111 1124455            444555444322210  


Q ss_pred             -------ccCCCCHHHHHHHHHHHhc--CCeEEEEecccCC--ChhhHHHHHhhCCCCCCCcEEEEecCChhH
Q 040913          242 -------VIIGEDYKLKKSILRDFLT--NKKYFIALDDVCH--NIEIWDDLEEVLPDNQNGSRVLITVINPSL  303 (425)
Q Consensus       242 -------~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~--~~~~~~~l~~~l~~~~~gskIivTTR~~~v  303 (425)
                             .....+...+...+..-+.  .++..+||||.--  +..--..+...+.....+-..|||||+.--
T Consensus       100 ~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~  172 (894)
T COG2909         100 EAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQ  172 (894)
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCC
Confidence                   1223344555555555554  3689999999731  333333445555556668899999999653

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.70  E-value=0.00016  Score=70.22  Aligned_cols=114  Identities=16%  Similarity=0.098  Sum_probs=69.9

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      -.+++|.+...+.+..++..+. ...++-++|++|+||||+|+.+++.  ....|-.           +       ....
T Consensus        20 ~~~~~~~~~~~~~l~~~~~~~~-~~~~lll~G~~G~GKT~la~~l~~~--~~~~~~~-----------i-------~~~~   78 (316)
T PHA02544         20 IDECILPAADKETFKSIVKKGR-IPNMLLHSPSPGTGKTTVAKALCNE--VGAEVLF-----------V-------NGSD   78 (316)
T ss_pred             HHHhcCcHHHHHHHHHHHhcCC-CCeEEEeeCcCCCCHHHHHHHHHHH--hCccceE-----------e-------ccCc
Confidence            3568999999999999988643 4567778999999999999999883  2222210           0       0000


Q ss_pred             CCHHHHHHHHHHHh-----cCCeEEEEecccCCCh---hhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          246 EDYKLKKSILRDFL-----TNKKYFIALDDVCHNI---EIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       246 ~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~~~---~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      .....+...+..+.     .+.+-+||+||+. ..   +..+.+...+.....++++|+||...
T Consensus        79 ~~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d-~l~~~~~~~~L~~~le~~~~~~~~Ilt~n~~  141 (316)
T PHA02544         79 CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFD-RLGLADAQRHLRSFMEAYSKNCSFIITANNK  141 (316)
T ss_pred             ccHHHHHHHHHHHHHhhcccCCCeEEEEECcc-cccCHHHHHHHHHHHHhcCCCceEEEEcCCh
Confidence            11222222232222     2345689999996 33   23344444454445577888888654

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.70  E-value=0.00013  Score=71.45  Aligned_cols=44  Identities=18%  Similarity=0.059  Sum_probs=37.2

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|++..++.+.+++..+.  .+.+.++|++|+||||+|+.+.+
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~GtGKT~la~~~~~   58 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSPN--LPHLLVQGPPGSGKTAAVRALAR   58 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHH
Confidence            568899999999999887654  44577999999999999998876

>PRK04195 replication factor C large subunit; Provisional

Probab=97.65  E-value=0.00018  Score=74.05  Aligned_cols=48  Identities=19%  Similarity=0.179  Sum_probs=40.0

Q ss_pred             CCCcccchhhHHHHHHHHhcCC--CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGP--IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~--~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|.+..++.+.+|+..-.  ...+.+.|+|++|+||||+|+.+.+.
T Consensus        13 l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~e   62 (482)
T PRK04195         13 LSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAND   62 (482)
T ss_pred             HHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3468999999999999987532  23678899999999999999999884

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.64  E-value=0.00023  Score=73.27  Aligned_cols=132  Identities=12%  Similarity=0.012  Sum_probs=73.3

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---HHHHHHHhCCCCCC-Cc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---LDDIIRSLMPPSRV-TV  242 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---~~~il~~l~~~~~~-~~  242 (425)
                      .+++|.+...+.|.+++..+. -...+.++|++|+||||+|+.+.+.-.....++..+|.   -..+.......... ..
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~-l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~   92 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR-LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDA   92 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecc
Confidence            468999998888888887754 34567899999999999999887743222222212222   01111000000000 00


Q ss_pred             cCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          243 IIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       243 ~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      ......+.+. .+.+.+     .+++-++|+|+++. +...++.+...+......+.+|++|..
T Consensus        93 ~~~~~vd~iR-~l~~~~~~~p~~~~~kVVIIDEad~ls~~a~naLLk~LEep~~~t~~Il~t~~  155 (504)
T PRK14963         93 ASNNSVEDVR-DLREKVLLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTE  155 (504)
T ss_pred             cccCCHHHHH-HHHHHHhhccccCCCeEEEEECccccCHHHHHHHHHHHHhCCCCEEEEEEcCC
Confidence            0111222222 233322     35677999999973 345677887777665555565555543

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

Probab=97.63  E-value=0.00015  Score=70.46  Aligned_cols=90  Identities=27%  Similarity=0.379  Sum_probs=56.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHH----hcCCeEE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDF----LTNKKYF  265 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~----l~~kr~L  265 (425)
                      +...-.||++|+||||||+.+..  .....|...                  ........++...+.+.    ..|++.+
T Consensus        48 l~SmIl~GPPG~GKTTlA~liA~--~~~~~f~~~------------------sAv~~gvkdlr~i~e~a~~~~~~gr~ti  107 (436)
T COG2256          48 LHSMILWGPPGTGKTTLARLIAG--TTNAAFEAL------------------SAVTSGVKDLREIIEEARKNRLLGRRTI  107 (436)
T ss_pred             CceeEEECCCCCCHHHHHHHHHH--hhCCceEEe------------------ccccccHHHHHHHHHHHHHHHhcCCceE
Confidence            55556899999999999999998  555566420                  11122334443333332    3589999


Q ss_pred             EEecccC-CChhhHHHHHhhCCCCCCCcEEEE--ecCChh
Q 040913          266 IALDDVC-HNIEIWDDLEEVLPDNQNGSRVLI--TVINPS  302 (425)
Q Consensus       266 lVLDdvw-~~~~~~~~l~~~l~~~~~gskIiv--TTR~~~  302 (425)
                      |++|.|- ++..+-+.   .||.-.+|.-|+|  ||-|..
T Consensus       108 LflDEIHRfnK~QQD~---lLp~vE~G~iilIGATTENPs  144 (436)
T COG2256         108 LFLDEIHRFNKAQQDA---LLPHVENGTIILIGATTENPS  144 (436)
T ss_pred             EEEehhhhcChhhhhh---hhhhhcCCeEEEEeccCCCCC
Confidence            9999994 13343333   3455566877776  455543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.62  E-value=0.00035  Score=73.84  Aligned_cols=132  Identities=11%  Similarity=0.089  Sum_probs=75.2

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccc---cchHHHHHHHHHHhCCCCCCC--
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF---DCLAWILDDIIRSLMPPSRVT--  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~il~~l~~~~~~~--  241 (425)
                      .+++|.+..++.|.+++..+. -.+.+.++|..|+||||+|+.+.+.-.....+   .|...   ...+.+.......  
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR-L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C---~sCr~I~~G~h~Dvi   91 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR-LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVC---RACREIDEGRFVDYV   91 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCccc---HHHHHHhcCCCceEE
Confidence            568999999999999988664 24455699999999999998776632111111   11100   0111111100000  


Q ss_pred             cc---CCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          242 VI---IGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       242 ~~---~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ..   .....+++.+.+...    ..++.-++|||++.. +...++.+...+..-....++|+||++.+
T Consensus        92 EIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~A~NALLKtLEEPP~~v~FILaTtd~~  160 (830)
T PRK07003         92 EMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQ  160 (830)
T ss_pred             EecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHHHHHHHHHHHHhcCCCeEEEEEECChh
Confidence            01   112233333333322    134566899999963 34678888777766555778777776643

>TIGR00767 rho transcription termination factor Rho

Probab=97.62  E-value=5.3e-05  Score=74.57  Aligned_cols=82  Identities=12%  Similarity=-0.011  Sum_probs=51.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---------HHHHHHHhCCCCCCC--ccCCCCHHHH----HHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------LDDIIRSLMPPSRVT--VIIGEDYKLK----KSI  254 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------~~~il~~l~~~~~~~--~~~~~~~~~l----~~~  254 (425)
                      -..++|+|++|+|||||++.+++..... ||+..+|+         ..++++++....-..  +.....-..+    .+.
T Consensus       168 Gq~~~IvG~~g~GKTtL~~~i~~~I~~n-hfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~  246 (415)
T TIGR00767       168 GQRGLIVAPPKAGKTVLLQKIAQAITRN-HPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEK  246 (415)
T ss_pred             CCEEEEECCCCCChhHHHHHHHHhhccc-CCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHH
Confidence            4568999999999999999999954333 79888888         667777763211100  0011110111    111


Q ss_pred             HHHH-hcCCeEEEEecccC
Q 040913          255 LRDF-LTNKKYFIALDDVC  272 (425)
Q Consensus       255 l~~~-l~~kr~LlVLDdvw  272 (425)
                      .... -.|++.+|++|.+.
T Consensus       247 Ae~~~~~GkdVVLlIDEit  265 (415)
T TIGR00767       247 AKRLVEHKKDVVILLDSIT  265 (415)
T ss_pred             HHHHHHcCCCeEEEEEChh
Confidence            1122 25899999999985

Members of this family differ in the specificity of RNA binding.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.61  E-value=8.8e-05  Score=68.26  Aligned_cols=40  Identities=13%  Similarity=0.047  Sum_probs=30.2

Q ss_pred             chhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          172 FERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       172 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+...+.+.+++...  ....+.++|++|+|||+||+.+++.
T Consensus        22 ~~~~~~~l~~~~~~~--~~~~lll~G~~G~GKT~la~~~~~~   61 (226)
T TIGR03420        22 NAELLAALRQLAAGK--GDRFLYLWGESGSGKSHLLQAACAA   61 (226)
T ss_pred             cHHHHHHHHHHHhcC--CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            344566666665432  3567889999999999999999873

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.

>PRK08727 hypothetical protein; Validated

Probab=97.60  E-value=0.00011  Score=68.27  Aligned_cols=41  Identities=12%  Similarity=0.020  Sum_probs=27.2

Q ss_pred             ccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          170 SEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|-.+....+.......  ....+.|+|..|+|||+|++.+++
T Consensus        23 ~~~~n~~~~~~~~~~~~--~~~~l~l~G~~G~GKThL~~a~~~   63 (233)
T PRK08727         23 AAPDGLLAQLQALAAGQ--SSDWLYLSGPAGTGKTHLALALCA   63 (233)
T ss_pred             CCcHHHHHHHHHHHhcc--CCCeEEEECCCCCCHHHHHHHHHH
Confidence            34434444443333222  234589999999999999999887

>PRK08116 hypothetical protein; Validated

Probab=97.57  E-value=9e-05  Score=70.19  Aligned_cols=102  Identities=17%  Similarity=0.170  Sum_probs=53.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchHHH-HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEec
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALD  269 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLD  269 (425)
                      ..+.++|..|+|||.||..+++.  +...-..++++ ..+++..+......  ....+...    +.+.+.+-. |||||
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~~~~ll~~i~~~~~~--~~~~~~~~----~~~~l~~~d-lLviD  185 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVNFPQLLNRIKSTYKS--SGKEDENE----IIRSLVNAD-LLILD  185 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHHHHHHHHHHHHhc--cccccHHH----HHHHhcCCC-EEEEe
Confidence            34779999999999999999993  32221122333 44444444322110  00112222    233344333 89999


Q ss_pred             ccCC-ChhhHHH--HHhhCCC-CCCCcEEEEecCCh
Q 040913          270 DVCH-NIEIWDD--LEEVLPD-NQNGSRVLITVINP  301 (425)
Q Consensus       270 dvw~-~~~~~~~--l~~~l~~-~~~gskIivTTR~~  301 (425)
                      |+.. ....|..  +...+.. -..|..+|+||...
T Consensus       186 Dlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        186 DLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            9941 2334432  3333321 13456788888653

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.55  E-value=0.00051  Score=71.74  Aligned_cols=134  Identities=10%  Similarity=0.052  Sum_probs=74.6

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCC--cc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVT--VI  243 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~--~~  243 (425)
                      -.+++|.+.....|.+++..+. -.+.+.++|+.|+||||+|+.+.+.-..........--.....+.+.......  ..
T Consensus        14 FddVIGQe~vv~~L~~aI~~gr-l~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEI   92 (702)
T PRK14960         14 FNELVGQNHVSRALSSALERGR-LHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEI   92 (702)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEe
Confidence            3568999999999999998764 34677899999999999999886621111000000000000001111100000  00


Q ss_pred             ---CCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          244 ---IGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       244 ---~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                         .....+++.+.+...    ..++.-++|+|++.. +....+.+...+.....+.++|++|.+
T Consensus        93 DAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~A~NALLKtLEEPP~~v~FILaTtd  157 (702)
T PRK14960         93 DAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTD  157 (702)
T ss_pred             cccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhcCCCCcEEEEEECC
Confidence               112233333222211    236777999999962 346777777777665556777777655

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.54  E-value=0.00046  Score=66.92  Aligned_cols=118  Identities=13%  Similarity=0.093  Sum_probs=67.8

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGE  246 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~  246 (425)
                      .+++|++..++.+..++..+.  .+.+.++|.+|+||||+|+.+.+.-. ...+.. .++      .+..      ....
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~~--~~~~ll~G~~G~GKt~~~~~l~~~l~-~~~~~~-~~i------~~~~------~~~~   80 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEKN--MPHLLFAGPPGTGKTTAALALARELY-GEDWRE-NFL------ELNA------SDER   80 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHHHc-CCcccc-ceE------Eecc------cccc
Confidence            458899999999999987654  44578999999999999999887311 111110 000      0000      0011


Q ss_pred             CHHHHHHHHHHHh-----c-CCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          247 DYKLKKSILRDFL-----T-NKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       247 ~~~~l~~~l~~~l-----~-~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      ........+....     . ..+-+|++|++.. .......+...+......+++|+++..
T Consensus        81 ~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~~~~~~L~~~le~~~~~~~lIl~~~~  141 (319)
T PRK00440         81 GIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNY  141 (319)
T ss_pred             chHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCHHHHHHHHHHHhcCCCCCeEEEEeCC
Confidence            1122222222222     1 2456899999862 234556666666554555677776643

>PLN03025 replication factor C subunit; Provisional

Probab=97.53  E-value=0.00078  Score=65.62  Aligned_cols=118  Identities=13%  Similarity=0.091  Sum_probs=65.8

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGE  246 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~  246 (425)
                      .+++|.++..+.|.+++..+.  .+-+-++|++|+||||+|+.+.+.-. ...|...+.       .+    +  ..+..
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~~--~~~lll~Gp~G~GKTtla~~la~~l~-~~~~~~~~~-------el----n--~sd~~   76 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDGN--MPNLILSGPPGTGKTTSILALAHELL-GPNYKEAVL-------EL----N--ASDDR   76 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHh-cccCcccee-------ee----c--ccccc
Confidence            457898888888887776544  34466899999999999999877210 111110000       00    0  00111


Q ss_pred             CHHHHHHHHHHHh-------cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          247 DYKLKKSILRDFL-------TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       247 ~~~~l~~~l~~~l-------~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      ..+.+...+....       .++.-+++||++.. +....+.+...+..-...+++|++|..
T Consensus        77 ~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~aq~aL~~~lE~~~~~t~~il~~n~  138 (319)
T PLN03025         77 GIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNT  138 (319)
T ss_pred             cHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHHHHHHHHHHHhcccCCceEEEEeCC
Confidence            2223333333221       24567999999962 234445555555443445777776654

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.53  E-value=0.00068  Score=67.26  Aligned_cols=133  Identities=13%  Similarity=0.057  Sum_probs=73.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccc---cch-HHHHHHHHHHhCCCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF---DCL-AWILDDIIRSLMPPSRVT  241 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~-~wv~~~il~~l~~~~~~~  241 (425)
                      -.+++|.+..++.+.+.+..+. -.+.+-++|+.|+||||+|+.+.+.-......   +|. +-.-.++...........
T Consensus        15 ~~~iiGq~~~~~~l~~~~~~~~-~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~   93 (363)
T PRK14961         15 FRDIIGQKHIVTAISNGLSLGR-IHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEI   93 (363)
T ss_pred             hhhccChHHHHHHHHHHHHcCC-CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEe
Confidence            3568999999999998887654 34667899999999999999987632111111   110 000111111110000000


Q ss_pred             cc-CCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          242 VI-IGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       242 ~~-~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      +. .....+++. .+.+.+     .+++-++|+|++.. +...++.+...+.......++|++|.+
T Consensus        94 ~~~~~~~v~~ir-~i~~~~~~~p~~~~~kviIIDEa~~l~~~a~naLLk~lEe~~~~~~fIl~t~~  158 (363)
T PRK14961         94 DAASRTKVEEMR-EILDNIYYSPSKSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTD  158 (363)
T ss_pred             cccccCCHHHHH-HHHHHHhcCcccCCceEEEEEChhhcCHHHHHHHHHHHhcCCCCeEEEEEcCC
Confidence            00 012223322 222222     24566999999963 334677777777665556777776654

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

Probab=97.51  E-value=0.00021  Score=70.52  Aligned_cols=99  Identities=19%  Similarity=0.131  Sum_probs=69.2

Q ss_pred             CcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCccccccc------cchHHH-------HHHHHH
Q 040913          168 DISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF------DCLAWI-------LDDIIR  232 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F------~~~~wv-------~~~il~  232 (425)
                      .+.+|+.+++++...|..-  ...+.-+-|+|.+|+|||+.++.+.+  ++.+..      ..-+|.       +..|++
T Consensus        18 ~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~   95 (366)
T COG1474          18 ELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVME--ELEESSANVEVVYINCLELRTPYQVLSKILN   95 (366)
T ss_pred             cccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEeeeeCCCHHHHHHHHHH
Confidence            3899999999999887653  22233388999999999999999988  443331      112222       667777


Q ss_pred             HhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccC
Q 040913          233 SLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVC  272 (425)
Q Consensus       233 ~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw  272 (425)
                      ++....    .......+....+.+.+.  ++.++||||++.
T Consensus        96 ~~~~~p----~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid  133 (366)
T COG1474          96 KLGKVP----LTGDSSLEILKRLYDNLSKKGKTVIVILDEVD  133 (366)
T ss_pred             HcCCCC----CCCCchHHHHHHHHHHHHhcCCeEEEEEcchh
Confidence            776221    223556677777777775  589999999996

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.50  E-value=0.00079  Score=61.91  Aligned_cols=107  Identities=18%  Similarity=0.181  Sum_probs=66.9

Q ss_pred             CCCCCCCcccchhhHHHHHHH---HhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCC
Q 040913          162 EGQPRLDISEFERAREEWFDL---LIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPS  238 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~---L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~  238 (425)
                      ..+.-.+++|.+..++.|++=   +..+. ...-+-++|..|.|||+|++.+.+...-+. ...           +... 
T Consensus        22 ~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~-pannvLL~G~rGtGKSSlVkall~~y~~~G-LRl-----------Iev~-   87 (249)
T PF05673_consen   22 DPIRLDDLIGIERQKEALIENTEQFLQGL-PANNVLLWGARGTGKSSLVKALLNEYADQG-LRL-----------IEVS-   87 (249)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHHcCC-CCcceEEecCCCCCHHHHHHHHHHHHhhcC-ceE-----------EEEC-
Confidence            345567899999999988653   33333 244456799999999999999988221111 000           0000 


Q ss_pred             CCCccCCCCHHHHHHHHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCCC
Q 040913          239 RVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLPD  287 (425)
Q Consensus       239 ~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~~  287 (425)
                         ...-.+...+.+.++.  +..||+|.+||+.+  ++..+..++..|..
T Consensus        88 ---k~~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeG  133 (249)
T PF05673_consen   88 ---KEDLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEG  133 (249)
T ss_pred             ---HHHhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcC
Confidence               0112334444444442  35799999999976  34678888888863

>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=97.48  E-value=0.00034  Score=58.14  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=19.2

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|++|+||||+|+.+.+.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            568999999999999999994

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 ....

>PRK09087 hypothetical protein; Validated

Probab=97.47  E-value=0.00054  Score=63.19  Aligned_cols=24  Identities=25%  Similarity=0.185  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.+.|+|..|+|||+|++.+++.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~   67 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREK   67 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHh
Confidence            456899999999999999998874

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.47  E-value=0.00075  Score=67.75  Aligned_cols=134  Identities=13%  Similarity=0.037  Sum_probs=73.8

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc--------------cccchHHHHHHHH
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF--------------YFDCLAWILDDII  231 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~--------------~F~~~~wv~~~il  231 (425)
                      -.+++|.+..++.|.+++..+. -...+-++|+.|+||||+|..+.+.-....              +-.|....  .+.
T Consensus        15 ~~eiiGq~~~~~~L~~~~~~~~-~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~--~~~   91 (397)
T PRK14955         15 FADITAQEHITRTIQNSLRMGR-VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCR--DFD   91 (397)
T ss_pred             HhhccChHHHHHHHHHHHHhCC-cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHH--HHh
Confidence            3468899999998888887654 345577899999999999988765211111              00111110  000


Q ss_pred             HHhCCCCCC-CccCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec-CChhH
Q 040913          232 RSLMPPSRV-TVIIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV-INPSL  303 (425)
Q Consensus       232 ~~l~~~~~~-~~~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT-R~~~v  303 (425)
                      .....+... ........+++.+ +.+.+     .+++-++|+|++.. +...++.+...+....+.+.+|++| +...+
T Consensus        92 ~~~~~n~~~~~~~~~~~id~Ir~-l~~~~~~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep~~~t~~Il~t~~~~kl  170 (397)
T PRK14955         92 AGTSLNISEFDAASNNSVDDIRL-LRENVRYGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKI  170 (397)
T ss_pred             cCCCCCeEeecccccCCHHHHHH-HHHHHhhchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcCCCCeEEEEEeCChHHh
Confidence            000000000 0001122344433 23333     35667899999862 3467888888877655567765554 43333

>PRK10536 hypothetical protein; Provisional

Probab=97.46  E-value=7.8e-05  Score=69.21  Aligned_cols=42  Identities=14%  Similarity=0.145  Sum_probs=34.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+.++......++.+|.+.    .++.+.|++|+|||+||..+..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~----~lV~i~G~aGTGKT~La~a~a~   96 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESK----QLIFATGEAGCGKTWISAAKAA   96 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcC----CeEEEECCCCCCHHHHHHHHHH
Confidence            44667888888888888763    3888999999999999987655

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.46  E-value=0.00051  Score=73.30  Aligned_cols=104  Identities=13%  Similarity=0.023  Sum_probs=64.2

Q ss_pred             CCCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhcCcc--c-cc---cc-----cch----HHH-
Q 040913          166 RLDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYNNNH--V-KF---YF-----DCL----AWI-  226 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~~~~--~-~~---~F-----~~~----~wv-  226 (425)
                      +..+.||++++++|...|...   .....++-|.|++|.|||+.++.|.+.-.  . +.   .|     .|.    .+. 
T Consensus       754 PD~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sI  833 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAA  833 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHH
Confidence            467889999999998888652   23346778999999999999999976311  0 00   11     110    111 


Q ss_pred             HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc---CCeEEEEecccC
Q 040913          227 LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT---NKKYFIALDDVC  272 (425)
Q Consensus       227 ~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~---~kr~LlVLDdvw  272 (425)
                      +..|..++.....   ............+...+.   +...+||||++.
T Consensus       834 YqvI~qqL~g~~P---~~GlsS~evLerLF~~L~k~~r~v~IIILDEID  879 (1164)
T PTZ00112        834 YQVLYKQLFNKKP---PNALNSFKILDRLFNQNKKDNRNVSILIIDEID  879 (1164)
T ss_pred             HHHHHHHHcCCCC---CccccHHHHHHHHHhhhhcccccceEEEeehHh
Confidence            5566667743322   122333445555555542   234599999996

>PRK08118 topology modulation protein; Reviewed

Probab=97.45  E-value=0.00027  Score=62.01  Aligned_cols=65  Identities=15%  Similarity=0.279  Sum_probs=43.1

Q ss_pred             EEEEEecCCCchHHHHHHhhcCcccc-ccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecc
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVK-FYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDD  270 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDd  270 (425)
                      -|.|+|++|+||||||+.+++...+. -+||..+|-          +    +....+.++....+.+.+++..  .|+|.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~----------~----~w~~~~~~~~~~~~~~~~~~~~--wVidG   66 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWK----------P----NWEGVPKEEQITVQNELVKEDE--WIIDG   66 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcc----------c----CCcCCCHHHHHHHHHHHhcCCC--EEEeC
Confidence            58899999999999999999955443 457777661          0    1112233455555566666655  57788


Q ss_pred             cC
Q 040913          271 VC  272 (425)
Q Consensus       271 vw  272 (425)
                      ..
T Consensus        67 ~~   68 (167)
T PRK08118         67 NY   68 (167)
T ss_pred             Cc
Confidence            75

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.43  E-value=0.00051  Score=71.63  Aligned_cols=131  Identities=11%  Similarity=0.044  Sum_probs=75.5

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc-----------ccccchHHHHHHHHHHhC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK-----------FYFDCLAWILDDIIRSLM  235 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~-----------~~F~~~~wv~~~il~~l~  235 (425)
                      .++||.+..++.|.+++..+. -.+.+.++|..|+||||+|+.+.+.-...           .+-.|...      ..+.
T Consensus        16 ddVIGQe~vv~~L~~al~~gR-LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC------~~I~   88 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR-LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRAC------TEID   88 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHH------HHHH
Confidence            468999999999999998764 34566889999999999998876522110           00011111      1110


Q ss_pred             CCCCCC--cc---CCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEE-EEecCChhHH
Q 040913          236 PPSRVT--VI---IGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRV-LITVINPSLL  304 (425)
Q Consensus       236 ~~~~~~--~~---~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskI-ivTTR~~~va  304 (425)
                      ......  ..   .....+++.+.+...    ..++.-++|+|++.. +...++.|...+-.-..++++ ++||....+.
T Consensus        89 aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~~AaNALLKTLEEPP~~v~FILaTtep~kLl  168 (700)
T PRK12323         89 AGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIP  168 (700)
T ss_pred             cCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCHHHHHHHHHhhccCCCCceEEEEeCChHhhh
Confidence            000000  00   112334443333332    245677999999963 456778887777654556664 5555544444

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.41  E-value=0.00087  Score=69.40  Aligned_cols=127  Identities=10%  Similarity=0.052  Sum_probs=72.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccc------cccccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHV------KFYFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~------~~~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+..+..|.+.+..+. -.+.+-++|+.|+||||+|+.+.+.-..      ..+..|....      .+.....
T Consensus        15 f~diiGq~~~v~~L~~~i~~~r-l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~------~i~~~~~   87 (546)
T PRK14957         15 FAEVAGQQHALNSLVHALETQK-VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCV------AINNNSF   87 (546)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHH------HHhcCCC
Confidence            3468899999999999887653 3455778999999999999988762110      1111221111      0000000


Q ss_pred             CC--------ccCCCCHHHHHHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecC
Q 040913          240 VT--------VIIGEDYKLKKSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVI  299 (425)
Q Consensus       240 ~~--------~~~~~~~~~l~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR  299 (425)
                      ..        .....+...+.+.+... ..+++-++|+|++.. +...++.+...+......+++|++|.
T Consensus        88 ~dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~a~naLLK~LEepp~~v~fIL~Tt  157 (546)
T PRK14957         88 IDLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATT  157 (546)
T ss_pred             CceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhccHHHHHHHHHHHhcCCCCceEEEEEC
Confidence            00        00011222333333321 246777999999952 44677788877776555666554443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.40  E-value=0.0011  Score=69.71  Aligned_cols=128  Identities=13%  Similarity=0.111  Sum_probs=71.6

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+..+..|.+++..+. -.+.+.++|..|+||||+|+.+.+.-....      +-.|..      .+.+.....
T Consensus        15 FddIIGQe~vv~~L~~ai~~~r-l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~s------Cr~i~~g~~   87 (709)
T PRK08691         15 FADLVGQEHVVKALQNALDEGR-LHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQS------CTQIDAGRY   87 (709)
T ss_pred             HHHHcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHH------HHHHhccCc
Confidence            3568999999999999988754 245678999999999999998866211111      111111      001100000


Q ss_pred             CC-----ccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          240 VT-----VIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       240 ~~-----~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      ..     .......+.+.+.+...    ..+++-++|+|++.. +....+.+...+..-...+++|++|.+
T Consensus        88 ~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~A~NALLKtLEEPp~~v~fILaTtd  158 (709)
T PRK08691         88 VDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTD  158 (709)
T ss_pred             cceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHHHHHHHHHHHHhCCCCcEEEEEeCC
Confidence            00     00112233333332211    235777999999962 334566666666544445666666644

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.39  E-value=0.00081  Score=67.30  Aligned_cols=50  Identities=18%  Similarity=0.040  Sum_probs=39.3

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          163 GQPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....++.|++..+++|.+.+...           -..++-|.++|++|+|||++|+.+++
T Consensus       127 ~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~  187 (389)
T PRK03992        127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH  187 (389)
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHH
Confidence            344567889999999998876431           12356688999999999999999998

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.38  E-value=0.0013  Score=67.74  Aligned_cols=135  Identities=12%  Similarity=0.036  Sum_probs=76.6

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc----------ccccchHHHHHHHHHHhCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK----------FYFDCLAWILDDIIRSLMP  236 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----------~~F~~~~wv~~~il~~l~~  236 (425)
                      .+++|.+.....|.+.+..+. -.+.+-++|+.|+||||+|+.+.+.-...          .+..|....  .|......
T Consensus        21 ~dliGq~~vv~~L~~ai~~~r-i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~--~i~~~~h~   97 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDR-LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCI--SFNNHNHP   97 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHH--HHhcCCCC
Confidence            468899999998888777654 34567889999999999999987632111          112221111  11100000


Q ss_pred             CCCC-CccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEE-EecCChhHH
Q 040913          237 PSRV-TVIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVL-ITVINPSLL  304 (425)
Q Consensus       237 ~~~~-~~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIi-vTTR~~~va  304 (425)
                      .... ........+++...+...    +.+++-++|+|+++. +...++.+...+......+.+| +||+...+.
T Consensus        98 Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~a~naLLk~LEepp~~~vfI~aTte~~kI~  172 (507)
T PRK06645         98 DIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIP  172 (507)
T ss_pred             cEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHHHHHHHHHHHhhcCCCEEEEEEeCChHHhh
Confidence            0000 000112334443333222    246778999999973 3567888888877655566655 455555544

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.37  E-value=0.00093  Score=64.61  Aligned_cols=108  Identities=19%  Similarity=0.213  Sum_probs=68.2

Q ss_pred             CCCCcccchhhHHHHHHHHhcCCC-CcEEEEEEecCCCchHHHHHHhhcCccccccc----cchHHH--HHHHHHHhCCC
Q 040913          165 PRLDISEFERAREEWFDLLIEGPI-GLSVVAILDSSGFDKTAFAADTYNNNHVKFYF----DCLAWI--LDDIIRSLMPP  237 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~~~-~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F----~~~~wv--~~~il~~l~~~  237 (425)
                      -++.+.+|+.+...+..++...+. -++.|-|.|..|.|||.+.+++++......-|    +|.-|-  +..|+.+....
T Consensus         4 l~~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~~~   83 (438)
T KOG2543|consen    4 LEPNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQLA   83 (438)
T ss_pred             cccCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhccC
Confidence            356788999999999999988765 35556899999999999999999965333222    111122  78888888522


Q ss_pred             CCCCccCC---CCHHHHHHHHHH--Hhc--CCeEEEEecccC
Q 040913          238 SRVTVIIG---EDYKLKKSILRD--FLT--NKKYFIALDDVC  272 (425)
Q Consensus       238 ~~~~~~~~---~~~~~l~~~l~~--~l~--~kr~LlVLDdvw  272 (425)
                      ...+....   ....+....+..  ...  ++.++||||++.
T Consensus        84 d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad  125 (438)
T KOG2543|consen   84 DKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNAD  125 (438)
T ss_pred             CCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHH
Confidence            22111111   111222222222  111  468999999996

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=97.34  E-value=0.00035  Score=66.98  Aligned_cols=96  Identities=23%  Similarity=0.221  Sum_probs=54.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHH--hcCCeEEEE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDF--LTNKKYFIA  267 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~--l~~kr~LlV  267 (425)
                      +..+-.||++|+||||||+.+.+..+-...|-...-            ..  .....+...+.+.-++.  +.++|..|.
T Consensus       162 ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelS------------At--~a~t~dvR~ife~aq~~~~l~krkTilF  227 (554)
T KOG2028|consen  162 IPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELS------------AT--NAKTNDVRDIFEQAQNEKSLTKRKTILF  227 (554)
T ss_pred             CCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEe------------cc--ccchHHHHHHHHHHHHHHhhhcceeEEE
Confidence            666778999999999999999985443332211000            00  11112223333333322  357889999


Q ss_pred             ecccC-CChhhHHHHHhhCCCCCCCcEEEE--ecCChh
Q 040913          268 LDDVC-HNIEIWDDLEEVLPDNQNGSRVLI--TVINPS  302 (425)
Q Consensus       268 LDdvw-~~~~~~~~l~~~l~~~~~gskIiv--TTR~~~  302 (425)
                      +|.|- ++..+-+   ..||.-.+|+-++|  ||.|.+
T Consensus       228 iDEiHRFNksQQD---~fLP~VE~G~I~lIGATTENPS  262 (554)
T KOG2028|consen  228 IDEIHRFNKSQQD---TFLPHVENGDITLIGATTENPS  262 (554)
T ss_pred             eHHhhhhhhhhhh---cccceeccCceEEEecccCCCc
Confidence            99994 1333222   34566666776555  565544

>PRK06526 transposase; Provisional

Probab=97.32  E-value=0.00028  Score=66.24  Aligned_cols=70  Identities=14%  Similarity=0.125  Sum_probs=39.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchHHH-HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEec
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALD  269 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLD  269 (425)
                      .-+.++|++|+|||+||..+.+... ...+. +.|+ ..+++..+.....     ..   .+...+...  .+.-|||+|
T Consensus        99 ~nlll~Gp~GtGKThLa~al~~~a~-~~g~~-v~f~t~~~l~~~l~~~~~-----~~---~~~~~l~~l--~~~dlLIID  166 (254)
T PRK06526         99 ENVVFLGPPGTGKTHLAIGLGIRAC-QAGHR-VLFATAAQWVARLAAAHH-----AG---RLQAELVKL--GRYPLLIVD  166 (254)
T ss_pred             ceEEEEeCCCCchHHHHHHHHHHHH-HCCCc-hhhhhHHHHHHHHHHHHh-----cC---cHHHHHHHh--ccCCEEEEc
Confidence            4578999999999999999876321 12222 2333 4444444432211     01   112222222  234589999


Q ss_pred             ccC
Q 040913          270 DVC  272 (425)
Q Consensus       270 dvw  272 (425)
                      |+.
T Consensus       167 D~g  169 (254)
T PRK06526        167 EVG  169 (254)
T ss_pred             ccc
Confidence            996

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.32  E-value=0.00075  Score=68.99  Aligned_cols=46  Identities=11%  Similarity=0.020  Sum_probs=36.9

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.+.....|...+..+. -.+.+-++|++|+||||+|+.+.+
T Consensus        13 ~~divGq~~i~~~L~~~i~~~~-l~~~~Lf~GPpGtGKTTlA~~lA~   58 (472)
T PRK14962         13 FSEVVGQDHVKKLIINALKKNS-ISHAYIFAGPRGTGKTTVARILAK   58 (472)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3568999888888877776654 335678999999999999999876

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.31  E-value=0.00071  Score=72.87  Aligned_cols=132  Identities=10%  Similarity=0.030  Sum_probs=73.4

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+..+..|.+++..+. -.+.+.++|+.|+||||+|+.+.+.-....      +..|..-.  .|.........
T Consensus        15 FddIIGQe~Iv~~LknaI~~~r-l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~--~i~~g~~~Dvi   91 (944)
T PRK14949         15 FEQMVGQSHVLHALTNALTQQR-LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCV--EIAQGRFVDLI   91 (944)
T ss_pred             HHHhcCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHH--HHhcCCCceEE
Confidence            3568999999999999887654 345567999999999999999887321111      11111100  01000000000


Q ss_pred             -CCccCCCCH---HHHHHHHHH-HhcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          240 -VTVIIGEDY---KLKKSILRD-FLTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       240 -~~~~~~~~~---~~l~~~l~~-~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                       .........   .++...+.. ...+++-++|+|++.. +....+.|...+-.-....++|++|.+
T Consensus        92 EidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~eAqNALLKtLEEPP~~vrFILaTTe  158 (944)
T PRK14949         92 EVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRSSFNALLKTLEEPPEHVKFLLATTD  158 (944)
T ss_pred             EeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHHHHHHHHHHHhccCCCeEEEEECCC
Confidence             000001122   233322221 1246778999999953 456778887777655556666555544

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.29  E-value=0.0016  Score=64.95  Aligned_cols=128  Identities=10%  Similarity=0.011  Sum_probs=70.4

Q ss_pred             CCcccchhhHHHHHHHHhcCCC--------CcEEEEEEecCCCchHHHHHHhhcCcccc--------ccccchHHHHHHH
Q 040913          167 LDISEFERAREEWFDLLIEGPI--------GLSVVAILDSSGFDKTAFAADTYNNNHVK--------FYFDCLAWILDDI  230 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~--------~~~vi~IvG~gGvGKTtLa~~v~~~~~~~--------~~F~~~~wv~~~i  230 (425)
                      .+++|.+..++.|.+.+..+..        -.+.+-++|+.|+||||+|..+.+.-...        .+-.|+.+.    
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~----   80 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVL----   80 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHh----
Confidence            4588999999999999987531        35668899999999999998875421100        011111111    


Q ss_pred             HHHhCCCCC--CCccCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          231 IRSLMPPSR--VTVIIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       231 l~~l~~~~~--~~~~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                       ..-.....  .++......+++.. +.+.+     .+++-++++|++.. +....+.+...+.....++.+|++|.+
T Consensus        81 -~~~hpD~~~i~~~~~~i~i~~iR~-l~~~~~~~p~~~~~kViiIDead~m~~~aanaLLk~LEep~~~~~fIL~a~~  156 (394)
T PRK07940         81 -AGTHPDVRVVAPEGLSIGVDEVRE-LVTIAARRPSTGRWRIVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPS  156 (394)
T ss_pred             -cCCCCCEEEeccccccCCHHHHHH-HHHHHHhCcccCCcEEEEEechhhcCHHHHHHHHHHhhcCCCCCeEEEEECC
Confidence             00000000  00001123333332 22222     24556888899963 345556676666555556666666655

>PRK08181 transposase; Validated

Probab=97.28  E-value=0.00024  Score=67.15  Aligned_cols=98  Identities=18%  Similarity=0.147  Sum_probs=50.1

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHH-HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecc
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDD  270 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDd  270 (425)
                      -+.++|++|+|||.||..+.+  ........+.++ ..+++..+.....     ..+.......+     .+-=||||||
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~--~a~~~g~~v~f~~~~~L~~~l~~a~~-----~~~~~~~l~~l-----~~~dLLIIDD  175 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGL--ALIENGWRVLFTRTTDLVQKLQVARR-----ELQLESAIAKL-----DKFDLLILDD  175 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHH--HHHHcCCceeeeeHHHHHHHHHHHHh-----CCcHHHHHHHH-----hcCCEEEEec
Confidence            478999999999999999987  332222122333 4444444432211     11222222222     2345999999


Q ss_pred             cCC-ChhhH--HHHHhhCCCCCCCcEEEEecCCh
Q 040913          271 VCH-NIEIW--DDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       271 vw~-~~~~~--~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      +.. ....|  ..+...+...-.+..+||||...
T Consensus       176 lg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        176 LAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             cccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            952 11222  22333332211123578888653

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.26  E-value=0.0017  Score=64.01  Aligned_cols=136  Identities=11%  Similarity=0.009  Sum_probs=72.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccc--cccc-cchHHH-HHHHHHHhCCCCCC-
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHV--KFYF-DCLAWI-LDDIIRSLMPPSRV-  240 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F-~~~~wv-~~~il~~l~~~~~~-  240 (425)
                      -.+++|.+..++.+.+++..+. -.+.+-++|++|+||||+|+.+...-..  ...| .|..+. -..+.......... 
T Consensus        13 ~~~iig~~~~~~~l~~~~~~~~-~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~~~~   91 (355)
T TIGR02397        13 FEDVIGQEHIVQTLKNAIKNGR-IAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVIEI   91 (355)
T ss_pred             HhhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEe
Confidence            3468999999999999887654 3456788999999999999877652110  0011 111000 00011000000000 


Q ss_pred             CccCCCCH---HHHHHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          241 TVIIGEDY---KLKKSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       241 ~~~~~~~~---~~l~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ........   ..+.+.+... ..+++-++|+|++.. +....+.+...+......+.+|++|.+..
T Consensus        92 ~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~~~~~~Ll~~le~~~~~~~lIl~~~~~~  158 (355)
T TIGR02397        92 DAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPH  158 (355)
T ss_pred             eccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCHHHHHHHHHHHhCCccceeEEEEeCCHH
Confidence            00001122   2233332211 234566899999852 34567777777755555667666665443

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.

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

Probab=97.25  E-value=0.00065  Score=68.08  Aligned_cols=100  Identities=15%  Similarity=0.078  Sum_probs=61.6

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-------HHHHHHHhCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-------LDDIIRSLMPPS  238 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-------~~~il~~l~~~~  238 (425)
                      ..++++.+...+.++..|...    +.|.++|++|+|||++|+.+.+......+|+...||       ..+.+..+....
T Consensus       174 l~d~~i~e~~le~l~~~L~~~----~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~  249 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTIK----KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNG  249 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhcC----CCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCC
Confidence            345788899999999998863    467789999999999999998743333455555555       445444332221


Q ss_pred             CCCccCCCCHHHHHHHHHHHh--cCCeEEEEecccC
Q 040913          239 RVTVIIGEDYKLKKSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       239 ~~~~~~~~~~~~l~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                      .  +.. ....-..+.+...-  .+++++||+|++.
T Consensus       250 v--gy~-~~~G~f~~~~~~A~~~p~~~~vliIDEIN  282 (459)
T PRK11331        250 V--GFR-RKDGIFYNFCQQAKEQPEKKYVFIIDEIN  282 (459)
T ss_pred             C--CeE-ecCchHHHHHHHHHhcccCCcEEEEehhh
Confidence            1  100 00111222222222  2478999999994

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.25  E-value=0.0015  Score=68.05  Aligned_cols=127  Identities=13%  Similarity=0.108  Sum_probs=70.5

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+..++.+.+.+..+. -.+.+-++|+.|+||||+|+.+.+.-....      +-.|..      .+.+.....
T Consensus        15 F~dIIGQe~iv~~L~~aI~~~r-l~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~s------Cr~i~~~~h   87 (605)
T PRK05896         15 FKQIIGQELIKKILVNAILNNK-LTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSV------CESINTNQS   87 (605)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHH------HHHHHcCCC
Confidence            3568899999999999887654 245678999999999999998866211111      111111      111111110


Q ss_pred             CC--cc---CCCCHHHHHHHH---HHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecC
Q 040913          240 VT--VI---IGEDYKLKKSIL---RDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVI  299 (425)
Q Consensus       240 ~~--~~---~~~~~~~l~~~l---~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR  299 (425)
                      ..  ..   .....+++...+   ... ..+++-++|+|++.. +...++.+...+......+.+|++|.
T Consensus        88 ~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~A~NaLLKtLEEPp~~tvfIL~Tt  157 (605)
T PRK05896         88 VDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTSAWNALLKTLEEPPKHVVFIFATT  157 (605)
T ss_pred             CceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHHHHHHHHHHHHhCCCcEEEEEECC
Confidence            00  00   112223332222   111 123455799999963 45677777777765454566555553

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.25  E-value=0.0015  Score=67.76  Aligned_cols=127  Identities=10%  Similarity=0.070  Sum_probs=71.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc------ccccchHHHHHHHHHHhCCCCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK------FYFDCLAWILDDIIRSLMPPSRV  240 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~------~~F~~~~wv~~~il~~l~~~~~~  240 (425)
                      .+++|.+..++.+.+++..+. -.+.+-++|+.|+||||+|+.+.+.-...      .+-.|..-      ..+......
T Consensus        16 ~divGq~~v~~~L~~~i~~~~-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C------~~i~~~~~~   88 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR-LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSAC------LEIDSGRFV   88 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHH------HHHhcCCCC
Confidence            568999999999999988754 23556789999999999998886521111      11111100      000000000


Q ss_pred             C----c-cCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          241 T----V-IIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       241 ~----~-~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      .    + ......+++.+.+...    ..+++-++|+|++.. +....+.+...+..-...+.+|++|.+
T Consensus        89 d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~a~naLLK~LEepp~~~~fIL~t~d  158 (527)
T PRK14969         89 DLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTD  158 (527)
T ss_pred             ceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHHHHHHHHHHHhCCCCCEEEEEEeCC
Confidence            0    0 0112233333222221    135677999999962 345677777777665556666655543

>PHA00729 NTP-binding motif containing protein

Probab=97.25  E-value=0.0017  Score=59.33  Aligned_cols=85  Identities=16%  Similarity=0.175  Sum_probs=48.2

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccccc-----chHHHHHHHHHHhCCCCCCCccCCCCHHHHHH
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFD-----CLAWILDDIIRSLMPPSRVTVIIGEDYKLKKS  253 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~-----~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~  253 (425)
                      +++.+....  ...|.|.|.+|+||||||..+.+  ++..++.     ...|          .+..  .....+.+.+..
T Consensus         8 ~~~~l~~~~--f~nIlItG~pGvGKT~LA~aLa~--~l~~~l~~l~~~~~~~----------d~~~--~~~fid~~~Ll~   71 (226)
T PHA00729          8 IVSAYNNNG--FVSAVIFGKQGSGKTTYALKVAR--DVFWKLNNLSTKDDAW----------QYVQ--NSYFFELPDALE   71 (226)
T ss_pred             HHHHHhcCC--eEEEEEECCCCCCHHHHHHHHHH--HHHhhcccccchhhHH----------hcCC--cEEEEEHHHHHH
Confidence            444454443  45688999999999999999887  3211110     0111          0000  112345677777


Q ss_pred             HHHHHhcC-Ce-EEEEeccc--CCChhhHH
Q 040913          254 ILRDFLTN-KK-YFIALDDV--CHNIEIWD  279 (425)
Q Consensus       254 ~l~~~l~~-kr-~LlVLDdv--w~~~~~~~  279 (425)
                      .+....++ .+ =|||+||+  |-+...|.
T Consensus        72 ~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh  101 (226)
T PHA00729         72 KIQDAIDNDYRIPLIIFDDAGIWLSKYVWY  101 (226)
T ss_pred             HHHHHHhcCCCCCEEEEeCCchhhcccchh
Confidence            77766644 22 37999994  42223455

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.24  E-value=0.0014  Score=68.94  Aligned_cols=134  Identities=9%  Similarity=0.056  Sum_probs=73.0

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc-------cc-cchHHHHHHHHHHhCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF-------YF-DCLAWILDDIIRSLMPP  237 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-------~F-~~~~wv~~~il~~l~~~  237 (425)
                      -.+++|-+..+..|.+++..+. -...+-++|..|+||||+|+.+.+.-....       .+ .|..-   ...+.+...
T Consensus        15 f~dviGQe~vv~~L~~~l~~~r-l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C---~~C~~i~~g   90 (618)
T PRK14951         15 FSEMVGQEHVVQALTNALTQQR-LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVC---QACRDIDSG   90 (618)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCcc---HHHHHHHcC
Confidence            3568898888888888888764 346678999999999999988844211000       00 11000   001111110


Q ss_pred             CCCC--cc---CCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec-CChhH
Q 040913          238 SRVT--VI---IGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV-INPSL  303 (425)
Q Consensus       238 ~~~~--~~---~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT-R~~~v  303 (425)
                      ....  ..   .....+++.+.+...    ..++.-++|+|+|.. +...++.+...+..-...+++|++| ....+
T Consensus        91 ~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEPP~~~~fIL~Ttd~~ki  167 (618)
T PRK14951         91 RFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKV  167 (618)
T ss_pred             CCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHHHHHHHHHhcccCCCCeEEEEEECCchhh
Confidence            0000  00   112233333322221    124566899999963 4567888887776655566665554 43333

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.23  E-value=0.0011  Score=62.61  Aligned_cols=45  Identities=11%  Similarity=0.085  Sum_probs=32.2

Q ss_pred             CcccchhhHHHHHHH---Hhc-------C---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDL---LIE-------G---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~---L~~-------~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.+..+++|.+.   +.-       +   .+...-+.++|++|+||||+|+.+.+
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHH
Confidence            478988887776433   311       1   12355677899999999999999876

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.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=97.22  E-value=0.0032  Score=65.66  Aligned_cols=55  Identities=15%  Similarity=0.216  Sum_probs=43.6

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC----CCCcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          164 QPRLDISEFERAREEWFDLLIEG----PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      .-+.+-+|.++.+++|++.|--.    .-.-+++..||++|+|||+|++.|..  -..+.|
T Consensus       320 iLd~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~--al~Rkf  378 (782)
T COG0466         320 ILDKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAK--ALGRKF  378 (782)
T ss_pred             HhcccccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHH--HhCCCE
Confidence            33566789999999999998642    33468999999999999999999987  444444

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.22  E-value=0.0011  Score=61.12  Aligned_cols=45  Identities=9%  Similarity=0.138  Sum_probs=29.3

Q ss_pred             cccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          169 ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.|..+.....+..+.........+.|+|..|+|||+||+.+++.
T Consensus        21 ~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~   65 (227)
T PRK08903         21 VAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVAD   65 (227)
T ss_pred             ccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            345544443333333332223456789999999999999999883

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.20  E-value=0.00038  Score=76.28  Aligned_cols=44  Identities=18%  Similarity=0.131  Sum_probs=37.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+++++++++.|.....+  -+.++|++|+|||++|+.+..
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~~~--n~lL~G~pGvGKTal~~~la~  222 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRTKN--NPILIGEPGVGKTAIAEGLAQ  222 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccccC--CeEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999876522  345899999999999988877

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.20  E-value=0.00078  Score=55.92  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+.|+|++|+||||+++.+...
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~   25 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARE   25 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhc
Confidence            57889999999999999999884

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.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.20  E-value=0.0024  Score=64.81  Aligned_cols=135  Identities=12%  Similarity=0.048  Sum_probs=73.5

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+.....|..++..+. -.+.+.++|+.|+||||+|+.+.+.-....      +..|...  ..|.........
T Consensus        17 f~dvVGQe~iv~~L~~~i~~~r-i~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC--~~i~~g~~~dvi   93 (484)
T PRK14956         17 FRDVIHQDLAIGALQNALKSGK-IGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSC--LEITKGISSDVL   93 (484)
T ss_pred             HHHHhChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHH--HHHHccCCccce
Confidence            3568999999999999888765 234678999999999999999876321110      1111111  111111111000


Q ss_pred             CCcc-CCCCH---HHHHHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEE-EecCChhH
Q 040913          240 VTVI-IGEDY---KLKKSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVL-ITVINPSL  303 (425)
Q Consensus       240 ~~~~-~~~~~---~~l~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIi-vTTR~~~v  303 (425)
                      .-+. .....   .++.+.+... ..++.-++|+|++.. +.+.++.+...+.........| .||....+
T Consensus        94 EIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~A~NALLKtLEEPp~~viFILaTte~~kI  164 (484)
T PRK14956         94 EIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKI  164 (484)
T ss_pred             eechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHHHHHHHHHHhhcCCCceEEEeecCChhhc
Confidence            0000 01112   2233333221 235667999999963 4567888877775544445544 44444444

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.19  E-value=0.0011  Score=61.64  Aligned_cols=23  Identities=4%  Similarity=0.118  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+.|+|+.|+|||+|++.+++
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~   67 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACA   67 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            45788999999999999999887

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=97.19  E-value=0.0022  Score=64.10  Aligned_cols=98  Identities=16%  Similarity=0.143  Sum_probs=58.3

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~i  230 (425)
                      |.+.-.++.|.+..+++|.+.+...           -...+-+.++|++|+|||+||+.+.+  ....+|-...  -..+
T Consensus       140 p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~--~l~~~fi~i~--~s~l  215 (398)
T PTZ00454        140 PDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAH--HTTATFIRVV--GSEF  215 (398)
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH--hcCCCEEEEe--hHHH
Confidence            3444567889999998887765421           12456788999999999999999998  4444442110  0111


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ......         .....+...+.........+|++|++.
T Consensus       216 ~~k~~g---------e~~~~lr~lf~~A~~~~P~ILfIDEID  248 (398)
T PTZ00454        216 VQKYLG---------EGPRMVRDVFRLARENAPSIIFIDEVD  248 (398)
T ss_pred             HHHhcc---------hhHHHHHHHHHHHHhcCCeEEEEECHh
Confidence            111110         112223333333334678999999975

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.19  E-value=0.00077  Score=74.02  Aligned_cols=44  Identities=11%  Similarity=0.081  Sum_probs=37.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+.++.++++.|.....  .-+.++|.+|+|||++|+.+..
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~~--~n~lL~G~pGvGKT~l~~~la~  221 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRTK--NNPVLIGEPGVGKTAIVEGLAQ  221 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCCc--CceEEECCCCCCHHHHHHHHHH
Confidence            4699999999999999987653  2344899999999999988877

>CHL00181 cbbX CbbX; Provisional

Probab=97.18  E-value=0.0028  Score=60.71  Aligned_cols=45  Identities=11%  Similarity=0.091  Sum_probs=30.9

Q ss_pred             CcccchhhHHHHHHHH---hcC----------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLL---IEG----------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L---~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +++|.+..+++|.++.   .-.          ......+.++|++|+||||+|+.+.+
T Consensus        24 ~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         24 ELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            4788777777664442   211          11233477899999999999999966

>TIGR00763 lon ATP-dependent protease La

Probab=97.18  E-value=0.004  Score=67.93  Aligned_cols=89  Identities=15%  Similarity=0.237  Sum_probs=56.1

Q ss_pred             hHHHHHHHHHHHHHhccCCCCCCCCccCCC-----c-ccccCC--------CCCCCCCCcccchhhHHHHHHHHhc----
Q 040913          124 VGLHSKIIDIRNRMQQLPPGDNGFDINEQR-----D-ELIHLS--------SEGQPRLDISEFERAREEWFDLLIE----  185 (425)
Q Consensus       124 ~~i~~~i~~i~~~l~~i~~~~~~~~~~~~~-----~-~~~~~~--------~~~~~~~~~vGr~~~~~~l~~~L~~----  185 (425)
                      ..+.+++.+-..|++.+......|.+....     + ++...+        ....-+.+++|.+..+++|.+++..    
T Consensus       263 ~~~~~~~~~e~~~~~~~~~~~~~~~~~~~yl~~~~~ip~~~~~~~~~~~~~~~~~l~~~~~G~~~~k~~i~~~~~~~~~~  342 (775)
T TIGR00763       263 EEVKKVIEKELTKLSLLEPSSSEFTVTRNYLDWLTDLPWGKYSKENLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLR  342 (775)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHHHCCCCcccccchhhHHHHHHHhhhhcCChHHHHHHHHHHHHHHHhh
Confidence            345556666666777777666666533211     0 111111        1111234588999999999887642    


Q ss_pred             CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          186 GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       186 ~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.....++.++|++|+|||++|+.+.+
T Consensus       343 ~~~~~~~lll~GppG~GKT~lAk~iA~  369 (775)
T TIGR00763       343 GKMKGPILCLVGPPGVGKTSLGKSIAK  369 (775)
T ss_pred             cCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            222345788999999999999999988

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>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=97.17  E-value=0.00061  Score=61.86  Aligned_cols=100  Identities=16%  Similarity=0.102  Sum_probs=54.6

Q ss_pred             CCCCcccchhhHHHHHHHHh---cCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCC
Q 040913          165 PRLDISEFERAREEWFDLLI---EGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVT  241 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~---~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~  241 (425)
                      .-.+++|.+.-+..+.-++.   .....+.-+-.+|++|+||||||..+.+  +....|..               ..  
T Consensus        22 ~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~--e~~~~~~~---------------~s--   82 (233)
T PF05496_consen   22 SLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIAN--ELGVNFKI---------------TS--   82 (233)
T ss_dssp             SCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHH--HCT--EEE---------------EE--
T ss_pred             CHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHh--ccCCCeEe---------------cc--
Confidence            45679999988888654444   3344577788999999999999999999  55555531               00  


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCeEEEEecccCC-ChhhHHHHHhhC
Q 040913          242 VIIGEDYKLKKSILRDFLTNKKYFIALDDVCH-NIEIWDDLEEVL  285 (425)
Q Consensus       242 ~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~l~~~l  285 (425)
                      ........++...+.. + +++-+|.+|.+-. +...-+.+.++.
T Consensus        83 g~~i~k~~dl~~il~~-l-~~~~ILFIDEIHRlnk~~qe~Llpam  125 (233)
T PF05496_consen   83 GPAIEKAGDLAAILTN-L-KEGDILFIDEIHRLNKAQQEILLPAM  125 (233)
T ss_dssp             CCC--SCHHHHHHHHT----TT-EEEECTCCC--HHHHHHHHHHH
T ss_pred             chhhhhHHHHHHHHHh-c-CCCcEEEEechhhccHHHHHHHHHHh
Confidence            1111223455544443 3 3455788899941 334444444443

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.

>PRK12377 putative replication protein; Provisional

Probab=97.15  E-value=0.00046  Score=64.44  Aligned_cols=100  Identities=14%  Similarity=0.061  Sum_probs=50.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEe
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIAL  268 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVL  268 (425)
                      ...+.++|.+|+|||+||..+.+.  .......++++ ..+++..+......    ..+...+.    +.+ .+--||||
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~~~l~~~l~~~~~~----~~~~~~~l----~~l-~~~dLLiI  169 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTVPDVMSRLHESYDN----GQSGEKFL----QEL-CKVDLLVL  169 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEHHHHHHHHHHHHhc----cchHHHHH----HHh-cCCCEEEE
Confidence            456889999999999999999983  33222222333 33444433222110    01112222    222 35569999


Q ss_pred             cccCC-ChhhHH--HHHhhCCCC-CCCcEEEEecCC
Q 040913          269 DDVCH-NIEIWD--DLEEVLPDN-QNGSRVLITVIN  300 (425)
Q Consensus       269 Ddvw~-~~~~~~--~l~~~l~~~-~~gskIivTTR~  300 (425)
                      ||+.. ....|.  .+...+... .+.--+||||..
T Consensus       170 DDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl  205 (248)
T PRK12377        170 DEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNL  205 (248)
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCC
Confidence            99941 123342  333333221 112336777754

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

Probab=97.15  E-value=0.00099  Score=72.17  Aligned_cols=44  Identities=18%  Similarity=0.079  Sum_probs=37.0

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+++++++++.|.....  .-+.++|++|+|||++|+.+.+
T Consensus       182 ~~~igr~~ei~~~~~~L~~~~~--~n~lL~G~pG~GKT~l~~~la~  225 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRRKK--NNPLLVGEPGVGKTAIAEGLAL  225 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcCCC--CceEEECCCCCCHHHHHHHHHH
Confidence            4689999999999998877642  2345899999999999998887

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.14  E-value=0.0028  Score=65.44  Aligned_cols=130  Identities=8%  Similarity=0.028  Sum_probs=73.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccccc---chHHHHHHHHHHhCCCCCCC--
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFD---CLAWILDDIIRSLMPPSRVT--  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~---~~~wv~~~il~~l~~~~~~~--  241 (425)
                      .++||-+..++.|.+++..+. -...+-++|+.|+||||+|+.+.+.-.....+.   |..   ......+.......  
T Consensus        16 ~divGq~~v~~~L~~~~~~~~-l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~---C~~C~~i~~g~~~d~~   91 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY-LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCND---CENCREIDEGRFPDLF   91 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCC---CHHHHHHhcCCCceEE
Confidence            568999999999999997764 245677999999999999988776221111110   000   00011111110000  


Q ss_pred             --c-cCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          242 --V-IIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       242 --~-~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                        + ......+++.+.+...    ..++.-++|+|++.. +....+.+...+..-...+++|++|.+
T Consensus        92 eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~a~naLLk~LEepp~~~~fIlattd  158 (509)
T PRK14958         92 EVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSHVKFILATTD  158 (509)
T ss_pred             EEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHHHHHHHHHHHhccCCCeEEEEEECC
Confidence              0 0112333333222211    135667899999963 446777777777665556776655543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.14  E-value=0.0017  Score=68.34  Aligned_cols=134  Identities=13%  Similarity=0.058  Sum_probs=74.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc---ccchHHHHHHHHHHhCCCCCCC-
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY---FDCLAWILDDIIRSLMPPSRVT-  241 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~---F~~~~wv~~~il~~l~~~~~~~-  241 (425)
                      -.++||.+..+..|.+.+..+. -.+.+-++|..|+||||+|+.+.+.-.....   ..|..   ....+.+....... 
T Consensus        15 f~divGQe~vv~~L~~~l~~~r-l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~---C~~C~~i~~g~~~D~   90 (647)
T PRK07994         15 FAEVVGQEHVLTALANALDLGR-LHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGE---CDNCREIEQGRFVDL   90 (647)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCC---CHHHHHHHcCCCCCc
Confidence            3568999999999998887764 3455678999999999999988763211100   01100   01112221111000 


Q ss_pred             -ccC---CCCHHHHH---HHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC-hhH
Q 040913          242 -VII---GEDYKLKK---SILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN-PSL  303 (425)
Q Consensus       242 -~~~---~~~~~~l~---~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~-~~v  303 (425)
                       ..+   ....+++.   ..+... ..+++-++|+|++.. +....+.+...+-.-....++|.+|.+ ..+
T Consensus        91 ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~a~NALLKtLEEPp~~v~FIL~Tt~~~kL  162 (647)
T PRK07994         91 IEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKL  162 (647)
T ss_pred             eeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHHHHHHHHHHHHcCCCCeEEEEecCCcccc
Confidence             000   12233332   222211 246777999999953 456777777777655556665554444 443

>PRK07261 topology modulation protein; Provisional

Probab=97.13  E-value=0.0007  Score=59.64  Aligned_cols=65  Identities=18%  Similarity=0.192  Sum_probs=42.5

Q ss_pred             EEEEEecCCCchHHHHHHhhcCcccc-ccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecc
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVK-FYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDD  270 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~-~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDd  270 (425)
                      -|.|+|++|+||||||+.+.....+. -+.|...|-            .  +....+.++....+.+.+.+.+  .|+|.
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~------------~--~~~~~~~~~~~~~~~~~~~~~~--wIidg   65 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQ------------P--NWQERDDDDMIADISNFLLKHD--WIIDG   65 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEec------------c--ccccCCHHHHHHHHHHHHhCCC--EEEcC
Confidence            47899999999999999987632221 123333330            0  1223455677888888887766  68888


Q ss_pred             cC
Q 040913          271 VC  272 (425)
Q Consensus       271 vw  272 (425)
                      .-
T Consensus        66 ~~   67 (171)
T PRK07261         66 NY   67 (171)
T ss_pred             cc
Confidence            75

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.12  E-value=0.003  Score=69.33  Aligned_cols=117  Identities=14%  Similarity=0.113  Sum_probs=65.5

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhcC----ccccccccchHHHHHHHHHHhC
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYNN----NHVKFYFDCLAWILDDIIRSLM  235 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~----~~~~~~F~~~~wv~~~il~~l~  235 (425)
                      ..++|.+..++.+.+.+...       .....++.++|+.|+|||.||+.+...    ..---.|++.-|.-..-...+.
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~~~l~  645 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTVSRLK  645 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhhcccc
Confidence            46889999999998887532       234568899999999999999776542    1111123333332111111221


Q ss_pred             CCCCCCccCCC-CHHHHHHHHHHHhcCCeEEEEecccCC-ChhhHHHHHhhCCCC
Q 040913          236 PPSRVTVIIGE-DYKLKKSILRDFLTNKKYFIALDDVCH-NIEIWDDLEEVLPDN  288 (425)
Q Consensus       236 ~~~~~~~~~~~-~~~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~  288 (425)
                      ....  +.... ....+...+++   ....+|+||++.. +.+.++.+...+..+
T Consensus       646 g~~~--gyvg~~~~g~L~~~v~~---~p~svvllDEieka~~~v~~~Llq~ld~g  695 (852)
T TIGR03345       646 GSPP--GYVGYGEGGVLTEAVRR---KPYSVVLLDEVEKAHPDVLELFYQVFDKG  695 (852)
T ss_pred             CCCC--CcccccccchHHHHHHh---CCCcEEEEechhhcCHHHHHHHHHHhhcc
Confidence            1111  11111 11223333332   4556999999963 346677777666543

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.12  E-value=0.0032  Score=64.34  Aligned_cols=136  Identities=14%  Similarity=0.058  Sum_probs=73.9

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC------ccccccccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN------NHVKFYFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~------~~~~~~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+...+.|.+.+..+. -...+-+.|+.|+||||+|+.+.+.      +....+=.|....  .|........-
T Consensus        12 f~dliGQe~vv~~L~~a~~~~r-i~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~--~i~~~~~~Dv~   88 (491)
T PRK14964         12 FKDLVGQDVLVRILRNAFTLNK-IPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCI--SIKNSNHPDVI   88 (491)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHH--HHhccCCCCEE
Confidence            3568999998888888887654 2347889999999999999887651      1111111111111  11110000000


Q ss_pred             C-CccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec-CChhHH
Q 040913          240 V-TVIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV-INPSLL  304 (425)
Q Consensus       240 ~-~~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT-R~~~va  304 (425)
                      . ........+++...+...    +.++.-++|+|++.. +....+.+...+..-.+.+++|++| ....+.
T Consensus        89 eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~A~NaLLK~LEePp~~v~fIlatte~~Kl~  160 (491)
T PRK14964         89 EIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIP  160 (491)
T ss_pred             EEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHHHHHHHHHHHhCCCCCeEEEEEeCChHHHH
Confidence            0 000112333333222221    235667899999952 4456777877777656667766555 444443

>PRK05642 DNA replication initiation factor; Validated

Probab=97.12  E-value=0.0011  Score=61.65  Aligned_cols=23  Identities=9%  Similarity=0.183  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+.|+|..|+|||.|++.+.+
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~   67 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACL   67 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            35678999999999999999987

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.09  E-value=0.0047  Score=65.09  Aligned_cols=130  Identities=10%  Similarity=0.046  Sum_probs=72.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc--------------cccchHHHHHHHHH
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF--------------YFDCLAWILDDIIR  232 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~--------------~F~~~~wv~~~il~  232 (425)
                      .+++|.+..+..|.+.+..+. -...+-++|+.|+||||+|..+.+.-....              +=.|...      +
T Consensus        16 ~eivGQe~i~~~L~~~i~~~r-i~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC------~   88 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDR-VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESC------R   88 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHH------H
Confidence            568899999999888887653 345578999999999999987765211111              0011111      1


Q ss_pred             HhCCCCCCC-----ccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec-CCh
Q 040913          233 SLMPPSRVT-----VIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV-INP  301 (425)
Q Consensus       233 ~l~~~~~~~-----~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT-R~~  301 (425)
                      .+.......     .......+++...+...    ..+++-++|+|++.. +....+.|...+..-...+.+|++| +..
T Consensus        89 ~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEePp~~tv~IL~t~~~~  168 (620)
T PRK14954         89 DFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELH  168 (620)
T ss_pred             HHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChh
Confidence            110000000     00112234444333222    235666899999862 3456777877776655556655444 433


Q ss_pred             hH
Q 040913          302 SL  303 (425)
Q Consensus       302 ~v  303 (425)
                      .+
T Consensus       169 kL  170 (620)
T PRK14954        169 KI  170 (620)
T ss_pred             hh
Confidence            33

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.09  E-value=0.0023  Score=61.16  Aligned_cols=45  Identities=9%  Similarity=0.077  Sum_probs=29.4

Q ss_pred             CcccchhhHHHHHHHHh---cC--------C--CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLI---EG--------P--IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~---~~--------~--~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.+..+++|.++..   ..        .  ....-+.++|++|+||||+|+.+..
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~   80 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQ   80 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHH
Confidence            37887777777654322   11        0  1122577899999999999966654

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.

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.08  E-value=0.0026  Score=63.22  Aligned_cols=119  Identities=10%  Similarity=0.082  Sum_probs=68.3

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc------ccccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK------FYFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~------~~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+...+.+.+.+..+. -.+.+-++|+.|+||||+|+.+.+.-...      ..|...+.       .+    .
T Consensus        16 ~~~iig~~~~~~~l~~~i~~~~-~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~-------~l----~   83 (367)
T PRK14970         16 FDDVVGQSHITNTLLNAIENNH-LAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIF-------EL----D   83 (367)
T ss_pred             HHhcCCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceE-------Ee----c
Confidence            3567899999999999998753 34578899999999999999886621110      11111000       00    0


Q ss_pred             CCccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec
Q 040913          240 VTVIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV  298 (425)
Q Consensus       240 ~~~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT  298 (425)
                        .....+.+++...+...    ..+++-+|++|++.. +...++.+...+......+.+|++|
T Consensus        84 --~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~~~~~~ll~~le~~~~~~~~Il~~  145 (367)
T PRK14970         84 --AASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILAT  145 (367)
T ss_pred             --cccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCHHHHHHHHHHHhCCCCceEEEEEe
Confidence              00111223333222221    234566899999852 3345677766665444455555555

>PRK06620 hypothetical protein; Validated

Probab=97.08  E-value=0.0031  Score=57.66  Aligned_cols=51  Identities=16%  Similarity=-0.116  Sum_probs=31.5

Q ss_pred             CCCCCCcccchh--hHHHHHHHHhcCCCCc--EEEEEEecCCCchHHHHHHhhcC
Q 040913          163 GQPRLDISEFER--AREEWFDLLIEGPIGL--SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       163 ~~~~~~~vGr~~--~~~~l~~~L~~~~~~~--~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..++-++|-.+  ....+.++-.....+.  +.+-|+|++|+|||+|++.+.+.
T Consensus        13 ~tfd~Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         13 YHPDEFIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             CCchhhEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHHHhc
Confidence            344555667522  2333344432211112  56889999999999999998874

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=97.07  E-value=0.039  Score=59.03  Aligned_cols=115  Identities=19%  Similarity=0.282  Sum_probs=74.3

Q ss_pred             CcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhh----cCccccccccchHHH-HHHHHHHhC
Q 040913          168 DISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTY----NNNHVKFYFDCLAWI-LDDIIRSLM  235 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~----~~~~~~~~F~~~~wv-~~~il~~l~  235 (425)
                      .++|.+.....+.+.+...       +...++...+|+.|||||.||+.+.    .++.---.||..=+. -..+-+-++
T Consensus       492 rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVSrLIG  571 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIG  571 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHHHHhC
Confidence            4899999999998887643       3456788889999999999887754    433333346665555 333334444


Q ss_pred             CCCCCCccCCCCHHHHHHHHHHHhcCCeE-EEEecccCC-ChhhHHHHHhhCCCC
Q 040913          236 PPSRVTVIIGEDYKLKKSILRDFLTNKKY-FIALDDVCH-NIEIWDDLEEVLPDN  288 (425)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~l~~kr~-LlVLDdvw~-~~~~~~~l~~~l~~~  288 (425)
                      .+.+   ....+.   -..|-+.++.|.| +|.||.|.- .++..+-+...|.++
T Consensus       572 aPPG---YVGyee---GG~LTEaVRr~PySViLlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         572 APPG---YVGYEE---GGQLTEAVRRKPYSVILLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             CCCC---Cceecc---ccchhHhhhcCCCeEEEechhhhcCHHHHHHHHHHhcCC
Confidence            4433   111111   2245556667877 888999962 346777788887654

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.07  E-value=0.005  Score=60.93  Aligned_cols=134  Identities=14%  Similarity=-0.006  Sum_probs=75.9

Q ss_pred             CCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc----c-c-----------cchHHHHH
Q 040913          165 PRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF----Y-F-----------DCLAWILD  228 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~-F-----------~~~~wv~~  228 (425)
                      ...+++|.+..++.+.+.+..+. -...+-++|+.|+||+|+|..+.+.--...    . +           .|...  +
T Consensus        17 ~~~~iiGq~~~~~~L~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c--~   93 (365)
T PRK07471         17 ETTALFGHAAAEAALLDAYRSGR-LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVA--R   93 (365)
T ss_pred             chhhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHH--H
Confidence            34678999999999999888764 345688999999999999966544210000    0 0           11111  0


Q ss_pred             HHHHHh-------CCCCCCCc---cCCCCHHHHHHHHHHHhc-----CCeEEEEecccCC-ChhhHHHHHhhCCCCCCCc
Q 040913          229 DIIRSL-------MPPSRVTV---IIGEDYKLKKSILRDFLT-----NKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGS  292 (425)
Q Consensus       229 ~il~~l-------~~~~~~~~---~~~~~~~~l~~~l~~~l~-----~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gs  292 (425)
                      .|...-       ........   ......++ ...+.+.+.     +++.++|+||+.. +....+.+...+..-..++
T Consensus        94 ~i~~~~HPDl~~i~~~~~~~~~~~~~~I~Vdq-iR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEepp~~~  172 (365)
T PRK07471         94 RIAAGAHGGLLTLERSWNEKGKRLRTVITVDE-VRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEPPARS  172 (365)
T ss_pred             HHHccCCCCeEEEecccccccccccccccHHH-HHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcCCCCe
Confidence            010000       00000000   01123344 233444432     5667999999963 5577777777776655567


Q ss_pred             EEEEecCChh
Q 040913          293 RVLITVINPS  302 (425)
Q Consensus       293 kIivTTR~~~  302 (425)
                      .+|++|.+.+
T Consensus       173 ~~IL~t~~~~  182 (365)
T PRK07471        173 LFLLVSHAPA  182 (365)
T ss_pred             EEEEEECCch
Confidence            7777776654

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

Probab=97.06  E-value=0.0045  Score=67.11  Aligned_cols=113  Identities=15%  Similarity=0.231  Sum_probs=64.6

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhcCcccccc---ccchHHHH-HHHHHHhC
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY---FDCLAWIL-DDIIRSLM  235 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~---F~~~~wv~-~~il~~l~  235 (425)
                      ..++|.+..++.|.+.+...       .....++.++|+.|+|||+||+.+...  ....   |++.-+.- ..+-+-++
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~--l~~~~~~~d~se~~~~~~~~~lig  531 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEA--LGVHLERFDMSEYMEKHTVSRLIG  531 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHH--hcCCeEEEeCchhhhcccHHHHhc
Confidence            45788888888888877642       223567889999999999999999873  2221   23322321 11222222


Q ss_pred             CCCCCCccCCCCHHHHHHHHHHHhcC-CeEEEEecccCC-ChhhHHHHHhhCCC
Q 040913          236 PPSRVTVIIGEDYKLKKSILRDFLTN-KKYFIALDDVCH-NIEIWDDLEEVLPD  287 (425)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~l~~-kr~LlVLDdvw~-~~~~~~~l~~~l~~  287 (425)
                      .+..   ....+..   ..+.+.++. ...+|+||++.. +.+.++.+...+..
T Consensus       532 ~~~g---yvg~~~~---~~l~~~~~~~p~~VvllDEieka~~~~~~~Ll~~ld~  579 (731)
T TIGR02639       532 APPG---YVGFEQG---GLLTEAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDY  579 (731)
T ss_pred             CCCC---Ccccchh---hHHHHHHHhCCCeEEEEechhhcCHHHHHHHHHhhcc
Confidence            2221   1111111   123333333 345999999963 34667777766653

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=97.04  E-value=0.00045  Score=63.81  Aligned_cols=34  Identities=24%  Similarity=0.288  Sum_probs=26.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchHHH
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI  226 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv  226 (425)
                      --++|+|..|+|||||...+..  .....|+.+.++
T Consensus        14 fr~viIG~sGSGKT~li~~lL~--~~~~~f~~I~l~   47 (241)
T PF04665_consen   14 FRMVIIGKSGSGKTTLIKSLLY--YLRHKFDHIFLI   47 (241)
T ss_pred             ceEEEECCCCCCHHHHHHHHHH--hhcccCCEEEEE
Confidence            3577999999999999998887  466667555444

This is thought to be an ATPase involved in viral DNA packaging [].

>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=97.03  E-value=0.0015  Score=60.02  Aligned_cols=47  Identities=13%  Similarity=0.002  Sum_probs=30.3

Q ss_pred             CCCcccchhh-HHHHHHHHhcC-CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERA-REEWFDLLIEG-PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~-~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++-++|-.+. .-.....+... ......+-|+|..|+|||.|.+++++
T Consensus         8 dnfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~   56 (219)
T PF00308_consen    8 DNFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIAN   56 (219)
T ss_dssp             CCS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHH
T ss_pred             ccCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHH
Confidence            4445674333 33444445443 33455678999999999999999998

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.

>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=97.01  E-value=0.00052  Score=56.40  Aligned_cols=22  Identities=23%  Similarity=0.336  Sum_probs=20.2

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ||.|.|++|+||||+|+.+.+.
T Consensus         1 vI~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            6899999999999999999883

...

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.95  E-value=0.0037  Score=62.66  Aligned_cols=94  Identities=26%  Similarity=0.293  Sum_probs=60.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHh---cCCeEEEEe
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFL---TNKKYFIAL  268 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l---~~kr~LlVL  268 (425)
                      ++.|.|+-++|||||++.+...  ..+.   .+++          ..   .....+...+.+.+..+.   ..++.+|+|
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~----------~~---~d~~~~~~~l~d~~~~~~~~~~~~~~yifL  100 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKG--LLEE---IIYI----------NF---DDLRLDRIELLDLLRAYIELKEREKSYIFL  100 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhh--CCcc---eEEE----------Ee---cchhcchhhHHHHHHHHHHhhccCCceEEE
Confidence            9999999999999999776662  2221   0000          00   000112222222233222   237789999


Q ss_pred             cccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          269 DDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       269 Ddvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      |.|. ....|......+.+.++. +|++|+-+.....
T Consensus       101 DEIq-~v~~W~~~lk~l~d~~~~-~v~itgsss~ll~  135 (398)
T COG1373         101 DEIQ-NVPDWERALKYLYDRGNL-DVLITGSSSSLLS  135 (398)
T ss_pred             eccc-CchhHHHHHHHHHccccc-eEEEECCchhhhc
Confidence            9999 999999988888887766 8999988766543

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.92  E-value=0.0062  Score=54.35  Aligned_cols=123  Identities=11%  Similarity=0.032  Sum_probs=61.6

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc---ccchHHHHHHHHHHhCCC-CC--CCccCCCCHHHH
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY---FDCLAWILDDIIRSLMPP-SR--VTVIIGEDYKLK  251 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~---F~~~~wv~~~il~~l~~~-~~--~~~~~~~~~~~l  251 (425)
                      .+.+.+..+. -...+.++|+.|+||||+|..+.+.-.-...   -.|........+..-..+ ..  .........+++
T Consensus         3 ~l~~~i~~~~-~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i   81 (188)
T TIGR00678         3 QLKRALEKGR-LAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQV   81 (188)
T ss_pred             HHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHH
Confidence            3455555443 3467889999999999999887652111100   011110000000000000 00  000011233444


Q ss_pred             HHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          252 KSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       252 ~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      ...+...    ..+.+-++|+|++.. +....+.+...+......+.+|++|++.
T Consensus        82 ~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~  136 (188)
T TIGR00678        82 RELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSP  136 (188)
T ss_pred             HHHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            3222222    135667899999852 3456777888877655567777777653

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.91  E-value=0.0008  Score=65.63  Aligned_cols=48  Identities=15%  Similarity=0.158  Sum_probs=40.9

Q ss_pred             CCCcccchhhHHHHHHHHhcC----CCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEG----PIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+++|.++.++++++++...    ....+++.++|++|+||||||+.+.+.
T Consensus        50 ~~~~~G~~~~i~~lv~~l~~~a~g~~~~r~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       50 DHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             chhccCcHHHHHHHHHHHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            337999999999999999763    235689999999999999999998773

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK09183 transposase/IS protein; Provisional

Probab=96.90  E-value=0.00052  Score=64.67  Aligned_cols=22  Identities=27%  Similarity=0.289  Sum_probs=19.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+.|+|++|+|||+||..+.+
T Consensus       103 ~~v~l~Gp~GtGKThLa~al~~  124 (259)
T PRK09183        103 ENIVLLGPSGVGKTHLAIALGY  124 (259)
T ss_pred             CeEEEEeCCCCCHHHHHHHHHH
Confidence            4577999999999999999866

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=96.90  E-value=0.0046  Score=67.27  Aligned_cols=133  Identities=13%  Similarity=0.081  Sum_probs=74.7

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc--c-cchHHHHHHHHHHhCCC--CCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY--F-DCLAWILDDIIRSLMPP--SRVT  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~--F-~~~~wv~~~il~~l~~~--~~~~  241 (425)
                      .+++|.+..++.|.+++..+. -.+.+.++|..|+||||+|+.+.+.-.....  . .|..-   .-.+.+...  ....
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r-i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C---~sC~~~~~g~~~~~d   90 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR-INHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGEC---DSCVALAPGGPGSLD   90 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCccc---HHHHHHHcCCCCCCc
Confidence            468999999999999988764 2356789999999999999888653211111  0 11000   000011000  0000


Q ss_pred             --cc---CCCCHHHHHHHHHHH-----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec-CChhHH
Q 040913          242 --VI---IGEDYKLKKSILRDF-----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV-INPSLL  304 (425)
Q Consensus       242 --~~---~~~~~~~l~~~l~~~-----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT-R~~~va  304 (425)
                        ..   .....+++.+ +.+.     ..++.-++|||++.. +...++.|...+..-...+.+|++| ....+.
T Consensus        91 v~eidaas~~~Vd~iR~-l~~~~~~~p~~~~~KV~IIDEad~lt~~a~NaLLK~LEEpP~~~~fIl~tt~~~kLl  164 (824)
T PRK07764         91 VTEIDAASHGGVDDARE-LRERAFFAPAESRYKIFIIDEAHMVTPQGFNALLKIVEEPPEHLKFIFATTEPDKVI  164 (824)
T ss_pred             EEEecccccCCHHHHHH-HHHHHHhchhcCCceEEEEechhhcCHHHHHHHHHHHhCCCCCeEEEEEeCChhhhh
Confidence              00   1122333332 2222     235666899999963 4577788888887665566655554 444443

>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=96.88  E-value=0.00012  Score=66.12  Aligned_cols=38  Identities=18%  Similarity=0.140  Sum_probs=25.1

Q ss_pred             cchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          171 EFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       171 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..+-...++.|..    ..++.+.|++|.|||.||....-
T Consensus         4 p~~~~Q~~~~~al~~----~~~v~~~G~AGTGKT~LA~a~Al   41 (205)
T PF02562_consen    4 PKNEEQKFALDALLN----NDLVIVNGPAGTGKTFLALAAAL   41 (205)
T ss_dssp             --SHHHHHHHHHHHH-----SEEEEE--TTSSTTHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh----CCeEEEECCCCCcHHHHHHHHHH
Confidence            344555666777773    55888999999999999976554

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

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.86  E-value=0.0079  Score=63.47  Aligned_cols=130  Identities=12%  Similarity=0.080  Sum_probs=73.1

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc---ccc-chHHHHHHHHHHhCCCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF---YFD-CLAWILDDIIRSLMPPSRVT  241 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F~-~~~wv~~~il~~l~~~~~~~  241 (425)
                      -.+++|.+..++.|.+++..+. -.+.+-++|+.|+||||+|+.+.+.-....   .+. |.   ..+..+.+.......
T Consensus        15 ~~eiiGq~~~~~~L~~~i~~~~-i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~---~c~~c~~i~~~~~~d   90 (585)
T PRK14950         15 FAELVGQEHVVQTLRNAIAEGR-VAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCG---TCEMCRAIAEGSAVD   90 (585)
T ss_pred             HHHhcCCHHHHHHHHHHHHhCC-CceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCc---cCHHHHHHhcCCCCe
Confidence            3578999999999988887654 345667899999999999998876321111   111 10   011122222111100


Q ss_pred             ----cc-CCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          242 ----VI-IGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       242 ----~~-~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                          +. .....+++.+ +.+.+     .+++-++|+|++.. +.+..+.|...+......+.+|++|.+
T Consensus        91 ~~~i~~~~~~~vd~ir~-ii~~~~~~p~~~~~kVvIIDEa~~L~~~a~naLLk~LEepp~~tv~Il~t~~  159 (585)
T PRK14950         91 VIEMDAASHTSVDDARE-IIERVQFRPALARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTE  159 (585)
T ss_pred             EEEEeccccCCHHHHHH-HHHHHhhCcccCCeEEEEEeChHhCCHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence                00 1122333322 22222     25677899999852 345677777776655556666666543

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

Probab=96.86  E-value=0.0019  Score=54.66  Aligned_cols=108  Identities=15%  Similarity=0.043  Sum_probs=61.4

Q ss_pred             ccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccc-cccccchHHHHHHHHHHhCCCCCCCccCCCCH
Q 040913          170 SEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHV-KFYFDCLAWILDDIIRSLMPPSRVTVIIGEDY  248 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~  248 (425)
                      ||.-..++++.+.+..-......|.|.|..|+||+++|+.++..... ...|...-                  ....+ 
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~------------------~~~~~-   61 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVID------------------CASLP-   61 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCC------------------HHCTC-
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEec------------------hhhCc-
Confidence            46666677777766653223455789999999999999999985332 22332210                  01112 


Q ss_pred             HHHHHHHHHHhcCCeEEEEecccCC-ChhhHHHHHhhCCC-CCCCcEEEEecCChh
Q 040913          249 KLKKSILRDFLTNKKYFIALDDVCH-NIEIWDDLEEVLPD-NQNGSRVLITVINPS  302 (425)
Q Consensus       249 ~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~-~~~gskIivTTR~~~  302 (425)
                         .+.+..   -+.--|+|+|+.. +.+....+...+.. .....|+|.||...-
T Consensus        62 ---~~~l~~---a~~gtL~l~~i~~L~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l  111 (138)
T PF14532_consen   62 ---AELLEQ---AKGGTLYLKNIDRLSPEAQRRLLDLLKRQERSNVRLIASSSQDL  111 (138)
T ss_dssp             ---HHHHHH---CTTSEEEEECGCCS-HHHHHHHHHHHHHCTTTTSEEEEEECC-C
T ss_pred             ---HHHHHH---cCCCEEEECChHHCCHHHHHHHHHHHHhcCCCCeEEEEEeCCCH
Confidence               111111   2555678999963 34555556555542 255789999987643

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.84  E-value=0.0018  Score=65.76  Aligned_cols=48  Identities=10%  Similarity=-0.030  Sum_probs=30.5

Q ss_pred             CCCCcccchhhH--HHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          165 PRLDISEFERAR--EEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       165 ~~~~~vGr~~~~--~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .++.++|-....  ....+....+. ...-+-|+|.+|+|||+|++.+.+.
T Consensus       104 FdnFv~g~~n~~a~~~~~~~~~~~~-~~n~l~lyG~~G~GKTHLl~ai~~~  153 (440)
T PRK14088        104 FENFVVGPGNSFAYHAALEVAKNPG-RYNPLFIYGGVGLGKTHLLQSIGNY  153 (440)
T ss_pred             ccccccCCchHHHHHHHHHHHhCcC-CCCeEEEEcCCCCcHHHHHHHHHHH
Confidence            344455744432  23333333222 2445889999999999999999983

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.84  E-value=0.0071  Score=59.51  Aligned_cols=49  Identities=16%  Similarity=0.075  Sum_probs=40.0

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          163 GQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.....++|.+...+.+...+..+. -...+-|.|+.|+||||+|..+.+
T Consensus        19 P~~~~~l~Gh~~a~~~L~~a~~~gr-l~ha~L~~G~~G~GKttlA~~lA~   67 (351)
T PRK09112         19 PSENTRLFGHEEAEAFLAQAYREGK-LHHALLFEGPEGIGKATLAFHLAN   67 (351)
T ss_pred             CCchhhccCcHHHHHHHHHHHHcCC-CCeeEeeECCCCCCHHHHHHHHHH
Confidence            3445678999999999999998764 345688999999999999987655

>PRK06696 uridine kinase; Validated

Probab=96.83  E-value=0.0015  Score=60.10  Aligned_cols=41  Identities=20%  Similarity=0.108  Sum_probs=33.9

Q ss_pred             chhhHHHHHHHHhc-CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          172 FERAREEWFDLLIE-GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       172 r~~~~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      |..-.++|.+.+.. ......+|+|.|.+|+||||||+.+.+
T Consensus         3 ~~~~~~~la~~~~~~~~~~~~iI~I~G~sgsGKSTlA~~L~~   44 (223)
T PRK06696          3 RKQLIKELAEHILTLNLTRPLRVAIDGITASGKTTFADELAE   44 (223)
T ss_pred             HHHHHHHHHHHHHHhCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            56667788887765 344688999999999999999999887

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

Probab=96.82  E-value=0.00023  Score=63.12  Aligned_cols=71  Identities=18%  Similarity=0.268  Sum_probs=40.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEe
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIAL  268 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVL  268 (425)
                      ..-+.++|..|+|||.||..+.+.. +...+. +.++ ..+++..+.....     ..........    +. +-=||||
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~-~~~g~~-v~f~~~~~L~~~l~~~~~-----~~~~~~~~~~----l~-~~dlLil  114 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEA-IRKGYS-VLFITASDLLDELKQSRS-----DGSYEELLKR----LK-RVDLLIL  114 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHH-HHTT---EEEEEHHHHHHHHHCCHC-----CTTHCHHHHH----HH-TSSCEEE
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHh-ccCCcc-eeEeecCceecccccccc-----ccchhhhcCc----cc-cccEecc
Confidence            3458899999999999999988732 112222 1223 5666666654322     1122232222    22 3357889


Q ss_pred             cccC
Q 040913          269 DDVC  272 (425)
Q Consensus       269 Ddvw  272 (425)
                      ||+.
T Consensus       115 DDlG  118 (178)
T PF01695_consen  115 DDLG  118 (178)
T ss_dssp             ETCT
T ss_pred             cccc
Confidence            9996

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.81  E-value=0.0066  Score=61.91  Aligned_cols=46  Identities=13%  Similarity=-0.073  Sum_probs=37.8

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.+..+..+.+++..+. -...+-++|+.|+||||+|+.+.+
T Consensus        16 ~~diiGq~~~v~~L~~~i~~~~-i~ha~Lf~Gp~G~GKtt~A~~lAk   61 (451)
T PRK06305         16 FSEILGQDAVVAVLKNALRFNR-AAHAYLFSGIRGTGKTTLARIFAK   61 (451)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CceEEEEEcCCCCCHHHHHHHHHH
Confidence            3578999999999999987654 245677899999999999988765

>TIGR03689 pup_AAA proteasome ATPase

Probab=96.80  E-value=0.0023  Score=65.64  Aligned_cols=51  Identities=20%  Similarity=0.096  Sum_probs=38.7

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          163 GQPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-.++.|.+..+++|.+.+..+           -...+-+.++|++|+|||++|+.+++.
T Consensus       178 ~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       178 DVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             CCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            344456788999999988876421           123456889999999999999999983

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.80  E-value=0.012  Score=64.73  Aligned_cols=116  Identities=16%  Similarity=0.157  Sum_probs=64.2

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhcCcc-ccc---cccchHHHHHHHHHHhC
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYNNNH-VKF---YFDCLAWILDDIIRSLM  235 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~-~~~---~F~~~~wv~~~il~~l~  235 (425)
                      ..++|.+..++.+...+...       +....++.++|+.|+|||+||+.+.+.-- -..   .|++.-+.-......+.
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~~~~Li  647 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLV  647 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhhHHHHh
Confidence            45889999988888877642       22345788999999999999999886211 011   12333232111222232


Q ss_pred             CCCCCCccCCCCHHHHHHHHHHHhcC-CeEEEEecccCC-ChhhHHHHHhhCCC
Q 040913          236 PPSRVTVIIGEDYKLKKSILRDFLTN-KKYFIALDDVCH-NIEIWDDLEEVLPD  287 (425)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~l~~-kr~LlVLDdvw~-~~~~~~~l~~~l~~  287 (425)
                      ....  +....+..   ..+.+.++. ..-+|+|||+.. +...++.+...+..
T Consensus       648 G~~p--gy~g~~~~---g~l~~~v~~~p~~vLllDEieka~~~v~~~Ll~ile~  696 (857)
T PRK10865        648 GAPP--GYVGYEEG---GYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDD  696 (857)
T ss_pred             CCCC--cccccchh---HHHHHHHHhCCCCeEEEeehhhCCHHHHHHHHHHHhh
Confidence            2211  11111111   123333332 335999999963 34677777666643

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.79  E-value=0.0031  Score=69.46  Aligned_cols=44  Identities=11%  Similarity=0.078  Sum_probs=36.8

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+.++.++++.|.....+  -+.++|++|+|||++|..+..
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~~~--n~lL~G~pGvGKT~l~~~la~  216 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRTKN--NPVLIGEPGVGKTAIVEGLAQ  216 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCCCC--ceEEEcCCCCCHHHHHHHHHH
Confidence            45899999999999999876533  334799999999999998877

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.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.79  E-value=0.01  Score=61.40  Aligned_cols=98  Identities=15%  Similarity=0.194  Sum_probs=55.6

Q ss_pred             CCCCCCCcccchhhHHHHHHHHh---cC-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLI---EG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDII  231 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il  231 (425)
                      +...-.+++|.+..++++.+++.   ..       ....+-+.++|++|+|||+||+.+.+.  ..-.|-..-  ..++.
T Consensus        50 ~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~--~~~~~~~i~--~~~~~  125 (495)
T TIGR01241        50 PKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE--AGVPFFSIS--GSDFV  125 (495)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH--cCCCeeecc--HHHHH
Confidence            34445678898877766655433   21       122345778999999999999999883  333331100  01111


Q ss_pred             HHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       232 ~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ....         ......+...+........++|++||+.
T Consensus       126 ~~~~---------g~~~~~l~~~f~~a~~~~p~Il~iDEid  157 (495)
T TIGR01241       126 EMFV---------GVGASRVRDLFEQAKKNAPCIIFIDEID  157 (495)
T ss_pred             HHHh---------cccHHHHHHHHHHHHhcCCCEEEEechh
Confidence            1110         1122333444444445567899999994

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=96.79  E-value=0.0018  Score=67.50  Aligned_cols=23  Identities=22%  Similarity=0.219  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+.|+|..|+|||.|++.+.+
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~  336 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGH  336 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHH
Confidence            34588999999999999999998

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=96.78  E-value=0.0019  Score=60.83  Aligned_cols=80  Identities=9%  Similarity=0.230  Sum_probs=49.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchH-HH--------HHHHHHHhCCCCCCC-------ccCCCCH-----H
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLA-WI--------LDDIIRSLMPPSRVT-------VIIGEDY-----K  249 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~-wv--------~~~il~~l~~~~~~~-------~~~~~~~-----~  249 (425)
                      .-++|.|..|+|||||++.+++  .++.+|+..+ ++        ..++++.+.......       ..+....     .
T Consensus        70 Qr~~If~~~G~GKTtLa~~i~~--~i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~  147 (274)
T cd01133          70 GKIGLFGGAGVGKTVLIMELIN--NIAKAHGGYSVFAGVGERTREGNDLYHEMKESGVLSKTALVYGQMNEPPGARARVA  147 (274)
T ss_pred             CEEEEecCCCCChhHHHHHHHH--HHHhcCCCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            4578999999999999999999  5554554333 33        566666664432211       0111111     1


Q ss_pred             HHHHHHHHHh--c-CCeEEEEecccC
Q 040913          250 LKKSILRDFL--T-NKKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~l~~~l--~-~kr~LlVLDdvw  272 (425)
                      ...-.+.+++  + ++.+||++||+-
T Consensus       148 ~~a~~~AEyfr~~~g~~Vl~~~Dslt  173 (274)
T cd01133         148 LTGLTMAEYFRDEEGQDVLLFIDNIF  173 (274)
T ss_pred             HHHHHHHHHHHHhcCCeEEEEEeChh
Confidence            2233455555  3 899999999994

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=96.77  E-value=0.024  Score=59.21  Aligned_cols=88  Identities=14%  Similarity=0.219  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHHHHhccCCCCCCCCccCCC-----c-ccccC--------CCCCCCCCCcccchhhHHHHHHHHhc----C
Q 040913          125 GLHSKIIDIRNRMQQLPPGDNGFDINEQR-----D-ELIHL--------SSEGQPRLDISEFERAREEWFDLLIE----G  186 (425)
Q Consensus       125 ~i~~~i~~i~~~l~~i~~~~~~~~~~~~~-----~-~~~~~--------~~~~~~~~~~vGr~~~~~~l~~~L~~----~  186 (425)
                      .+-+-+.+=..+++.+......|++..+-     + +|...        .+...-+.+-+|.++-+++|++.+--    +
T Consensus       355 ~v~kv~~eEl~kL~~le~~~sEfnvtrNYLdwlt~LPWgk~S~En~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~kLrg  434 (906)
T KOG2004|consen  355 HVLKVIDEELTKLKLLEPSSSEFNVTRNYLDWLTSLPWGKSSTENLDLARAKEILDEDHYGMEDVKERILEFIAVGKLRG  434 (906)
T ss_pred             HHHHHHHHHHHHHhccCccccchhHHHHHHHHHHhCCCCCCChhhhhHHHHHHhhcccccchHHHHHHHHHHHHHHhhcc
Confidence            34455666667788888888888765431     1 22111        22223356678999999999999864    3


Q ss_pred             CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          187 PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       187 ~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+-+++..+|++|||||++|+.|..
T Consensus       435 s~qGkIlCf~GPPGVGKTSI~kSIA~  460 (906)
T KOG2004|consen  435 SVQGKILCFVGPPGVGKTSIAKSIAR  460 (906)
T ss_pred             cCCCcEEEEeCCCCCCcccHHHHHHH
Confidence            45689999999999999999999987

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.77  E-value=0.0015  Score=66.82  Aligned_cols=48  Identities=10%  Similarity=-0.025  Sum_probs=30.8

Q ss_pred             CCCcccchhh--HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERA--REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~--~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++.++|....  ......+..........+.|+|..|+|||+|++.+.+.
T Consensus       122 d~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~  171 (450)
T PRK00149        122 DNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNY  171 (450)
T ss_pred             cccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3445565443  23333333332233456889999999999999999983

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.75  E-value=0.0021  Score=58.08  Aligned_cols=109  Identities=13%  Similarity=0.089  Sum_probs=59.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchHHHHH---HHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEE
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILD---DIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIA  267 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~---~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlV  267 (425)
                      ++|.|+|+.|+||||++..+..  .+..+....++.+.   +....-....-.......+.....+.++..+....=.|+
T Consensus         2 GlilI~GptGSGKTTll~~ll~--~~~~~~~~~i~t~e~~~E~~~~~~~~~i~q~~vg~~~~~~~~~i~~aLr~~pd~ii   79 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMID--YINKNKTHHILTIEDPIEFVHESKRSLINQREVGLDTLSFENALKAALRQDPDVIL   79 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH--HhhhcCCcEEEEEcCCccccccCccceeeecccCCCccCHHHHHHHHhcCCcCEEE
Confidence            4789999999999999987665  22222222222200   000000000000000011223455667777777777999


Q ss_pred             ecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          268 LDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       268 LDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      +|.+. +.+.........   ..|..|+.|+...++..
T Consensus        80 ~gEir-d~e~~~~~l~~a---~~G~~v~~t~Ha~~~~~  113 (198)
T cd01131          80 VGEMR-DLETIRLALTAA---ETGHLVMSTLHTNSAAK  113 (198)
T ss_pred             EcCCC-CHHHHHHHHHHH---HcCCEEEEEecCCcHHH
Confidence            99998 776555443332   23566888887766554

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.74  E-value=0.017  Score=60.55  Aligned_cols=134  Identities=11%  Similarity=0.009  Sum_probs=74.2

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccc---cchHHHHHHHHHHhCCCCCC--C
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF---DCLAWILDDIIRSLMPPSRV--T  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F---~~~~wv~~~il~~l~~~~~~--~  241 (425)
                      .+++|.+...+.|.+++..+. -.+.+.+.|+.|+||||+|+.+.+.-......   .|..   ....+.+......  .
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r-~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~---C~~C~~i~~~~~~~~d   88 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR-INHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGV---CESCVALAPNGPGSID   88 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccc---cHHHHHhhcccCCCce
Confidence            468999999999999998754 34567899999999999998887632111100   1100   0011111110000  0


Q ss_pred             --cc---CCCCHHHH---HHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEE-ecCChhHH
Q 040913          242 --VI---IGEDYKLK---KSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLI-TVINPSLL  304 (425)
Q Consensus       242 --~~---~~~~~~~l---~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIiv-TTR~~~va  304 (425)
                        ..   .....+++   .+.+... ..+++-++|+|++.. +....+.|...+..-...+.+|+ ||....+.
T Consensus        89 vieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~A~NALLK~LEEpp~~~~fIL~tte~~kll  162 (584)
T PRK14952         89 VVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVL  162 (584)
T ss_pred             EEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHHHHHHHHHHHhcCCCCeEEEEEeCChHhhH
Confidence              00   11123333   2222111 235666899999853 45677788777776555666554 54444443

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.74  E-value=0.012  Score=64.89  Aligned_cols=116  Identities=16%  Similarity=0.162  Sum_probs=64.8

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhcCc----cccccccchHHHHHHHHHHhC
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYNNN----HVKFYFDCLAWILDDIIRSLM  235 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~----~~~~~F~~~~wv~~~il~~l~  235 (425)
                      ..++|.+..++.+.+.+...       .....++.++|+.|+|||++|+.+...-    .---.|++.-+.-..-...+.
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~~~l~  644 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSVARLI  644 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchHHHhc
Confidence            45899999999998888752       1235678899999999999999987621    101123332222111112221


Q ss_pred             CCCCCCccCCC-CHHHHHHHHHHHhcCCeEEEEecccCC-ChhhHHHHHhhCCC
Q 040913          236 PPSRVTVIIGE-DYKLKKSILRDFLTNKKYFIALDDVCH-NIEIWDDLEEVLPD  287 (425)
Q Consensus       236 ~~~~~~~~~~~-~~~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~  287 (425)
                      ....  +.... ....+...++.   ....+|+||++.. +.+.++.+...+..
T Consensus       645 g~~~--g~~g~~~~g~l~~~v~~---~p~~vlllDeieka~~~v~~~Ll~~l~~  693 (852)
T TIGR03346       645 GAPP--GYVGYEEGGQLTEAVRR---KPYSVVLFDEVEKAHPDVFNVLLQVLDD  693 (852)
T ss_pred             CCCC--CccCcccccHHHHHHHc---CCCcEEEEeccccCCHHHHHHHHHHHhc
Confidence            1111  11111 11223223221   2335999999963 34677777777753

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.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.73  E-value=0.0078  Score=54.90  Aligned_cols=118  Identities=17%  Similarity=0.186  Sum_probs=71.9

Q ss_pred             CCCCCCCcccchhhHHHHHHH---HhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCC
Q 040913          162 EGQPRLDISEFERAREEWFDL---LIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPS  238 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~---L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~  238 (425)
                      +.++-..++|.+..++.+++-   +..+. ...-|..||.-|.||++|++++.+  ++....-..+              
T Consensus        55 ~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~-pANnVLLwGaRGtGKSSLVKA~~~--e~~~~glrLV--------------  117 (287)
T COG2607          55 DPIDLADLVGVDRQKEALVRNTEQFAEGL-PANNVLLWGARGTGKSSLVKALLN--EYADEGLRLV--------------  117 (287)
T ss_pred             CCcCHHHHhCchHHHHHHHHHHHHHHcCC-cccceEEecCCCCChHHHHHHHHH--HHHhcCCeEE--------------
Confidence            344556789999999888753   22332 233467899999999999999998  4332211000              


Q ss_pred             CCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccCC--ChhhHHHHHhhCCCC---CCCcEEEEecCC
Q 040913          239 RVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVCH--NIEIWDDLEEVLPDN---QNGSRVLITVIN  300 (425)
Q Consensus       239 ~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~--~~~~~~~l~~~l~~~---~~gskIivTTR~  300 (425)
                         +....+...+ -.|.+.|+  ..||.|..||+.+  ....+..++..|..+   .+...++..|.|
T Consensus       118 ---EV~k~dl~~L-p~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~ve~rP~NVl~YATSN  182 (287)
T COG2607         118 ---EVDKEDLATL-PDLVELLRARPEKFILFCDDLSFEEGDDAYKALKSALEGGVEGRPANVLFYATSN  182 (287)
T ss_pred             ---EEcHHHHhhH-HHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHHHhcCCcccCCCeEEEEEecC
Confidence               1111122222 23344443  5899999999975  346888899888743   233344444544

>PRK07667 uridine kinase; Provisional

Probab=96.72  E-value=0.0021  Score=57.75  Aligned_cols=37  Identities=19%  Similarity=0.179  Sum_probs=31.7

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.|.+.+........+|+|-|.+|+||||+|+.+..
T Consensus         3 ~~~~~~~~~~~~~~~~iIgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667          3 TNELINIMKKHKENRFILGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             HHHHHHHHHhcCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4677777877666779999999999999999998877

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.71  E-value=0.0048  Score=62.16  Aligned_cols=47  Identities=11%  Similarity=-0.036  Sum_probs=30.0

Q ss_pred             CCCcccchhhH--HHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAR--EEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~--~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++.++|.....  ..+..+..........+.|+|..|+|||+|++.+++
T Consensus       110 d~fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~  158 (405)
T TIGR00362       110 DNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGN  158 (405)
T ss_pred             cccccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHH
Confidence            34456755442  222233332222345678999999999999999998

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>TIGR00602 rad24 checkpoint protein rad24

Probab=96.71  E-value=0.011  Score=62.25  Aligned_cols=47  Identities=15%  Similarity=0.076  Sum_probs=39.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCC---CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGP---IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~---~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|-++.++++..++....   ....++.++|++|+||||+++.+..
T Consensus        83 ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~  132 (637)
T TIGR00602        83 QHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSK  132 (637)
T ss_pred             HHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999987642   2346799999999999999999987

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.69  E-value=0.013  Score=60.21  Aligned_cols=45  Identities=11%  Similarity=-0.091  Sum_probs=37.2

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|.+.....+.+++..+. -.+.+.++|+.|+||||+|+.+..
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~-i~hayLf~Gp~G~GKTtlAr~lAk   60 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR-VSHAYIFAGPRGTGKTTIARILAK   60 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468899999999999997754 345667899999999999988765

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=96.69  E-value=0.014  Score=61.46  Aligned_cols=134  Identities=10%  Similarity=0.028  Sum_probs=73.5

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc-------cccchHHHHHHHHHHhCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF-------YFDCLAWILDDIIRSLMPPS  238 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-------~F~~~~wv~~~il~~l~~~~  238 (425)
                      -.+++|.+..++.|.+.+..+. -...+-++|+.|+||||+|+.+.+.-....       .++.+-+.  .-.+.+....
T Consensus        23 f~dliGq~~~v~~L~~~~~~gr-i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c--~~C~~i~~g~   99 (598)
T PRK09111         23 FDDLIGQEAMVRTLTNAFETGR-IAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVG--EHCQAIMEGR   99 (598)
T ss_pred             HHHhcCcHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCccc--HHHHHHhcCC
Confidence            3578999999999999988764 344677899999999999998876321111       01111111  0001111111


Q ss_pred             CCC--c---cCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec-CChhH
Q 040913          239 RVT--V---IIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV-INPSL  303 (425)
Q Consensus       239 ~~~--~---~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT-R~~~v  303 (425)
                      ...  .   ......+++.+ +.+.+     .+++-++|+|++.. +....+.+...+..-..++++|++| ....+
T Consensus       100 h~Dv~e~~a~s~~gvd~IRe-Iie~~~~~P~~a~~KVvIIDEad~Ls~~a~naLLKtLEePp~~~~fIl~tte~~kl  175 (598)
T PRK09111        100 HVDVLEMDAASHTGVDDIRE-IIESVRYRPVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKV  175 (598)
T ss_pred             CCceEEecccccCCHHHHHH-HHHHHHhchhcCCcEEEEEEChHhCCHHHHHHHHHHHHhCCCCeEEEEEeCChhhh
Confidence            000  0   01122333332 22222     24566899999952 4456777777776555567765544 44443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.69  E-value=0.0082  Score=61.21  Aligned_cols=47  Identities=15%  Similarity=0.005  Sum_probs=29.6

Q ss_pred             CCCcccchhh--HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERA--REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~--~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++-++|..+.  ......+...+......+-|+|..|+|||+|++.+.+
T Consensus       115 dnFv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~  163 (450)
T PRK14087        115 ENFVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKN  163 (450)
T ss_pred             hcccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHH
Confidence            3445575443  2222233332222345578999999999999999988

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

Probab=96.68  E-value=0.0021  Score=69.24  Aligned_cols=44  Identities=20%  Similarity=0.108  Sum_probs=36.7

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+.++.++++.|.....  .-+.++|++|+|||++|+.+.+
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~~--~n~LLvGppGvGKT~lae~la~  229 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRRK--NNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccCC--CCeEEECCCCCCHHHHHHHHHH
Confidence            4589999999999999987542  2234799999999999999886

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.68  E-value=0.009  Score=65.62  Aligned_cols=45  Identities=16%  Similarity=0.090  Sum_probs=38.4

Q ss_pred             CcccchhhHHHHHHHHhcC-CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIEG-PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++||+.+.+.|...+..- .....++.+.|..|+|||+|++.|..
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~   46 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHK   46 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHH
Confidence            3789999999999888764 23466999999999999999999987

>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=96.67  E-value=0.0033  Score=53.19  Aligned_cols=88  Identities=16%  Similarity=0.149  Sum_probs=45.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCH-----HHHHHHHHHHhcCCeEEE
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDY-----KLKKSILRDFLTNKKYFI  266 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~-----~~l~~~l~~~l~~kr~Ll  266 (425)
                      +|.++|++|+||||+|+.+..... ..+++     .+.+...+..............     ..+...+...+..... +
T Consensus         1 lii~~G~pgsGKSt~a~~l~~~~~-~~~i~-----~D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~-~   73 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAKRLG-AVVIS-----QDEIRRRLAGEDPPSPSDYIEAEERAYQILNAAIRKALRNGNS-V   73 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHST-EEEEE-----HHHHHHHHCCSSSGCCCCCHHHHHHHHHHHHHHHHHHHHTT-E-E
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC-CEEEe-----HHHHHHHHcccccccchhHHHHHHHHHHHHHHHHHHHHHcCCC-c
Confidence            578899999999999999885211 11111     4555666665322111111111     1223444455544444 6


Q ss_pred             EecccCCChhhHHHHHhhCC
Q 040913          267 ALDDVCHNIEIWDDLEEVLP  286 (425)
Q Consensus       267 VLDdvw~~~~~~~~l~~~l~  286 (425)
                      |+|+-......+..+...+.
T Consensus        74 vvd~~~~~~~~r~~~~~~~~   93 (143)
T PF13671_consen   74 VVDNTNLSREERARLRELAR   93 (143)
T ss_dssp             EEESS--SHHHHHHHHHHHH
T ss_pred             eeccCcCCHHHHHHHHHHHH
Confidence            66755324555556655554

...

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.66  E-value=0.0014  Score=57.97  Aligned_cols=30  Identities=27%  Similarity=0.331  Sum_probs=24.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      ...+|.+.|+.|+||||+|+.+++  +....+
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~--~l~~~~   35 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYE--RLKLKY   35 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH--HHHHcC
Confidence            356899999999999999999987  444333

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.65  E-value=0.013  Score=61.39  Aligned_cols=133  Identities=12%  Similarity=0.087  Sum_probs=71.5

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc---cccchHHHHHHHHHHhCCCCCCC--
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF---YFDCLAWILDDIIRSLMPPSRVT--  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F~~~~wv~~~il~~l~~~~~~~--  241 (425)
                      .+++|-+..+..|.+.+..+. -...+-++|+.|+||||+|+.+.+.-....   ...|..   ....+.+.......  
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r-i~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~---C~sC~~i~~g~hpDv~   91 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR-VAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNT---CEQCRKVTQGMHVDVV   91 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcc---cHHHHHHhcCCCCceE
Confidence            467898888888888887653 246677899999999999988876321111   001100   00001111110000  


Q ss_pred             cc---CCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC-hhHH
Q 040913          242 VI---IGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN-PSLL  304 (425)
Q Consensus       242 ~~---~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~-~~va  304 (425)
                      ..   .....+++. .+.+.+     .+++-+||+|++.. +....+.|...+..-.....+|++|.+ ..+.
T Consensus        92 eId~a~~~~Id~iR-~L~~~~~~~p~~g~~kVIIIDEad~Lt~~a~naLLk~LEEP~~~~ifILaTt~~~kll  163 (624)
T PRK14959         92 EIDGASNRGIDDAK-RLKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFP  163 (624)
T ss_pred             EEecccccCHHHHH-HHHHHHHhhhhcCCceEEEEEChHhCCHHHHHHHHHHhhccCCCEEEEEecCChhhhh
Confidence            00   011222222 233222     35677999999962 346677777777544445555555544 4433

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

Probab=96.63  E-value=0.012  Score=63.48  Aligned_cols=113  Identities=14%  Similarity=0.210  Sum_probs=64.4

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhcCcccccc---ccchHHHHHHHHHHhCC
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY---FDCLAWILDDIIRSLMP  236 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~---F~~~~wv~~~il~~l~~  236 (425)
                      ..++|.+..++.|.+.+...       ......+.++|++|+|||+||+.+...  ....   |++.-+.-..-...+..
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~--l~~~~i~id~se~~~~~~~~~LiG  535 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA--LGIELLRFDMSEYMERHTVSRLIG  535 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHH--hCCCcEEeechhhcccccHHHHcC
Confidence            34789999999988887632       223567889999999999999988773  2222   23333321111233322


Q ss_pred             CCCCCccCCCCHHHHHHHHHHHhcC-CeEEEEecccCC-ChhhHHHHHhhCC
Q 040913          237 PSRVTVIIGEDYKLKKSILRDFLTN-KKYFIALDDVCH-NIEIWDDLEEVLP  286 (425)
Q Consensus       237 ~~~~~~~~~~~~~~l~~~l~~~l~~-kr~LlVLDdvw~-~~~~~~~l~~~l~  286 (425)
                      ...  +....+..   ..+.+.++. ...+|+||++.. ..+.++.+...+.
T Consensus       536 ~~~--gyvg~~~~---g~L~~~v~~~p~sVlllDEieka~~~v~~~LLq~ld  582 (758)
T PRK11034        536 APP--GYVGFDQG---GLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMD  582 (758)
T ss_pred             CCC--Cccccccc---chHHHHHHhCCCcEEEeccHhhhhHHHHHHHHHHHh
Confidence            211  11111111   122333333 446999999962 3366777776664

>PRK06921 hypothetical protein; Provisional

Probab=96.62  E-value=0.0011  Score=62.59  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+.++|..|+|||+||..+.+.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~  140 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE  140 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH
Confidence            456889999999999999999883

>PRK08939 primosomal protein DnaI; Reviewed

Probab=96.61  E-value=0.0026  Score=61.34  Aligned_cols=118  Identities=18%  Similarity=0.144  Sum_probs=60.3

Q ss_pred             cchhhHHHHHHHHhcCC--CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-HHHHHHHhCCCCCCCccCCCC
Q 040913          171 EFERAREEWFDLLIEGP--IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-LDDIIRSLMPPSRVTVIIGED  247 (425)
Q Consensus       171 Gr~~~~~~l~~~L~~~~--~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-~~~il~~l~~~~~~~~~~~~~  247 (425)
                      ++........+++..-.  ...+-+-++|..|+|||.||..+.+..- ...+.+. ++ ..+++..+.....     ..+
T Consensus       135 ~~~~~~~~~~~fi~~~~~~~~~~gl~L~G~~G~GKThLa~Aia~~l~-~~g~~v~-~~~~~~l~~~lk~~~~-----~~~  207 (306)
T PRK08939        135 DRLDALMAALDFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELA-KKGVSST-LLHFPEFIRELKNSIS-----DGS  207 (306)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCeEEEECCCCCCHHHHHHHHHHHHH-HcCCCEE-EEEHHHHHHHHHHHHh-----cCc
Confidence            44444555566665322  1345688999999999999999998421 2222221 22 2233333322111     012


Q ss_pred             HHHHHHHHHHHhcCCeEEEEecccCC-ChhhHHH--HHhhC-CCC-CCCcEEEEecCC
Q 040913          248 YKLKKSILRDFLTNKKYFIALDDVCH-NIEIWDD--LEEVL-PDN-QNGSRVLITVIN  300 (425)
Q Consensus       248 ~~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~--l~~~l-~~~-~~gskIivTTR~  300 (425)
                      .......    + .+-=||||||+.. ....|..  +...+ ... ..+..+|+||..
T Consensus       208 ~~~~l~~----l-~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl  260 (306)
T PRK08939        208 VKEKIDA----V-KEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNF  260 (306)
T ss_pred             HHHHHHH----h-cCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCC
Confidence            2222222    2 2456899999962 2346643  43333 221 234557777743

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.59  E-value=0.011  Score=62.06  Aligned_cols=132  Identities=11%  Similarity=0.059  Sum_probs=72.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc------ccccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK------FYFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~------~~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+..+..|.+.+..+. -.+.+-++|+.|+||||+|+.+.+.--..      .+-.|...      ..+.....
T Consensus        15 f~~iiGq~~v~~~L~~~i~~~~-~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c------~~i~~g~~   87 (576)
T PRK14965         15 FSDLTGQEHVSRTLQNAIDTGR-VAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPC------VEITEGRS   87 (576)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHH------HHHhcCCC
Confidence            3578999999999999988764 34566789999999999998876631111      11111111      11111000


Q ss_pred             CC-----ccCCCCHHH---HHHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEE-ecCChhHH
Q 040913          240 VT-----VIIGEDYKL---KKSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLI-TVINPSLL  304 (425)
Q Consensus       240 ~~-----~~~~~~~~~---l~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIiv-TTR~~~va  304 (425)
                      ..     .......++   +...+... ..+++-++|+|++.. +....+.|...+..-...+.+|+ ||....+.
T Consensus        88 ~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~a~naLLk~LEepp~~~~fIl~t~~~~kl~  163 (576)
T PRK14965         88 VDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVP  163 (576)
T ss_pred             CCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHHHHHHHHHHHHcCCCCeEEEEEeCChhhhh
Confidence            00     001112223   22222211 134566899999852 44667777777765555666554 44444443

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=96.59  E-value=0.017  Score=62.82  Aligned_cols=88  Identities=13%  Similarity=0.146  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHhccCCCCCCCCccCCC-----c-ccccCC--------CCCCCCCCcccchhhHHHHHHHHhcC----
Q 040913          125 GLHSKIIDIRNRMQQLPPGDNGFDINEQR-----D-ELIHLS--------SEGQPRLDISEFERAREEWFDLLIEG----  186 (425)
Q Consensus       125 ~i~~~i~~i~~~l~~i~~~~~~~~~~~~~-----~-~~~~~~--------~~~~~~~~~vGr~~~~~~l~~~L~~~----  186 (425)
                      ...+++.+=.+|++.+......|++..+-     + +|...+        +...-+.+.+|.++.+++|+++|...    
T Consensus       266 ~~~~~~~~e~~~~~~~~~~~~e~~~~~~yl~~~~~~pw~~~~~~~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~~~  345 (784)
T PRK10787        266 EAKEKAEAELQKLKMMSPMSAEATVVRGYIDWMVQVPWNARSKVKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSRVN  345 (784)
T ss_pred             HHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHhCCCCCCCcccccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHhcc
Confidence            44455555556777777666666544321     0 222211        11223456899999999999888742    


Q ss_pred             CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          187 PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       187 ~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....++.++|++|+||||+|+.+..
T Consensus       346 ~~~g~~i~l~GppG~GKTtl~~~ia~  371 (784)
T PRK10787        346 KIKGPILCLVGPPGVGKTSLGQSIAK  371 (784)
T ss_pred             cCCCceEEEECCCCCCHHHHHHHHHH
Confidence            22456789999999999999999887

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.58  E-value=0.0096  Score=52.48  Aligned_cols=116  Identities=13%  Similarity=0.111  Sum_probs=68.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccc------ccc---------------------------------chHHH----
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKF------YFD---------------------------------CLAWI----  226 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~---------------------------------~~~wv----  226 (425)
                      -..+-++|++|.|||||.+.+|..++-..      .|+                                 .+++.    
T Consensus        28 Gef~fl~GpSGAGKSTllkLi~~~e~pt~G~i~~~~~dl~~l~~~~iP~LRR~IGvVFQD~rLL~~~tvyeNVA~pL~v~  107 (223)
T COG2884          28 GEFVFLTGPSGAGKSTLLKLIYGEERPTRGKILVNGHDLSRLKGREIPFLRRQIGVVFQDFRLLPDRTVYENVALPLRVI  107 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhhcCCCceEEECCeecccccccccchhhheeeeEeeeccccccchHhhhhhhhhhcc
Confidence            45788999999999999999997544221      011                                 11111    


Q ss_pred             ----------HHHHHHHhCCCCCCC--ccCCCCHHHHHHHHHHHhcCCeEEEEecccCC---ChhhHHHHHhhCCCCCCC
Q 040913          227 ----------LDDIIRSLMPPSRVT--VIIGEDYKLKKSILRDFLTNKKYFIALDDVCH---NIEIWDDLEEVLPDNQNG  291 (425)
Q Consensus       227 ----------~~~il~~l~~~~~~~--~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~---~~~~~~~l~~~l~~~~~g  291 (425)
                                ....+...+......  ...-+.-++-.-.|...+-++.-+++=|.---   ..-.|+-+.-.-.-+..|
T Consensus       108 G~~~~~i~~rV~~~L~~VgL~~k~~~lP~~LSGGEQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~G  187 (223)
T COG2884         108 GKPPREIRRRVSEVLDLVGLKHKARALPSQLSGGEQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLG  187 (223)
T ss_pred             CCCHHHHHHHHHHHHHHhccchhhhcCccccCchHHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcC
Confidence                      333333333322211  11223334445567777778888888886421   234665554433346679


Q ss_pred             cEEEEecCChhHHH
Q 040913          292 SRVLITVINPSLLT  305 (425)
Q Consensus       292 skIivTTR~~~va~  305 (425)
                      +.||++|.+.++-.
T Consensus       188 tTVl~ATHd~~lv~  201 (223)
T COG2884         188 TTVLMATHDLELVN  201 (223)
T ss_pred             cEEEEEeccHHHHH
Confidence            99999999988654

>CHL00176 ftsH cell division protein; Validated

Probab=96.55  E-value=0.011  Score=62.82  Aligned_cols=96  Identities=17%  Similarity=0.220  Sum_probs=54.7

Q ss_pred             CCCCCcccchhhHHHHHH---HHhcCC-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFD---LLIEGP-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRS  233 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~---~L~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~  233 (425)
                      ..-.++.|.++.++++.+   .+....       ...+-+.++|++|+|||+||+.+.+.  ....|-..-  ..++...
T Consensus       180 ~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e--~~~p~i~is--~s~f~~~  255 (638)
T CHL00176        180 ITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE--AEVPFFSIS--GSEFVEM  255 (638)
T ss_pred             CCHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH--hCCCeeecc--HHHHHHH
Confidence            344568887776666544   444332       22456889999999999999999883  332331100  0011000


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      .         .......+...+........++|++||+.
T Consensus       256 ~---------~g~~~~~vr~lF~~A~~~~P~ILfIDEID  285 (638)
T CHL00176        256 F---------VGVGAARVRDLFKKAKENSPCIVFIDEID  285 (638)
T ss_pred             h---------hhhhHHHHHHHHHHHhcCCCcEEEEecch
Confidence            0         00112233444455556788999999994

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.52  E-value=0.015  Score=61.49  Aligned_cols=129  Identities=9%  Similarity=0.075  Sum_probs=73.2

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc----------ccccchHHHHHHHHHHhCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK----------FYFDCLAWILDDIIRSLMP  236 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----------~~F~~~~wv~~~il~~l~~  236 (425)
                      .+++|.+...+.|.+++..+. -.+.+-++|+.|+||||+|+.+...-...          .+=.|+.|-     .  ..
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~-l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~-----~--~~   88 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK-LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFN-----E--QR   88 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHh-----c--CC
Confidence            568999999999999998764 34567899999999999998766521100          000111111     0  00


Q ss_pred             CCCCC---ccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEE-ecCChhH
Q 040913          237 PSRVT---VIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLI-TVINPSL  303 (425)
Q Consensus       237 ~~~~~---~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIiv-TTR~~~v  303 (425)
                      ..+..   .......+++...+...    ..+++-++|+|++.. +...++.+...+..-..++.+|+ ||....+
T Consensus        89 ~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~a~naLLK~LEepp~~tifIL~tt~~~kI  164 (614)
T PRK14971         89 SYNIHELDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKI  164 (614)
T ss_pred             CCceEEecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHHHHHHHHHHHhCCCCCeEEEEEeCCchhc
Confidence            00000   00112233333333221    234666889999863 45678888888776555666555 4444443

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.52  E-value=0.0027  Score=61.81  Aligned_cols=23  Identities=13%  Similarity=0.125  Sum_probs=20.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-+.++|..|+|||+||..+.+.
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~  206 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKE  206 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH
Confidence            56889999999999999999883

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.50  E-value=0.0053  Score=62.42  Aligned_cols=24  Identities=13%  Similarity=0.245  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+.|+|+.|+|||+|++.+.+.
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~  164 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHA  164 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHH
Confidence            356789999999999999999983

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.48  E-value=0.021  Score=62.74  Aligned_cols=115  Identities=13%  Similarity=0.180  Sum_probs=63.8

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhcC----ccccccccchHHH-HHHHHHHh
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYNN----NHVKFYFDCLAWI-LDDIIRSL  234 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~----~~~~~~F~~~~wv-~~~il~~l  234 (425)
                      ..++|.+..++.|.+.+...       +....++.++|+.|+|||+||+.+.+.    ..---.|+..-+. ...+.+-+
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~~~l~  588 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLI  588 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccHHHhc
Confidence            56889999999998887632       223456778999999999999887652    1111112222221 11111112


Q ss_pred             CCCCCCCccCCCCHHHHHHHHHHHhcCCe-EEEEecccCC-ChhhHHHHHhhCCC
Q 040913          235 MPPSRVTVIIGEDYKLKKSILRDFLTNKK-YFIALDDVCH-NIEIWDDLEEVLPD  287 (425)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~l~~kr-~LlVLDdvw~-~~~~~~~l~~~l~~  287 (425)
                      +.+..   ....+..   ..+.+.++.+. .+|+||++.. +.+.++.+...+..
T Consensus       589 g~~~g---yvg~~~~---~~l~~~~~~~p~~VvllDeieka~~~v~~~Llq~le~  637 (821)
T CHL00095        589 GSPPG---YVGYNEG---GQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQILDD  637 (821)
T ss_pred             CCCCc---ccCcCcc---chHHHHHHhCCCeEEEECChhhCCHHHHHHHHHHhcc
Confidence            22211   1111111   12344444444 5899999963 34677777777654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.47  E-value=0.0057  Score=66.43  Aligned_cols=96  Identities=20%  Similarity=0.198  Sum_probs=57.6

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIR  232 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~  232 (425)
                      ..-+++.|.+..+++|.+++...           -...+-|.++|++|+||||||+.+.+  .....|-.. - ..++..
T Consensus       175 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~--~~~~~~i~i-~-~~~i~~  250 (733)
T TIGR01243       175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVAN--EAGAYFISI-N-GPEIMS  250 (733)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHH--HhCCeEEEE-e-cHHHhc
Confidence            44456889999999988776421           02345678999999999999999988  333333100 0 011111


Q ss_pred             HhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          233 SLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       233 ~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      .         ........+...+.........+|+||++.
T Consensus       251 ~---------~~g~~~~~l~~lf~~a~~~~p~il~iDEid  281 (733)
T TIGR01243       251 K---------YYGESEERLREIFKEAEENAPSIIFIDEID  281 (733)
T ss_pred             c---------cccHHHHHHHHHHHHHHhcCCcEEEeehhh
Confidence            1         011122334444444445667899999984

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.46  E-value=0.0032  Score=64.77  Aligned_cols=45  Identities=16%  Similarity=0.135  Sum_probs=38.8

Q ss_pred             CcccchhhHHHHHHHHhc----CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIE----GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +++|.++.+++|++.|..    -....+++.++|++|+||||||+.+.+
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~  125 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKS  125 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHH
Confidence            689999999999999943    244568999999999999999998876

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.43  E-value=0.021  Score=53.10  Aligned_cols=58  Identities=21%  Similarity=0.214  Sum_probs=35.2

Q ss_pred             CCCHHHHH-HHHHHHhcCCeEEEEecccCC--C---hhhHHHHHhhCCCCCCCcEEEEecCChhHH
Q 040913          245 GEDYKLKK-SILRDFLTNKKYFIALDDVCH--N---IEIWDDLEEVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       245 ~~~~~~l~-~~l~~~l~~kr~LlVLDdvw~--~---~~~~~~l~~~l~~~~~gskIivTTR~~~va  304 (425)
                      ..+-.+.+ -.|.+.|..+.=|++||.--.  +   ....-.+..-+...  |..|+++|.+-+..
T Consensus       139 ~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~e--g~tIl~vtHDL~~v  202 (254)
T COG1121         139 ELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQE--GKTVLMVTHDLGLV  202 (254)
T ss_pred             ccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHC--CCEEEEEeCCcHHh
Confidence            33444443 456677888999999997531  1   12333333333332  88899999886654

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.38  E-value=0.029  Score=58.74  Aligned_cols=133  Identities=8%  Similarity=-0.049  Sum_probs=73.4

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc---cccchHHH-HHHHHHHhCCCCC-CC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF---YFDCLAWI-LDDIIRSLMPPSR-VT  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F~~~~wv-~~~il~~l~~~~~-~~  241 (425)
                      .+++|-+..+..|.+++..+. -.+.+-++|+.|+||||+|+.+.+.--...   .++|..-. -+.|...-..... ..
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~-i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv~~id   94 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK-IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVIEID   94 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCeEEec
Confidence            468999999999999998754 355678999999999999998876321110   11110000 0111110000000 00


Q ss_pred             ccCCCCHHHHHHHH---HH-HhcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          242 VIIGEDYKLKKSIL---RD-FLTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       242 ~~~~~~~~~l~~~l---~~-~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      +......+++.+..   .. -..+++-++|+|++.. +...++.+...+..-...+.+|.+|..
T Consensus        95 gas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~a~naLLK~LEepp~~~vfI~~tte  158 (563)
T PRK06647         95 GASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTE  158 (563)
T ss_pred             CcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHHHHHHHHHhhccCCCCEEEEEecCC
Confidence            01112333333322   11 1235667899999852 446777787777665556666655533

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

Probab=96.36  E-value=0.0023  Score=60.09  Aligned_cols=25  Identities=24%  Similarity=0.232  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..-+.++|.+|+|||.||.++.+.
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~  128 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNE  128 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHH
Confidence            3556789999999999999999984

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.34  E-value=0.033  Score=52.72  Aligned_cols=126  Identities=14%  Similarity=0.048  Sum_probs=70.0

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc---ccc-chHHH---HHHHHHHhCCCCCCC---ccC
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF---YFD-CLAWI---LDDIIRSLMPPSRVT---VII  244 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F~-~~~wv---~~~il~~l~~~~~~~---~~~  244 (425)
                      ..+.++..|.... ...-++|+|..|.|||||.+.+.....-..   .|+ ..+-+   ..++...+..-....   ..+
T Consensus        97 ~~~~~l~~l~~~~-~~~~~~i~g~~g~GKttl~~~l~~~~~~~~G~i~~~g~~v~~~d~~~ei~~~~~~~~q~~~~~r~~  175 (270)
T TIGR02858        97 AADKLLPYLVRNN-RVLNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVDERSEIAGCVNGVPQHDVGIRTD  175 (270)
T ss_pred             cHHHHHHHHHhCC-CeeEEEEEcCCCCCHHHHHHHHhCccCCCCceEEECCEEeecchhHHHHHHHhccccccccccccc
Confidence            4455555565432 356789999999999999999987322110   121 11111   234433322111110   011


Q ss_pred             CCCHHHHHHHHHHHhc-CCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          245 GEDYKLKKSILRDFLT-NKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       245 ~~~~~~l~~~l~~~l~-~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      ..+.......+...+. ...-++++|.+- ..+.+..+...+.   .|..||+||.+..+..
T Consensus       176 v~~~~~k~~~~~~~i~~~~P~villDE~~-~~e~~~~l~~~~~---~G~~vI~ttH~~~~~~  233 (270)
T TIGR02858       176 VLDGCPKAEGMMMLIRSMSPDVIVVDEIG-REEDVEALLEALH---AGVSIIATAHGRDVED  233 (270)
T ss_pred             ccccchHHHHHHHHHHhCCCCEEEEeCCC-cHHHHHHHHHHHh---CCCEEEEEechhHHHH
Confidence            1111111222333333 477899999997 7776776666653   4788999999877643

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=96.33  E-value=0.0059  Score=55.27  Aligned_cols=73  Identities=15%  Similarity=0.034  Sum_probs=42.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHH-----H-HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAW-----I-LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNK  262 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~w-----v-~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~k  262 (425)
                      .+.+|+|-|.+|+||||+|+.+++  .++..+-..+-     . ....-..-....+-..+...+.+-+.+.|...++|+
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~--~~~~~~~~~I~~D~YYk~~~~~~~~~~~~~n~d~p~A~D~dLl~~~L~~L~~g~   84 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSE--QLGVEKVVVISLDDYYKDQSHLPFEERNKINYDHPEAFDLDLLIEHLKDLKQGK   84 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHH--HhCcCcceEeeccccccchhhcCHhhcCCcCccChhhhcHHHHHHHHHHHHcCC
Confidence            468999999999999999999988  33322111100     0 000000000001000344567788888888888887


Q ss_pred             e
Q 040913          263 K  263 (425)
Q Consensus       263 r  263 (425)
                      .
T Consensus        85 ~   85 (218)
T COG0572          85 P   85 (218)
T ss_pred             c
Confidence            7

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.32  E-value=0.0038  Score=58.16  Aligned_cols=38  Identities=16%  Similarity=0.048  Sum_probs=26.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..+.+...........+.++|.+|+|||+||..+.+.
T Consensus        85 l~~a~~~~~~~~~~~~~~~l~G~~GtGKThLa~aia~~  122 (244)
T PRK07952         85 LSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNE  122 (244)
T ss_pred             HHHHHHHHHhhccCCceEEEECCCCCCHHHHHHHHHHH
Confidence            33444444332223456789999999999999999984

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=96.29  E-value=0.031  Score=58.59  Aligned_cols=46  Identities=15%  Similarity=0.009  Sum_probs=38.1

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.+...+.+.+++..+. -.+.+-++|+.|+||||+|+.+.+
T Consensus        15 f~~viGq~~v~~~L~~~i~~~~-~~hayLf~Gp~GtGKTt~Ak~lAk   60 (559)
T PRK05563         15 FEDVVGQEHITKTLKNAIKQGK-ISHAYLFSGPRGTGKTSAAKIFAK   60 (559)
T ss_pred             HHhccCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999998764 345677899999999999988755

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=96.28  E-value=0.033  Score=57.66  Aligned_cols=132  Identities=9%  Similarity=-0.008  Sum_probs=73.4

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc------cccccccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN------HVKFYFDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~------~~~~~F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|-+...+.+...+..+. -.++.-++|+.|+||||+|+.+.+.-      ....+..|....  .+........-
T Consensus        13 fdeiiGqe~v~~~L~~~I~~gr-l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~--~~~~~~h~dv~   89 (535)
T PRK08451         13 FDELIGQESVSKTLSLALDNNR-LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQ--SALENRHIDII   89 (535)
T ss_pred             HHHccCcHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHH--HHhhcCCCeEE
Confidence            3568999999999999887664 34567899999999999998765521      111111111110  00000000000


Q ss_pred             C-CccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          240 V-TVIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       240 ~-~~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      . ........+++.+.+...    ..+++-++|+|++.. +.+..+.+...+..-...+++|++|.+
T Consensus        90 eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~A~NALLK~LEEpp~~t~FIL~ttd  156 (535)
T PRK08451         90 EMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTD  156 (535)
T ss_pred             EeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHHHHHHHHHHHhhcCCceEEEEEECC
Confidence            0 000111244444444321    125667999999962 446677777777655556776666654

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.28  E-value=0.0087  Score=54.67  Aligned_cols=115  Identities=12%  Similarity=0.147  Sum_probs=58.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccc--cccccchHHH----HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHh--cC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHV--KFYFDCLAWI----LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFL--TN  261 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F~~~~wv----~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l--~~  261 (425)
                      .+++.|+|+.|.|||||.+.+......  ...|-.....    +..+...+........ ...+...-...+...+  ..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~~~~si~~-~~S~f~~el~~l~~~l~~~~  107 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSS-GQSAFMIDLYQVSKALRLAT  107 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeCCccChhh-ccchHHHHHHHHHHHHHhCC
Confidence            478899999999999999887632111  0111100001    2333333333222110 1112222223333332  36


Q ss_pred             CeEEEEecccCCChh--h-----HHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          262 KKYFIALDDVCHNIE--I-----WDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       262 kr~LlVLDdvw~~~~--~-----~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      ++-|++||..-...+  .     +..+......+..+..+|+||.+.+.+.
T Consensus       108 ~~slvllDE~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH~~~l~~  158 (213)
T cd03281         108 RRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFN  158 (213)
T ss_pred             CCcEEEeccccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcChHHHHH
Confidence            789999999862221  1     1222222222223468999999988775

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.26  E-value=0.032  Score=59.11  Aligned_cols=130  Identities=9%  Similarity=0.055  Sum_probs=72.0

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc-----ccchHHHHHHHHHHhCCCCCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY-----FDCLAWILDDIIRSLMPPSRVT  241 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~-----F~~~~wv~~~il~~l~~~~~~~  241 (425)
                      .+++|.+.....|..++..+. -.+.+-++|+.|+||||+|+.+.+.--....     -.|.   ..+..+.+.......
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r-l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg---~C~~C~~i~~g~h~D   91 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR-IAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCG---KCELCRAIAAGNALD   91 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC-CCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCc---ccHHHHHHhcCCCcc
Confidence            568899999999999888754 2345778999999999999988763211100     0111   001111111111000


Q ss_pred             -----ccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          242 -----VIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       242 -----~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                           .......+.+.+.+...    ..+++-++|+|++.. +.+.++.|...+..-...+.+|++|.+
T Consensus        92 ~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~a~naLLK~LEePp~~tvfIL~t~~  160 (620)
T PRK14948         92 VIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTD  160 (620)
T ss_pred             EEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHHHHHHHHHHHhcCCcCeEEEEEeCC
Confidence                 00112233333333221    125666899999962 446777787777654445555554443

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=96.26  E-value=0.021  Score=57.48  Aligned_cols=22  Identities=23%  Similarity=0.218  Sum_probs=19.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -.+++|+|+.|+||||||+.+.
T Consensus       362 G~~lgIIGPSgSGKSTLaR~lv  383 (580)
T COG4618         362 GEALGIIGPSGSGKSTLARLLV  383 (580)
T ss_pred             CceEEEECCCCccHHHHHHHHH
Confidence            4589999999999999999976

>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=96.25  E-value=0.046  Score=47.62  Aligned_cols=129  Identities=16%  Similarity=0.072  Sum_probs=69.7

Q ss_pred             cchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccc----hHHHHHHHHHHhCCCCCC--Ccc-
Q 040913          171 EFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDC----LAWILDDIIRSLMPPSRV--TVI-  243 (425)
Q Consensus       171 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~----~~wv~~~il~~l~~~~~~--~~~-  243 (425)
                      |-++..+.|.+.+..+. -...+-++|..|+||+|+|..+.+.---......    .-. -+.+...-......  +.. 
T Consensus         1 gq~~~~~~L~~~~~~~~-l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~-c~~~~~~~~~d~~~~~~~~~   78 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR-LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRS-CRRIEEGNHPDFIIIKPDKK   78 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC---SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHH-HHHHHTT-CTTEEEEETTTS
T ss_pred             CcHHHHHHHHHHHHcCC-cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHH-HHHHHhccCcceEEEecccc
Confidence            44556666777666553 3456789999999999999776552111111100    000 01111100000000  000 


Q ss_pred             -CCCCHHHHHHHHHHHhc-----CCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          244 -IGEDYKLKKSILRDFLT-----NKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       244 -~~~~~~~l~~~l~~~l~-----~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                       .....+++. .+.+.+.     ++.-++|+||+.. +.+..+.+...+-.-..++.+|++|++.+
T Consensus        79 ~~~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~~~a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen   79 KKSIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLTEEAQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SSSBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS-HHHHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             cchhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhhHHHHHHHHHHhcCCCCCEEEEEEECChH
Confidence             123455555 4444442     3566899999963 45788888888877677899888888755

...

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.21  E-value=0.0098  Score=59.09  Aligned_cols=50  Identities=10%  Similarity=-0.142  Sum_probs=32.9

Q ss_pred             CCCCCCcccchhhHHHH-HHHH-hcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          163 GQPRLDISEFERAREEW-FDLL-IEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l-~~~L-~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..++-++|-......- ...+ ..+......+-|+|..|.|||.|++++.|
T Consensus        84 ytFdnFv~g~~N~~A~aa~~~va~~~g~~~nplfi~G~~GlGKTHLl~Aign  135 (408)
T COG0593          84 YTFDNFVVGPSNRLAYAAAKAVAENPGGAYNPLFIYGGVGLGKTHLLQAIGN  135 (408)
T ss_pred             CchhheeeCCchHHHHHHHHHHHhccCCcCCcEEEECCCCCCHHHHHHHHHH
Confidence            34445556755443332 2222 22333477899999999999999999999

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.20  E-value=0.0036  Score=56.25  Aligned_cols=21  Identities=29%  Similarity=0.371  Sum_probs=19.6

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ||+|.|.+|+||||||+.+..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~   21 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQ   21 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            799999999999999999876

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=96.20  E-value=0.04  Score=48.71  Aligned_cols=22  Identities=32%  Similarity=0.348  Sum_probs=19.6

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ||.|+|++|+||||+|+.+...
T Consensus         1 ~i~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         1 VVFVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999998773

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.19  E-value=0.012  Score=57.34  Aligned_cols=47  Identities=13%  Similarity=-0.074  Sum_probs=38.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..++|....+.++.+.+..-.....-|.|+|..|+||+++|+.++..
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~   52 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYL   52 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            45899999999998887764333455789999999999999999863

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.18  E-value=0.0048  Score=67.72  Aligned_cols=44  Identities=14%  Similarity=0.097  Sum_probs=37.3

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+.++.++++.|.....+  -+.++|.+|+||||+|+.+.+
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~~~--n~lLvG~pGvGKTal~~~La~  230 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRRQN--NPILTGEAGVGKTAVVEGLAL  230 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCCcC--ceeEECCCCCCHHHHHHHHHH
Confidence            57899999999999999876522  345899999999999998887

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.

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=96.18  E-value=0.0053  Score=62.03  Aligned_cols=54  Identities=20%  Similarity=0.118  Sum_probs=39.7

Q ss_pred             CCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          165 PRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      .-.++.|.+..+++|.+.+.-.           -...+-+.++|++|+|||+||+.+.+  +....|
T Consensus       181 ~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~--el~~~f  245 (438)
T PTZ00361        181 SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVAN--ETSATF  245 (438)
T ss_pred             CHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHH--hhCCCE
Confidence            3456788999998888776421           12345677899999999999999998  444444

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.14  E-value=0.0044  Score=56.37  Aligned_cols=25  Identities=28%  Similarity=0.399  Sum_probs=22.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+|+|.|.+|+|||||++.+...
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999873

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=96.13  E-value=0.0048  Score=57.62  Aligned_cols=47  Identities=19%  Similarity=0.181  Sum_probs=39.1

Q ss_pred             CCCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.++-++++-=.+...   ...+--+.++|++|.||||||.-+.+
T Consensus        25 l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~   74 (332)
T COG2255          25 LDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIAN   74 (332)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHH
Confidence            457999999999886666543   44677889999999999999999999

>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=96.13  E-value=0.0041  Score=51.32  Aligned_cols=20  Identities=25%  Similarity=0.293  Sum_probs=18.8

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.|.|.+|+||||+|+.+..
T Consensus         1 I~i~G~~GsGKtTia~~L~~   20 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAE   20 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999888

...

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=96.12  E-value=0.0067  Score=56.08  Aligned_cols=26  Identities=23%  Similarity=0.258  Sum_probs=23.1

Q ss_pred             CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          187 PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       187 ~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....+|+|.|..|+|||||++.+..
T Consensus        30 ~~~~~iigi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         30 PQRRTIVGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34688999999999999999998876

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=96.11  E-value=0.012  Score=56.88  Aligned_cols=127  Identities=20%  Similarity=0.338  Sum_probs=70.0

Q ss_pred             CCCccc---chhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHh----------hcCcccc-cccc----------
Q 040913          166 RLDISE---FERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADT----------YNNNHVK-FYFD----------  221 (425)
Q Consensus       166 ~~~~vG---r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v----------~~~~~~~-~~F~----------  221 (425)
                      +..+.|   |..+..--+++|.+++  ...|++.|.+|.|||.||-+.          |+.--+. ..++          
T Consensus       220 ~~~vwGi~prn~eQ~~ALdlLld~d--I~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGfLPG  297 (436)
T COG1875         220 DQEVWGIRPRNAEQRVALDLLLDDD--IDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGFLPG  297 (436)
T ss_pred             chhhhccCcccHHHHHHHHHhcCCC--CCeEEeeccCCccHhHHHHHHHHHHHHHHhhhceEEEecCCcCcccccCcCCC
Confidence            334445   5555555578888776  889999999999999998543          2211111 0111          


Q ss_pred             -----chHHH--HHHHHHHhCCCCCCCccCCCCHHHHHHHH---------HHHhcCCe---EEEEecccCCChhhHHHHH
Q 040913          222 -----CLAWI--LDDIIRSLMPPSRVTVIIGEDYKLKKSIL---------RDFLTNKK---YFIALDDVCHNIEIWDDLE  282 (425)
Q Consensus       222 -----~~~wv--~~~il~~l~~~~~~~~~~~~~~~~l~~~l---------~~~l~~kr---~LlVLDdvw~~~~~~~~l~  282 (425)
                           ..-|.  ..+=+..+.....      ...+.+...+         ..+++|+.   -+||+|... +-.. .+++
T Consensus       298 ~eEeKm~PWmq~i~DnLE~L~~~~~------~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQ-NLTp-heik  369 (436)
T COG1875         298 TEEEKMGPWMQAIFDNLEVLFSPNE------PGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQ-NLTP-HELK  369 (436)
T ss_pred             chhhhccchHHHHHhHHHHHhcccc------cchHHHHHHHhccceeeeeeeeecccccccceEEEehhh-ccCH-HHHH
Confidence                 12243  3333333333322      1112222221         12345644   489999887 5422 3455


Q ss_pred             hhCCCCCCCcEEEEecCChh
Q 040913          283 EVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       283 ~~l~~~~~gskIivTTR~~~  302 (425)
                      ..+...+.||||+.|---.+
T Consensus       370 TiltR~G~GsKIVl~gd~aQ  389 (436)
T COG1875         370 TILTRAGEGSKIVLTGDPAQ  389 (436)
T ss_pred             HHHHhccCCCEEEEcCCHHH
Confidence            56666678999998864433

>PRK08233 hypothetical protein; Provisional

Probab=96.10  E-value=0.0046  Score=54.59  Aligned_cols=24  Identities=21%  Similarity=0.254  Sum_probs=21.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+|+|.|.+|+||||||+.+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            478999999999999999999863

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=96.10  E-value=0.0076  Score=55.89  Aligned_cols=27  Identities=15%  Similarity=0.198  Sum_probs=22.9

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ..+.+|.++||+|+||||..|.++.+-
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl   43 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHL   43 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHH
Confidence            346788889999999999999998753

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.10  E-value=0.04  Score=58.84  Aligned_cols=132  Identities=11%  Similarity=0.070  Sum_probs=71.9

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc---cc-cchHHHHHHHHHHhCCCCCCCc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF---YF-DCLAWILDDIIRSLMPPSRVTV  242 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F-~~~~wv~~~il~~l~~~~~~~~  242 (425)
                      .+++|.+...+.|.+++..+. -.+.+-++|+.|+||||+|+.+.+.--...   .+ .|..- .    .........-.
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r-l~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C-~----~~~~~~~Dvie   91 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK-ISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQEC-I----ENVNNSLDIIE   91 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHH-H----HhhcCCCcEEE
Confidence            468899999999999998754 345667899999999999988765211100   01 11100 0    00011000000


Q ss_pred             cC---CCCHH---HHHHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEE-EecCChhHH
Q 040913          243 II---GEDYK---LKKSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVL-ITVINPSLL  304 (425)
Q Consensus       243 ~~---~~~~~---~l~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIi-vTTR~~~va  304 (425)
                      ..   ....+   ++.+.+... ..+++-++|+|++.. +...++.+...+-.-...+.+| +||....+.
T Consensus        92 idaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~A~NALLKtLEEPP~~tifILaTte~~KLl  162 (725)
T PRK07133         92 MDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIP  162 (725)
T ss_pred             EeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHHHHHHHHHHhhcCCCceEEEEEcCChhhhh
Confidence            00   11222   233222211 235677999999853 4467777777766544455544 555444443

>TIGR00235 udk uridine kinase

Probab=96.06  E-value=0.0049  Score=55.99  Aligned_cols=24  Identities=29%  Similarity=0.313  Sum_probs=22.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|++|+|||||++.+..
T Consensus         5 ~g~vi~I~G~sGsGKSTl~~~l~~   28 (207)
T TIGR00235         5 KGIIIGIGGGSGSGKTTVARKIYE   28 (207)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999986

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.04  E-value=0.014  Score=51.72  Aligned_cols=115  Identities=15%  Similarity=0.104  Sum_probs=60.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcccc-c----------cccchHHH-----HHHHHHHhCCCCCCC-ccCCCC-HHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVK-F----------YFDCLAWI-----LDDIIRSLMPPSRVT-VIIGED-YKLK  251 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~-~----------~F~~~~wv-----~~~il~~l~~~~~~~-~~~~~~-~~~l  251 (425)
                      -.+++|+|..|.|||||.+.+..-.... .          .++...|.     +..++..+.-..... .....+ -+..
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~~q  104 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSGGERQ  104 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHHHH
Confidence            4689999999999999999998642110 0          11111111     112344433221100 111122 2333


Q ss_pred             HHHHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCCCC-CC-CcEEEEecCChhHH
Q 040913          252 KSILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLPDN-QN-GSRVLITVINPSLL  304 (425)
Q Consensus       252 ~~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~~~-~~-gskIivTTR~~~va  304 (425)
                      .-.+...+-...-+++||+.-.  +....+.+...+..- .. |..||++|.+....
T Consensus       105 rl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~~~~  161 (180)
T cd03214         105 RVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDLNLA  161 (180)
T ss_pred             HHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHH
Confidence            3445666667778999999751  223344444444321 22 66788888775543

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.03  E-value=0.025  Score=49.96  Aligned_cols=115  Identities=17%  Similarity=0.150  Sum_probs=60.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc-cc--ccc---cc--chHHH-HHHHHHHhCCCCC--CCccCCCCH-HHHHHHHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN-HV--KFY---FD--CLAWI-LDDIIRSLMPPSR--VTVIIGEDY-KLKKSILRD  257 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~-~~--~~~---F~--~~~wv-~~~il~~l~~~~~--~~~~~~~~~-~~l~~~l~~  257 (425)
                      -.+++|+|+.|+|||||.+.+..+. ++  ...   |.  ...|+ ..+.+..+.-...  .......+. +...-.+..
T Consensus        21 G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~~q~~~l~~~~L~~~~~~~~~~~LSgGq~qrl~lar  100 (176)
T cd03238          21 NVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFIDQLQFLIDVGLGYLTLGQKLSTLSGGELQRVKLAS  100 (176)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEEhHHHHHHHcCCCccccCCCcCcCCHHHHHHHHHHH
Confidence            4689999999999999999986321 11  111   10  12233 3345555553211  111122222 222333444


Q ss_pred             HhcCC--eEEEEecccCC--ChhhHHHHHhhCCC-CCCCcEEEEecCChhHH
Q 040913          258 FLTNK--KYFIALDDVCH--NIEIWDDLEEVLPD-NQNGSRVLITVINPSLL  304 (425)
Q Consensus       258 ~l~~k--r~LlVLDdvw~--~~~~~~~l~~~l~~-~~~gskIivTTR~~~va  304 (425)
                      .+-.+  .-+++||..-.  +......+...+.. ...|..||++|.+.+..
T Consensus       101 al~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~~~~  152 (176)
T cd03238         101 ELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVL  152 (176)
T ss_pred             HHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHH
Confidence            55555  67888898741  22333334333332 12467788888887654

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.01  E-value=0.028  Score=54.90  Aligned_cols=45  Identities=18%  Similarity=-0.044  Sum_probs=34.6

Q ss_pred             cccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          169 ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++|....+.++.+.+..-.....-|.|.|..|+||+++|+.+++.
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHh
Confidence            467777777877777654333455789999999999999999864

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

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.99  E-value=0.11  Score=51.62  Aligned_cols=24  Identities=21%  Similarity=0.286  Sum_probs=20.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|+++|++|+||||++..+..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999888754

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=95.98  E-value=0.064  Score=52.10  Aligned_cols=40  Identities=10%  Similarity=0.071  Sum_probs=33.2

Q ss_pred             hhhHHHHHHHHhcCC-CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          173 ERAREEWFDLLIEGP-IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       173 ~~~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.-.+.|.+.|...+ ....+|+|.|.-|+||||+.+.+.+
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~IgL~G~WGsGKSs~l~~l~~   42 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDSDDPFVIGLYGEWGSGKSSFLNMLKE   42 (325)
T ss_pred             hHHHHHHHHHHhccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            445677788887764 6789999999999999999998876

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PTZ00301 uridine kinase; Provisional

Probab=95.98  E-value=0.0055  Score=55.80  Aligned_cols=23  Identities=22%  Similarity=0.394  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|.|.+|+||||||+.+.+
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHH
Confidence            57999999999999999987765

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=95.97  E-value=0.011  Score=54.53  Aligned_cols=25  Identities=20%  Similarity=0.094  Sum_probs=21.9

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-.++.|+|.+|+|||+|+.++.-
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~   41 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAV   41 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999998864

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

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

Probab=95.97  E-value=0.041  Score=53.28  Aligned_cols=130  Identities=12%  Similarity=0.108  Sum_probs=70.1

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc---cccchHHHHHHHHHHhCCCCCCC---
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF---YFDCLAWILDDIIRSLMPPSRVT---  241 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F~~~~wv~~~il~~l~~~~~~~---  241 (425)
                      .++|-+....++..+..........+-+.|++|+||||+|..+.+.---..   ...+...   .....+.......   
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~---~~~~~~~~~~~~d~le   78 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHC---RSCKLIPAGNHPDFLE   78 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccch---hhhhHHhhcCCCceEE
Confidence            466777888888888886544455688999999999999988776211000   0000000   0000000000000   


Q ss_pred             ----ccCCCC-HHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          242 ----VIIGED-YKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       242 ----~~~~~~-~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                          +....+ ..+....+.+..     .++.-++++|++.. +.+.-+.+...+......+.+|++|..
T Consensus        79 l~~s~~~~~~i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~~A~nallk~lEep~~~~~~il~~n~  148 (325)
T COG0470          79 LNPSDLRKIDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTEDAANALLKTLEEPPKNTRFILITND  148 (325)
T ss_pred             ecccccCCCcchHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhHHHHHHHHHHhccCCCCeEEEEEcCC
Confidence                011111 222233333332     14678999999962 234556666666666667888888873

>TIGR01817 nifA Nif-specific regulatory protein

Probab=95.96  E-value=0.021  Score=59.74  Aligned_cols=50  Identities=18%  Similarity=-0.053  Sum_probs=40.2

Q ss_pred             CCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          164 QPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .....++|....+.++.+.+..-......|.|+|..|+|||++|+.+++.
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHh
Confidence            34567999999999998888754333445679999999999999999974

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.

>PRK06547 hypothetical protein; Provisional

Probab=95.96  E-value=0.01  Score=52.26  Aligned_cols=25  Identities=32%  Similarity=0.311  Sum_probs=22.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+|.|.|++|+||||+|+.+.+.
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999998763

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=95.94  E-value=0.035  Score=50.81  Aligned_cols=58  Identities=16%  Similarity=0.294  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCCC--CCCCcEEEEecCChhHHHH
Q 040913          249 KLKKSILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLPD--NQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       249 ~~l~~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~~--~~~gskIivTTR~~~va~~  306 (425)
                      ++-.-.+.+.|-...-+|+-|.--.  +...=+.+...+..  ...|..||+.|.+..+|..
T Consensus       147 qqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VTHd~~lA~~  208 (226)
T COG1136         147 QQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVTHDPELAKY  208 (226)
T ss_pred             HHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHh
Confidence            4444567777788888899997531  11222233333332  2347889999999999873

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=95.93  E-value=0.026  Score=49.89  Aligned_cols=24  Identities=21%  Similarity=0.192  Sum_probs=21.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||++.+..-
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            457999999999999999999874

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

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

Probab=95.92  E-value=0.044  Score=54.07  Aligned_cols=24  Identities=25%  Similarity=0.335  Sum_probs=20.1

Q ss_pred             CcEEEEEEecCCCchHH-HHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTA-FAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTt-La~~v~~  212 (425)
                      +-++|.+||+.|+|||| ||+....
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar  226 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAAR  226 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHH
Confidence            37999999999999998 7776544

>PRK13531 regulatory ATPase RavA; Provisional

Probab=95.91  E-value=0.016  Score=58.85  Aligned_cols=40  Identities=20%  Similarity=0.152  Sum_probs=35.4

Q ss_pred             cccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          169 ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|+++.++.+...+..+.    -|-+.|++|+|||+||+.+..
T Consensus        22 i~gre~vI~lll~aalag~----hVLL~GpPGTGKT~LAraLa~   61 (498)
T PRK13531         22 LYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKF   61 (498)
T ss_pred             ccCcHHHHHHHHHHHccCC----CEEEECCCChhHHHHHHHHHH
Confidence            8999999999988887753    467899999999999999987

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.89  E-value=0.0054  Score=52.49  Aligned_cols=23  Identities=17%  Similarity=0.177  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-|.|.||+|+|||||++.+.+
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e   27 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAE   27 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHH
Confidence            34588999999999999999987

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=95.88  E-value=0.022  Score=52.06  Aligned_cols=23  Identities=17%  Similarity=0.121  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|+|||||.+.+..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (220)
T cd03263          28 GEIFGLLGHNGAGKTTTLKMLTG   50 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

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

Probab=95.88  E-value=0.021  Score=52.36  Aligned_cols=28  Identities=18%  Similarity=0.090  Sum_probs=22.7

Q ss_pred             cCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          185 EGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       185 ~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+=..-.++.|+|.+|+|||+|+.++..
T Consensus        14 GG~~~g~v~~I~G~~GsGKT~l~~~ia~   41 (226)
T cd01393          14 GGIPTGRITEIFGEFGSGKTQLCLQLAV   41 (226)
T ss_pred             CCCcCCcEEEEeCCCCCChhHHHHHHHH
Confidence            3334567999999999999999988764

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=95.85  E-value=0.049  Score=51.54  Aligned_cols=125  Identities=14%  Similarity=0.091  Sum_probs=71.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCcc--
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVI--  243 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~--  243 (425)
                      -.+++|.+...+-|.+.+...  ..+....+|++|.|||+-|..+...---.+.|++++--      .-.....+...  
T Consensus        35 ~de~~gQe~vV~~L~~a~~~~--~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~------lnaSderGisvvr  106 (346)
T KOG0989|consen   35 FDELAGQEHVVQVLKNALLRR--ILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLE------LNASDERGISVVR  106 (346)
T ss_pred             HHhhcchHHHHHHHHHHHhhc--CCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhh------hcccccccccchh
Confidence            356889999999999888873  47888899999999999887766522223456654431      00000000000  


Q ss_pred             -CCCCHHHHHHHHHHHh--cCCe-EEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEec
Q 040913          244 -IGEDYKLKKSILRDFL--TNKK-YFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITV  298 (425)
Q Consensus       244 -~~~~~~~l~~~l~~~l--~~kr-~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTT  298 (425)
                       ...+...+........  ..+. -.||||++.. ..+.|..++..+.+....++-|..|
T Consensus       107 ~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsdaq~aLrr~mE~~s~~trFiLIc  166 (346)
T KOG0989|consen  107 EKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSDAQAALRRTMEDFSRTTRFILIC  166 (346)
T ss_pred             hhhcCHHHHhhccccccCCCCCcceEEEEechhhhhHHHHHHHHHHHhccccceEEEEEc
Confidence             0011111111111000  0133 3789999963 3589999998887766566644433

>PRK06762 hypothetical protein; Provisional

Probab=95.80  E-value=0.0073  Score=52.65  Aligned_cols=23  Identities=26%  Similarity=0.310  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|++|+||||+|+.+.+
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~   24 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQE   24 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999887

>PRK12608 transcription termination factor Rho; Provisional

Probab=95.79  E-value=0.0078  Score=59.10  Aligned_cols=37  Identities=16%  Similarity=0.030  Sum_probs=27.7

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++++.+..-..+ .-+.|+|.+|+|||||++.+.+
T Consensus       119 ~~~RvID~l~PiGkG-QR~LIvG~pGtGKTTLl~~la~  155 (380)
T PRK12608        119 LSMRVVDLVAPIGKG-QRGLIVAPPRAGKTVLLQQIAA  155 (380)
T ss_pred             hhHhhhhheeecCCC-ceEEEECCCCCCHHHHHHHHHH
Confidence            345578877753322 3458999999999999999877

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.76  E-value=0.031  Score=57.44  Aligned_cols=97  Identities=18%  Similarity=0.234  Sum_probs=62.4

Q ss_pred             CCCCCCcccchhhHHHHHHHHhc---CC-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHH
Q 040913          163 GQPRLDISEFERAREEWFDLLIE---GP-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIR  232 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~---~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~  232 (425)
                      .+.-.++=|.+....++.+++..   ++       ...+=|.++|++|.|||.||+.+.+  +..-.|-.+.  .-+|+.
T Consensus       186 nv~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAg--el~vPf~~is--ApeivS  261 (802)
T KOG0733|consen  186 NVSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAG--ELGVPFLSIS--APEIVS  261 (802)
T ss_pred             CcchhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhh--hcCCceEeec--chhhhc
Confidence            33445667889888888777653   21       2355577999999999999999999  4444441100  011111


Q ss_pred             HhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          233 SLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       233 ~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                               +....+++.+.+-+.+.-..-.+++++|++.
T Consensus       262 ---------GvSGESEkkiRelF~~A~~~aPcivFiDeID  292 (802)
T KOG0733|consen  262 ---------GVSGESEKKIRELFDQAKSNAPCIVFIDEID  292 (802)
T ss_pred             ---------ccCcccHHHHHHHHHHHhccCCeEEEeeccc
Confidence                     2233455555555555666789999999995

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.73  E-value=0.011  Score=53.56  Aligned_cols=25  Identities=16%  Similarity=0.027  Sum_probs=21.8

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.-.++-|+|++|+|||+|+.++..
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~   34 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAV   34 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4568999999999999999988764

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

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=95.73  E-value=0.05  Score=51.79  Aligned_cols=102  Identities=14%  Similarity=0.107  Sum_probs=65.0

Q ss_pred             CCCcccchh---hHHHHHHHHhcCC-CCcEEEEEEecCCCchHHHHHHhhcCcccc-----ccccchHHH----------
Q 040913          166 RLDISEFER---AREEWFDLLIEGP-IGLSVVAILDSSGFDKTAFAADTYNNNHVK-----FYFDCLAWI----------  226 (425)
Q Consensus       166 ~~~~vGr~~---~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~-----~~F~~~~wv----------  226 (425)
                      .+..+|...   ..+++.++|..+. ...+-+.|||.+|.|||++++......-..     ..+ .++.|          
T Consensus        33 ~~rWIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~-PVv~vq~P~~p~~~~  111 (302)
T PF05621_consen   33 ADRWIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERI-PVVYVQMPPEPDERR  111 (302)
T ss_pred             cCCeecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccc-cEEEEecCCCCChHH
Confidence            344666443   3455555565553 346778999999999999999988632111     111 11122          


Q ss_pred             -HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcC-CeEEEEecccC
Q 040913          227 -LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTN-KKYFIALDDVC  272 (425)
Q Consensus       227 -~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~-kr~LlVLDdvw  272 (425)
                       ...|+.+++.+...    ..+...+...+...++. +--+||+|.+-
T Consensus       112 ~Y~~IL~~lgaP~~~----~~~~~~~~~~~~~llr~~~vrmLIIDE~H  155 (302)
T PF05621_consen  112 FYSAILEALGAPYRP----RDRVAKLEQQVLRLLRRLGVRMLIIDEFH  155 (302)
T ss_pred             HHHHHHHHhCcccCC----CCCHHHHHHHHHHHHHHcCCcEEEeechH
Confidence             78999999988652    23445555566566654 55689999996

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=95.73  E-value=0.0072  Score=44.50  Aligned_cols=21  Identities=29%  Similarity=0.370  Sum_probs=19.1

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|.|.|..|+||||+++.+.+
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~   21 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAE   21 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999998887

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=95.69  E-value=0.094  Score=51.29  Aligned_cols=128  Identities=9%  Similarity=0.019  Sum_probs=69.5

Q ss_pred             Cccc-chhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccc------cchHHHHHHHHHHhCCCCCC
Q 040913          168 DISE-FERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF------DCLAWILDDIIRSLMPPSRV  240 (425)
Q Consensus       168 ~~vG-r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F------~~~~wv~~~il~~l~~~~~~  240 (425)
                      .++| -+...+.+.+.+..+. -.+..-++|+.|+||||+|..+.+.--.....      .|...      +.+......
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~-l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c------~~~~~~~hp   78 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNR-LSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNC------KRIDSGNHP   78 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCC-CCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHH------HHHhcCCCC
Confidence            3556 5666777777776543 45667899999999999998775421111000      01110      011000000


Q ss_pred             C------ccCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          241 T------VIIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       241 ~------~~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .      +......+++.+.+...    ..+.+-++|+|++.. +.+.-+.+...+..-..++.+|++|.+..
T Consensus        79 D~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~  151 (329)
T PRK08058         79 DVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKH  151 (329)
T ss_pred             CEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChH
Confidence            0      00112334443333221    235566799999853 44567778778776666777777776533

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=95.67  E-value=0.03  Score=60.46  Aligned_cols=48  Identities=21%  Similarity=0.003  Sum_probs=38.3

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...++|....+..+.+.+..-.....-|-|.|..|+|||++|+.+++.
T Consensus       375 ~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        375 FGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             ccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHh
Confidence            346999999999988777643333446789999999999999999874

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=95.67  E-value=0.042  Score=53.02  Aligned_cols=24  Identities=17%  Similarity=0.112  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|+.|.|||||.+.+...
T Consensus        28 Gei~~l~G~NGaGKTTLl~~l~Gl   51 (301)
T TIGR03522        28 GRIVGFLGPNGAGKSTTMKIITGY   51 (301)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999998753

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>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=95.65  E-value=0.043  Score=48.12  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=18.5

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++.++|++|+||||++..+..
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~   22 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLAL   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            678999999999999887765

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.

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=95.65  E-value=0.045  Score=50.66  Aligned_cols=23  Identities=26%  Similarity=0.239  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|+|||||++.+..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (237)
T cd03252          28 GEVVGIVGRSGSGKSTLTKLIQR   50 (237)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999998875

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=95.64  E-value=0.092  Score=51.26  Aligned_cols=108  Identities=13%  Similarity=0.067  Sum_probs=58.3

Q ss_pred             CCCcEEEEEEecCCCchHHHHHHhhcCcccc------ccccchHHHHHHHHHHhCCCCCCC-----c----cCCCCHHHH
Q 040913          187 PIGLSVVAILDSSGFDKTAFAADTYNNNHVK------FYFDCLAWILDDIIRSLMPPSRVT-----V----IIGEDYKLK  251 (425)
Q Consensus       187 ~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~------~~F~~~~wv~~~il~~l~~~~~~~-----~----~~~~~~~~l  251 (425)
                      ..-...+.+.|+.|+||||+|..+.+.--..      .+=.|....      .+... ..+     .    ......+++
T Consensus        19 ~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~------~~~~g-~HPD~~~i~~~~~~~~i~id~i   91 (328)
T PRK05707         19 GRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQ------LLRAG-SHPDNFVLEPEEADKTIKVDQV   91 (328)
T ss_pred             CCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHH------HHhcC-CCCCEEEEeccCCCCCCCHHHH
Confidence            3346678899999999999998765521111      111111110      00000 000     0    011234444


Q ss_pred             HHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          252 KSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       252 ~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .+ +.+.+     .+++-++|+|++.. +.+..+.+...+-.-..++.+|+||.+.+
T Consensus        92 R~-l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~  147 (328)
T PRK05707         92 RE-LVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPS  147 (328)
T ss_pred             HH-HHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChh
Confidence            43 22322     24555667899964 55777777777766555777777777654

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=95.64  E-value=0.033  Score=57.85  Aligned_cols=48  Identities=15%  Similarity=-0.008  Sum_probs=40.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...++|....+.++.+.+..-.....-|.|.|..|+|||++|+.+++.
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            456999999999998888765444556789999999999999999874

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=95.64  E-value=0.027  Score=52.53  Aligned_cols=117  Identities=11%  Similarity=0.104  Sum_probs=67.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccc---cccchHH----H------HHHHHHHhCCCCCCC---ccCCCCHHHHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKF---YFDCLAW----I------LDDIIRSLMPPSRVT---VIIGEDYKLKKS  253 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~---~F~~~~w----v------~~~il~~l~~~~~~~---~~~~~~~~~l~~  253 (425)
                      -.++++||..|.|||||++.+..=.+-..   .|+..-.    .      ..+++..++.....-   ....+..+.-.-
T Consensus        39 ge~~glVGESG~GKSTlgr~i~~L~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQRi  118 (268)
T COG4608          39 GETLGLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQRI  118 (268)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHcCcCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhhH
Confidence            56899999999999999999987332111   2443211    1      556666666332211   112222233334


Q ss_pred             HHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCCC--CCCCcEEEEecCChhHHHH
Q 040913          254 ILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLPD--NQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       254 ~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~~--~~~gskIivTTR~~~va~~  306 (425)
                      .+...|.-+.-|||.|..-+  +...-.++...+.+  ...|-..+..|.+-.|+..
T Consensus       119 ~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL~vv~~  175 (268)
T COG4608         119 GIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDLSVVRY  175 (268)
T ss_pred             HHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEHHhhhh
Confidence            57777888999999998752  11112233333321  2236667777777777653

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=95.63  E-value=0.01  Score=52.99  Aligned_cols=111  Identities=14%  Similarity=0.071  Sum_probs=55.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHH-------HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcC--C
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTN--K  262 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~--k  262 (425)
                      ++.|.|..|.||||+.+.+.-..- -.+-.+.++.       ...++..+...... .....+...-...+...+..  +
T Consensus         1 ~~~ltG~N~~GKst~l~~i~~~~~-la~~G~~v~a~~~~~~~~d~il~~~~~~d~~-~~~~s~fs~~~~~l~~~l~~~~~   78 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGLIVI-MAQIGSFVPAESAELPVFDRIFTRIGASDSL-AQGLSTFMVEMKETANILKNATE   78 (185)
T ss_pred             CEEEECCCCCcHHHHHHHHHHHHH-HHHhCCCeeehheEecccceEEEEeCCCCch-hccccHHHHHHHHHHHHHHhCCC
Confidence            467999999999999998873211 1111111111       22333222222111 11111222223345555554  8


Q ss_pred             eEEEEecccCC--Chhh----HHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          263 KYFIALDDVCH--NIEI----WDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       263 r~LlVLDdvw~--~~~~----~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      +-|+++|..-.  +...    ...+...+.. ..++.+|++|.+.++..
T Consensus        79 ~~llllDEp~~g~d~~~~~~~~~~~l~~l~~-~~~~~iii~TH~~~l~~  126 (185)
T smart00534       79 NSLVLLDELGRGTSTYDGVAIAAAVLEYLLE-KIGALTLFATHYHELTK  126 (185)
T ss_pred             CeEEEEecCCCCCCHHHHHHHHHHHHHHHHh-cCCCeEEEEecHHHHHH
Confidence            89999999852  1111    1122222222 23678999998877654

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.60  E-value=0.041  Score=48.28  Aligned_cols=24  Identities=25%  Similarity=0.141  Sum_probs=21.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        28 G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          28 GEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHcC
Confidence            468999999999999999999874

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). 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.

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=95.58  E-value=0.028  Score=56.08  Aligned_cols=105  Identities=11%  Similarity=0.043  Sum_probs=68.7

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-----------HHHH
Q 040913          164 QPRLDISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------LDDI  230 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-----------~~~i  230 (425)
                      ..+..++||+.+++.+.+++...  ....+.+-|.|.+|.|||.+...++.+..-...=.+++++           +..|
T Consensus       147 ~~p~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~~aiF~kI  226 (529)
T KOG2227|consen  147 APPGTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEASAIFKKI  226 (529)
T ss_pred             CCCCCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccchHHHHHHH
Confidence            34567899999999999998765  3356778889999999999999998853211110111222           5555


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCC--eEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNK--KYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~k--r~LlVLDdvw  272 (425)
                      ...+......    .....+.+..+.....+.  -+|+|||...
T Consensus       227 ~~~~~q~~~s----~~~~~~~~~~~~~h~~q~k~~~llVlDEmD  266 (529)
T KOG2227|consen  227 FSSLLQDLVS----PGTGMQHLEKFEKHTKQSKFMLLLVLDEMD  266 (529)
T ss_pred             HHHHHHHhcC----CchhHHHHHHHHHHHhcccceEEEEechhh
Confidence            5555222221    112256667777776653  5899999886

>PRK03839 putative kinase; Provisional

Probab=95.58  E-value=0.0088  Score=52.96  Aligned_cols=22  Identities=23%  Similarity=0.326  Sum_probs=19.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .|.|.|++|+||||+++.+.+.
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999883

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.58  E-value=0.025  Score=48.95  Aligned_cols=111  Identities=13%  Similarity=0.125  Sum_probs=58.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc-----Ccccc-ccccchHHH--HHHHHHHhCCCCCC-----C-ccCCCCH-------H
Q 040913          191 SVVAILDSSGFDKTAFAADTYN-----NNHVK-FYFDCLAWI--LDDIIRSLMPPSRV-----T-VIIGEDY-------K  249 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~-----~~~~~-~~F~~~~wv--~~~il~~l~~~~~~-----~-~~~~~~~-------~  249 (425)
                      +.|-|++..|.||||+|-...-     ..++. -.|-..-|-  -..++..+.. ...     . .....+.       .
T Consensus         3 G~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~vQFlKg~~~~gE~~~l~~l~~-v~~~~~g~~~~~~~~~~~~~~~~a~   81 (159)
T cd00561           3 GLIQVYTGNGKGKTTAALGLALRALGHGYRVGVVQFLKGGWKYGELKALERLPN-IEIHRMGRGFFWTTENDEEDIAAAA   81 (159)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEEeCCCCccCHHHHHHhCCC-cEEEECCCCCccCCCChHHHHHHHH
Confidence            4678888899999999865432     11111 012111122  3334444420 000     0 0000111       1


Q ss_pred             HHHHHHHHHhcCC-eEEEEecccCC----ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          250 LKKSILRDFLTNK-KYFIALDDVCH----NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       250 ~l~~~l~~~l~~k-r~LlVLDdvw~----~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ...+..++.+... -=|||||++-.    ..-..+.+...+.....+.-||+|.|+..
T Consensus        82 ~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p  139 (159)
T cd00561          82 EGWAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAP  139 (159)
T ss_pred             HHHHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCC
Confidence            1233344444444 44999999851    12355667777766666788999999954

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=95.57  E-value=0.029  Score=49.34  Aligned_cols=24  Identities=25%  Similarity=0.200  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||.+.+..-
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~   51 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGL   51 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            458999999999999999999863

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.57  E-value=0.018  Score=54.72  Aligned_cols=77  Identities=10%  Similarity=0.141  Sum_probs=49.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcccc--ccccchHHH---HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVK--FYFDCLAWI---LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKY  264 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~--~~F~~~~wv---~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~  264 (425)
                      -++|.++|++|.|||+|.+.+++.-.++  +.+....-+   -.++..+.+...+      .-...+-++|.+.++++..
T Consensus       177 NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESg------KlV~kmF~kI~ELv~d~~~  250 (423)
T KOG0744|consen  177 NRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESG------KLVAKMFQKIQELVEDRGN  250 (423)
T ss_pred             eeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhh------hHHHHHHHHHHHHHhCCCc
Confidence            5889999999999999999999864333  223222211   3344444433332      3456677788888877554


Q ss_pred             --EEEecccC
Q 040913          265 --FIALDDVC  272 (425)
Q Consensus       265 --LlVLDdvw  272 (425)
                        ++.+|.|.
T Consensus       251 lVfvLIDEVE  260 (423)
T KOG0744|consen  251 LVFVLIDEVE  260 (423)
T ss_pred             EEEEEeHHHH
Confidence              55678885

>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=95.57  E-value=0.01  Score=53.38  Aligned_cols=23  Identities=26%  Similarity=0.328  Sum_probs=18.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++||.+||+.|+||||.+-++..
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa   23 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAA   23 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHH
Confidence            47999999999999996655443

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 ....

>PRK14527 adenylate kinase; Provisional

Probab=95.56  E-value=0.078  Score=47.41  Aligned_cols=24  Identities=25%  Similarity=0.165  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|+|++|+||||+|+.+.+
T Consensus         5 ~~~~i~i~G~pGsGKsT~a~~La~   28 (191)
T PRK14527          5 KNKVVIFLGPPGAGKGTQAERLAQ   28 (191)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999876

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.56  E-value=0.01  Score=52.71  Aligned_cols=24  Identities=13%  Similarity=0.173  Sum_probs=21.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.|+|++|+||||+++.+..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999999999875

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.

>PRK04296 thymidine kinase; Provisional

Probab=95.55  E-value=0.012  Score=52.74  Aligned_cols=107  Identities=13%  Similarity=0.039  Sum_probs=55.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCcccc--------ccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVK--------FYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNK  262 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~--------~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~k  262 (425)
                      .++.|.|..|.||||++..........        ..|+.+.- ...+...++....  ........++...+.+ ..++
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~k~~~d~~~~-~~~i~~~lg~~~~--~~~~~~~~~~~~~~~~-~~~~   78 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVFKPAIDDRYG-EGKVVSRIGLSRE--AIPVSSDTDIFELIEE-EGEK   78 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEEecccccccc-CCcEecCCCCccc--ceEeCChHHHHHHHHh-hCCC
Confidence            467789999999999987766522111        11111100 1223333321111  1111234555555555 3334


Q ss_pred             eEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChhH
Q 040913          263 KYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPSL  303 (425)
Q Consensus       263 r~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~v  303 (425)
                      .-+||+|.+.. +.+....+...+  ...|..||+|.++.+.
T Consensus        79 ~dvviIDEaq~l~~~~v~~l~~~l--~~~g~~vi~tgl~~~~  118 (190)
T PRK04296         79 IDCVLIDEAQFLDKEQVVQLAEVL--DDLGIPVICYGLDTDF  118 (190)
T ss_pred             CCEEEEEccccCCHHHHHHHHHHH--HHcCCeEEEEecCccc
Confidence            55899999863 233233333332  2447889999998553

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=95.55  E-value=0.017  Score=53.18  Aligned_cols=32  Identities=22%  Similarity=0.150  Sum_probs=24.5

Q ss_pred             HHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          181 DLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       181 ~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|..+=..-.++.|+|.+|+|||+||.++..
T Consensus        14 ~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~   45 (225)
T PRK09361         14 ELLGGGFERGTITQIYGPPGSGKTNICLQLAV   45 (225)
T ss_pred             HHhcCCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            33333334568999999999999999988775

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=95.54  E-value=0.07  Score=45.40  Aligned_cols=103  Identities=13%  Similarity=0.108  Sum_probs=54.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEec
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALD  269 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLD  269 (425)
                      -.+++|+|..|.|||||++.+..-....   ...+++-..  ..+..     -..-+..+...-.+...+..+.-++++|
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~~---~G~i~~~~~--~~i~~-----~~~lS~G~~~rv~laral~~~p~illlD   95 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELEPD---EGIVTWGST--VKIGY-----FEQLSGGEKMRLALAKLLLENPNLLLLD   95 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCCC---ceEEEECCe--EEEEE-----EccCCHHHHHHHHHHHHHhcCCCEEEEe
Confidence            4688999999999999999998743211   111111000  00000     0001122333344566666677789999


Q ss_pred             ccCC--ChhhHHHHHhhCCCCCCCcEEEEecCChhHH
Q 040913          270 DVCH--NIEIWDDLEEVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       270 dvw~--~~~~~~~l~~~l~~~~~gskIivTTR~~~va  304 (425)
                      +.-.  +......+...+...  +..||++|.+...+
T Consensus        96 EP~~~LD~~~~~~l~~~l~~~--~~til~~th~~~~~  130 (144)
T cd03221          96 EPTNHLDLESIEALEEALKEY--PGTVILVSHDRYFL  130 (144)
T ss_pred             CCccCCCHHHHHHHHHHHHHc--CCEEEEEECCHHHH
Confidence            8752  233444444444322  24677787775544

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=95.54  E-value=0.0078  Score=54.18  Aligned_cols=21  Identities=29%  Similarity=0.433  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|.+|+|||||++.+..
T Consensus         1 iigi~G~~GsGKSTl~~~l~~   21 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIE   21 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999876

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.50  E-value=0.028  Score=48.94  Aligned_cols=106  Identities=14%  Similarity=0.031  Sum_probs=56.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---------HHHHHH-HhCCCCCCCccCCCCHHHHHHHHHHHh
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------LDDIIR-SLMPPSRVTVIIGEDYKLKKSILRDFL  259 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------~~~il~-~l~~~~~~~~~~~~~~~~l~~~l~~~l  259 (425)
                      -.+++|+|..|.|||||.+.+..-...   ....+++         ..+..+ .++.     -..-+.-+...-.+...+
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~~~~---~~G~v~~~g~~~~~~~~~~~~~~~i~~-----~~qLS~G~~qrl~laral   97 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGLYKP---DSGEILVDGKEVSFASPRDARRAGIAM-----VYQLSVGERQMVEIARAL   97 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCC---CCeEEEECCEECCcCCHHHHHhcCeEE-----EEecCHHHHHHHHHHHHH
Confidence            458999999999999999999863211   1111111         000000 0000     000112223334455556


Q ss_pred             cCCeEEEEecccCC--ChhhHHHHHhhCCC-CCCCcEEEEecCChhH
Q 040913          260 TNKKYFIALDDVCH--NIEIWDDLEEVLPD-NQNGSRVLITVINPSL  303 (425)
Q Consensus       260 ~~kr~LlVLDdvw~--~~~~~~~l~~~l~~-~~~gskIivTTR~~~v  303 (425)
                      -.+.-+++||+.-.  +......+...+.. ...|..||++|.+...
T Consensus        98 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~~~  144 (163)
T cd03216          98 ARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRLDE  144 (163)
T ss_pred             hcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHH
Confidence            66778899999752  22333344444432 1236678888887653

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=95.49  E-value=0.066  Score=48.97  Aligned_cols=23  Identities=17%  Similarity=0.267  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        30 Ge~~~i~G~nGsGKSTLl~~l~G   52 (221)
T cd03244          30 GEKVGIVGRTGSGKSSLLLALFR   52 (221)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHc
Confidence            46899999999999999999875

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.47  E-value=0.064  Score=47.50  Aligned_cols=22  Identities=23%  Similarity=0.321  Sum_probs=19.8

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .|.|.|.+|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3679999999999999999884

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=95.42  E-value=0.029  Score=54.38  Aligned_cols=83  Identities=13%  Similarity=0.060  Sum_probs=45.4

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLT  260 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~  260 (425)
                      +.-+++-|.|++|+||||||.++.-.  ....-...+|+      -...+.+++.....- -....+.++....+...++
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~  130 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVR  130 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHh
Confidence            45678889999999999999887642  11111122233      111222222211100 1112345666666666554


Q ss_pred             C-CeEEEEecccC
Q 040913          261 N-KKYFIALDDVC  272 (425)
Q Consensus       261 ~-kr~LlVLDdvw  272 (425)
                      . .--+||+|-|-
T Consensus       131 s~~~~lIVIDSva  143 (325)
T cd00983         131 SGAVDLIVVDSVA  143 (325)
T ss_pred             ccCCCEEEEcchH
Confidence            3 56699999974

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK04040 adenylate kinase; Provisional

Probab=95.41  E-value=0.012  Score=52.53  Aligned_cols=23  Identities=22%  Similarity=0.361  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|+|++|+||||+++.+.+
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH
Confidence            46899999999999999999877

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=95.41  E-value=0.074  Score=49.26  Aligned_cols=24  Identities=25%  Similarity=0.173  Sum_probs=21.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||++.+..-
T Consensus        29 Ge~~~l~G~nGsGKSTLl~~i~G~   52 (238)
T cd03249          29 GKTVALVGSSGCGKSTVVSLLERF   52 (238)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHhcc
Confidence            468999999999999999998753

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.41  E-value=0.023  Score=55.91  Aligned_cols=109  Identities=13%  Similarity=0.058  Sum_probs=63.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---HHHHHHHhCCC-CCCCccCCCCHHHHHHHHHHHhcCCeEE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---LDDIIRSLMPP-SRVTVIIGEDYKLKKSILRDFLTNKKYF  265 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---~~~il~~l~~~-~~~~~~~~~~~~~l~~~l~~~l~~kr~L  265 (425)
                      ...|.|.|+.|+||||+...+.+  .+..+...+++.   ..++...-... ....+. ..+.......++..|+...=.
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~--~i~~~~~~~i~tiEdp~E~~~~~~~~~i~q~ev-g~~~~~~~~~l~~~lr~~pd~  198 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMID--YINKNAAGHIITIEDPIEYVHRNKRSLINQREV-GLDTLSFANALRAALREDPDV  198 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH--hhCcCCCCEEEEEcCChhhhccCccceEEcccc-CCCCcCHHHHHHHhhccCCCE
Confidence            47899999999999999998776  333333333333   00111000000 000000 112234566677888888889


Q ss_pred             EEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          266 IALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       266 lVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      |++|.+. +.+.+......   ...|..|+.|+...++..
T Consensus       199 i~vgEir-d~~~~~~~l~a---a~tGh~v~~T~Ha~~~~~  234 (343)
T TIGR01420       199 ILIGEMR-DLETVELALTA---AETGHLVFGTLHTNSAAQ  234 (343)
T ss_pred             EEEeCCC-CHHHHHHHHHH---HHcCCcEEEEEcCCCHHH
Confidence            9999998 77766553332   233666777777766654

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.

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=95.41  E-value=0.076  Score=48.05  Aligned_cols=23  Identities=13%  Similarity=0.268  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        34 G~~~~i~G~nGsGKSTLl~~l~G   56 (207)
T cd03369          34 GEKIGIVGRTGAGKSTLILALFR   56 (207)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999875

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=95.40  E-value=0.0088  Score=54.93  Aligned_cols=21  Identities=19%  Similarity=0.164  Sum_probs=19.2

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|.+|+||||||+.+.+
T Consensus         1 IigI~G~sGSGKTTla~~L~~   21 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQA   21 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHH
Confidence            589999999999999998876

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=95.40  E-value=0.057  Score=50.06  Aligned_cols=94  Identities=14%  Similarity=0.080  Sum_probs=56.6

Q ss_pred             CCCCcccchhhHHHHHHHHhcC----C-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHH
Q 040913          165 PRLDISEFERAREEWFDLLIEG----P-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRS  233 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~----~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~  233 (425)
                      ..+++=|-.+.+++|-+....+    +       +.++=|..+|++|.|||-+|++|.|  +...+|-.++=.  ++...
T Consensus       175 ty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravan--rtdacfirvigs--elvqk  250 (435)
T KOG0729|consen  175 TYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVAN--RTDACFIRVIGS--ELVQK  250 (435)
T ss_pred             ccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhc--ccCceEEeehhH--HHHHH
Confidence            3345556777777776554322    1       3466678899999999999999999  777777433211  11111


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcC-CeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTN-KKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~-kr~LlVLDdvw  272 (425)
                      ..          .....+...+.+.-+. |-|+|.+|.+.
T Consensus       251 yv----------gegarmvrelf~martkkaciiffdeid  280 (435)
T KOG0729|consen  251 YV----------GEGARMVRELFEMARTKKACIIFFDEID  280 (435)
T ss_pred             Hh----------hhhHHHHHHHHHHhcccceEEEEeeccc
Confidence            00          1112333444444444 66899999884

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.40  E-value=0.032  Score=53.17  Aligned_cols=23  Identities=13%  Similarity=0.049  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        33 Ge~~~i~G~nGsGKSTLl~~l~G   55 (279)
T PRK13650         33 GEWLSIIGHNGSGKSTTVRLIDG   55 (279)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999875

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

Probab=95.39  E-value=0.016  Score=50.80  Aligned_cols=46  Identities=17%  Similarity=0.046  Sum_probs=33.8

Q ss_pred             cccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          169 ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ++|....+.++++.+..-.....-|-|+|..|+||+.+|+.+++.-
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s   46 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNS   46 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCS
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            4788888888888877643223456699999999999999999853

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 ....

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=95.38  E-value=0.013  Score=52.95  Aligned_cols=22  Identities=9%  Similarity=-0.010  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++.|+|..|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            6899999999999999999884

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.38  E-value=0.023  Score=47.58  Aligned_cols=40  Identities=15%  Similarity=0.076  Sum_probs=28.3

Q ss_pred             hhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          174 RAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       174 ~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++..++.+.|...-..-.+|.+.|.-|.|||||++.+.+.
T Consensus         6 ~~t~~l~~~l~~~l~~~~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150         6 KAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             HHHHHHHHHHHHhCCCCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            3444555545433223568999999999999999999874

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.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.38  E-value=0.025  Score=51.29  Aligned_cols=113  Identities=10%  Similarity=0.029  Sum_probs=57.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcccc--ccccchHHH----HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHh--cC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVK--FYFDCLAWI----LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFL--TN  261 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~--~~F~~~~wv----~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l--~~  261 (425)
                      ..++.|.|+.|.||||+.+.+....-..  ..|-+....    .+.|...+....... ....+...-...+...+  ..
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~I~~~~~~~d~~~-~~~S~fs~e~~~~~~il~~~~  107 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSNDDSME-RNLSTFASEMSETAYILDYAD  107 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhheeEecCCccccc-hhhhHHHHHHHHHHHHHHhcC
Confidence            4789999999999999988876421100  112110000    444444444332110 00001111111222222  35


Q ss_pred             CeEEEEecccCC--Chhh----HHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          262 KKYFIALDDVCH--NIEI----WDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       262 kr~LlVLDdvw~--~~~~----~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      ++-|++||..-.  +..+    ...+...+.  ..|+.+|++|....++.
T Consensus       108 ~~~lvllDE~~~gt~~~~~~~l~~~il~~l~--~~~~~~i~~TH~~~l~~  155 (204)
T cd03282         108 GDSLVLIDELGRGTSSADGFAISLAILECLI--KKESTVFFATHFRDIAA  155 (204)
T ss_pred             CCcEEEeccccCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHH
Confidence            678999999841  2221    112222232  23789999999988775

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=95.37  E-value=0.072  Score=49.25  Aligned_cols=24  Identities=25%  Similarity=0.192  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||.+.+..-
T Consensus        27 Ge~~~l~G~nGsGKSTLl~~i~Gl   50 (236)
T cd03253          27 GKKVAIVGPSGSGKSTILRLLFRF   50 (236)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            468999999999999999998753

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=95.36  E-value=0.071  Score=49.20  Aligned_cols=23  Identities=22%  Similarity=0.183  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||++.+..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (234)
T cd03251          28 GETVALVGPSGSGKSTLVNLIPR   50 (234)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999998875

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=95.35  E-value=0.022  Score=54.55  Aligned_cols=139  Identities=15%  Similarity=0.069  Sum_probs=78.3

Q ss_pred             CCcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcC-cccccccc-----chHHH----HHHHHHHh
Q 040913          167 LDISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNN-NHVKFYFD-----CLAWI----LDDIIRSL  234 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~-~~~~~~F~-----~~~wv----~~~il~~l  234 (425)
                      ..++|-.++..++-.++...  .....-+.|+|+.|+|||+|...+..+ +++.++|=     .-+-.    ++.|.+|+
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~al~~I~rql  103 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIALKGITRQL  103 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHHHHHHHHHH
Confidence            45889888888888887653  122445678999999999998877765 34555552     11111    66666666


Q ss_pred             CCCCCCCccCCCCHHHHHHHHHHHhc------CCeEEEEecccCC----Chh--hHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          235 MPPSRVTVIIGEDYKLKKSILRDFLT------NKKYFIALDDVCH----NIE--IWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~l~------~kr~LlVLDdvw~----~~~--~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ............+..+...++-..|+      +-++.+|+|...-    ..+  -++.+-..-....|-+-|-+|||-..
T Consensus       104 ~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~  183 (408)
T KOG2228|consen  104 ALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDI  183 (408)
T ss_pred             HHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccH
Confidence            54433211222333344444555553      2347788877641    111  11211111112345677889998865


Q ss_pred             HHH
Q 040913          303 LLT  305 (425)
Q Consensus       303 va~  305 (425)
                      .-.
T Consensus       184 lE~  186 (408)
T KOG2228|consen  184 LEL  186 (408)
T ss_pred             HHH
Confidence            443

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.35  E-value=0.099  Score=53.77  Aligned_cols=93  Identities=13%  Similarity=0.085  Sum_probs=51.6

Q ss_pred             CCCcccchhhHHHHHHHHhc--------CCCCcEEEEEEecCCCchHHHHHHhhcCccccccc-cchHHHHHHHHHHhCC
Q 040913          166 RLDISEFERAREEWFDLLIE--------GPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-DCLAWILDDIIRSLMP  236 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~--------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~il~~l~~  236 (425)
                      -.++-|.+..++.+.+....        +-...+-|.++|++|+|||.+|+.+.+  +..-.| ...   ..    .+..
T Consensus       227 ~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~--e~~~~~~~l~---~~----~l~~  297 (489)
T CHL00195        227 ISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAN--DWQLPLLRLD---VG----KLFG  297 (489)
T ss_pred             HHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHH--HhCCCEEEEE---hH----Hhcc
Confidence            34577877766665542211        112356688999999999999999988  333332 110   00    1111


Q ss_pred             CCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          237 PSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       237 ~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ..     ...+...+.+.+...-...+++|++|++.
T Consensus       298 ~~-----vGese~~l~~~f~~A~~~~P~IL~IDEID  328 (489)
T CHL00195        298 GI-----VGESESRMRQMIRIAEALSPCILWIDEID  328 (489)
T ss_pred             cc-----cChHHHHHHHHHHHHHhcCCcEEEehhhh
Confidence            10     11222333333333334578999999985

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=95.35  E-value=0.021  Score=55.80  Aligned_cols=26  Identities=12%  Similarity=0.087  Sum_probs=23.5

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+..++|+|++|.|||.+|+.+++.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999993

>TIGR02012 tigrfam_recA protein RecA

Probab=95.34  E-value=0.031  Score=54.10  Aligned_cols=85  Identities=16%  Similarity=0.061  Sum_probs=46.7

Q ss_pred             CCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHH
Q 040913          186 GPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDF  258 (425)
Q Consensus       186 ~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~  258 (425)
                      +=+.-+++-|.|++|+||||||.++...  ....=..++|+      -.....+++.....- .....+.++....+...
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~l  128 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETL  128 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHH
Confidence            3345679999999999999999886652  21111122233      111223332221100 11123455566666555


Q ss_pred             hc-CCeEEEEecccC
Q 040913          259 LT-NKKYFIALDDVC  272 (425)
Q Consensus       259 l~-~kr~LlVLDdvw  272 (425)
                      ++ +.--+||+|-|-
T Consensus       129 i~~~~~~lIVIDSv~  143 (321)
T TIGR02012       129 VRSGAVDIIVVDSVA  143 (321)
T ss_pred             hhccCCcEEEEcchh
Confidence            54 456699999984

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PRK14738 gmk guanylate kinase; Provisional

Probab=95.30  E-value=0.015  Score=52.79  Aligned_cols=30  Identities=30%  Similarity=0.311  Sum_probs=24.9

Q ss_pred             HhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          183 LIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       183 L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..+......|.|+|++|+|||||++.+.+
T Consensus         6 ~~~~~~~~~~ivi~GpsG~GK~tl~~~L~~   35 (206)
T PRK14738          6 LFNKPAKPLLVVISGPSGVGKDAVLARMRE   35 (206)
T ss_pred             ccCCCCCCeEEEEECcCCCCHHHHHHHHHh
Confidence            444445678899999999999999999876

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=95.30  E-value=0.013  Score=51.75  Aligned_cols=23  Identities=13%  Similarity=0.216  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .++.|+|+.|+|||||++.+...
T Consensus         2 ~~~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         2 RLIYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            37899999999999999998663

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.

>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A

Probab=95.28  E-value=0.015  Score=49.38  Aligned_cols=22  Identities=23%  Similarity=0.296  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|+|..|+|||||++.+.+
T Consensus         1 pvv~VvG~~~sGKTTl~~~Li~   22 (140)
T PF03205_consen    1 PVVQVVGPKNSGKTTLIRKLIN   22 (140)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4899999999999999999988

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.28  E-value=1.1  Score=44.35  Aligned_cols=23  Identities=13%  Similarity=0.205  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++.++|+.|+||||++..+..
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~  228 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGW  228 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999998877764

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=95.28  E-value=0.042  Score=50.38  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G   48 (223)
T TIGR03740        26 NSVYGLLGPNGAGKSTLLKMITG   48 (223)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999998875

Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.26  E-value=0.042  Score=57.19  Aligned_cols=48  Identities=10%  Similarity=-0.053  Sum_probs=36.5

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|....+.++++.+..-...-.-|-|+|..|+||++||+.+++.
T Consensus       203 f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~  250 (520)
T PRK10820        203 FSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLR  250 (520)
T ss_pred             ccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHh
Confidence            346899988888888777542222334779999999999999998763

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=95.26  E-value=0.028  Score=48.25  Aligned_cols=44  Identities=18%  Similarity=0.181  Sum_probs=29.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCC
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPP  237 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~  237 (425)
                      +|.|-|.+|+||||+|+.+.++  ..-.|-..-.++++|.+..+-.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~--~gl~~vsaG~iFR~~A~e~gms   45 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEH--LGLKLVSAGTIFREMARERGMS   45 (179)
T ss_pred             EEEeccCCCCChhHHHHHHHHH--hCCceeeccHHHHHHHHHcCCC
Confidence            6899999999999999999883  3333322223355666655443

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=95.26  E-value=0.018  Score=61.48  Aligned_cols=126  Identities=10%  Similarity=0.069  Sum_probs=69.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc-ccc-----chHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF-YFD-----CLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-~F~-----~~~wv~~~il~~l~~~~~  239 (425)
                      -+.++||++++.++++.|.....+-+|  .+|.+|||||+++.-+..  ++.. .-+     ..++ .-++-.-+.... 
T Consensus       169 lDPvIGRd~EI~r~iqIL~RR~KNNPv--LiGEpGVGKTAIvEGLA~--rIv~g~VP~~L~~~~i~-sLD~g~LvAGak-  242 (786)
T COG0542         169 LDPVIGRDEEIRRTIQILSRRTKNNPV--LVGEPGVGKTAIVEGLAQ--RIVNGDVPESLKDKRIY-SLDLGSLVAGAK-  242 (786)
T ss_pred             CCCCcChHHHHHHHHHHHhccCCCCCe--EecCCCCCHHHHHHHHHH--HHhcCCCCHHHcCCEEE-EecHHHHhcccc-
Confidence            345899999999999999987655554  489999999997655544  2211 110     0111 011111111111 


Q ss_pred             CCccCCCCHHHHHHHHHHHhc-CCeEEEEecccCC-----C-----hhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          240 VTVIIGEDYKLKKSILRDFLT-NKKYFIALDDVCH-----N-----IEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       240 ~~~~~~~~~~~l~~~l~~~l~-~kr~LlVLDdvw~-----~-----~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                          --.+.++....+.+.++ .++..|++|.+-.     .     -+.-+-++++|..+. --.|=.||=++.
T Consensus       243 ----yRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPaLARGe-L~~IGATT~~EY  311 (786)
T COG0542         243 ----YRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARGE-LRCIGATTLDEY  311 (786)
T ss_pred             ----ccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHHHhcCC-eEEEEeccHHHH
Confidence                11345555555555554 4589999999841     1     112334555554332 234556665544

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=95.26  E-value=0.081  Score=48.65  Aligned_cols=23  Identities=26%  Similarity=0.231  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        29 G~~~~i~G~nGsGKSTLl~~l~G   51 (229)
T cd03254          29 GETVAIVGPTGAGKTTLINLLMR   51 (229)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45799999999999999999875

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). 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.

>PLN02318 phosphoribulokinase/uridine kinase

Probab=95.24  E-value=0.022  Score=59.01  Aligned_cols=34  Identities=29%  Similarity=0.389  Sum_probs=27.6

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++.+........+|+|.|..|+||||||+.+..
T Consensus        54 a~qlL~~~~~~riIIGIaGpSGSGKTTLAk~Lag   87 (656)
T PLN02318         54 ACQLLAQKNDGIILVGVAGPSGAGKTVFTEKVLN   87 (656)
T ss_pred             HHHHHHhcCCCeEEEEEECCCCCcHHHHHHHHHh
Confidence            3445555555689999999999999999999876

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.23  E-value=0.18  Score=50.53  Aligned_cols=23  Identities=26%  Similarity=0.189  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++.++|++|+||||++..+..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~  245 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAA  245 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999988765

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.22  E-value=0.062  Score=56.94  Aligned_cols=24  Identities=21%  Similarity=0.246  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       375 ~G~~vaIvG~SGsGKSTL~~lL~g  398 (588)
T PRK11174        375 AGQRIALVGPSGAGKTSLLNALLG  398 (588)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            457899999999999999999865

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=95.22  E-value=0.052  Score=56.67  Aligned_cols=24  Identities=29%  Similarity=0.158  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|+.|+|||||++.+..
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g  383 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTG  383 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            457899999999999999999864

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=95.20  E-value=0.052  Score=57.49  Aligned_cols=24  Identities=21%  Similarity=0.164  Sum_probs=20.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       360 ~G~~v~IvG~sGsGKSTLl~lL~g  383 (588)
T PRK13657        360 PGQTVAIVGPTGAGKSTLINLLQR  383 (588)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356799999999999999999864

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=95.20  E-value=0.064  Score=48.35  Aligned_cols=24  Identities=21%  Similarity=0.288  Sum_probs=21.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||.+.+...
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          26 GEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999998774

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional

Probab=95.18  E-value=0.017  Score=50.81  Aligned_cols=24  Identities=25%  Similarity=0.222  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++|+|..|+|||||++.+..
T Consensus         5 ~~~ii~ivG~sgsGKTTLi~~li~   28 (173)
T PRK10751          5 MIPLLAIAAWSGTGKTTLLKKLIP   28 (173)
T ss_pred             CceEEEEECCCCChHHHHHHHHHH
Confidence            467999999999999999998886

>TIGR03263 guanyl_kin guanylate kinase

Probab=95.18  E-value=0.015  Score=51.33  Aligned_cols=22  Identities=18%  Similarity=0.314  Sum_probs=20.5

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|+|+.|+|||||++.+.+
T Consensus         2 ~ii~l~G~~GsGKsTl~~~L~~   23 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLE   23 (180)
T ss_pred             cEEEEECCCCCCHHHHHHHHHc
Confidence            4789999999999999999987

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.

>PRK09354 recA recombinase A; Provisional

Probab=95.17  E-value=0.037  Score=54.07  Aligned_cols=91  Identities=16%  Similarity=0.011  Sum_probs=49.7

Q ss_pred             HHHHh-cCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHH
Q 040913          180 FDLLI-EGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLK  251 (425)
Q Consensus       180 ~~~L~-~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l  251 (425)
                      -.+|- .+=+.-+++-|+|++|+|||||+.++....  ...=...+|+      -.....+++.....- .....+.++.
T Consensus        49 D~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~--~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~  126 (349)
T PRK09354         49 DIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEA--QKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQA  126 (349)
T ss_pred             HHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHH--HHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHH
Confidence            33444 333456788999999999999998876522  1111223333      112233333221100 1112245566


Q ss_pred             HHHHHHHhc-CCeEEEEecccC
Q 040913          252 KSILRDFLT-NKKYFIALDDVC  272 (425)
Q Consensus       252 ~~~l~~~l~-~kr~LlVLDdvw  272 (425)
                      ...+...++ ++--+||+|-|-
T Consensus       127 l~i~~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        127 LEIADTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             HHHHHHHhhcCCCCEEEEeChh
Confidence            666666554 456699999985

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=95.17  E-value=0.13  Score=53.44  Aligned_cols=112  Identities=21%  Similarity=0.193  Sum_probs=60.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc-----ccc-------ccccchH-----------HH-----------HHHHHHHhC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN-----HVK-------FYFDCLA-----------WI-----------LDDIIRSLM  235 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~-----~~~-------~~F~~~~-----------wv-----------~~~il~~l~  235 (425)
                      -.-|+|+|+.|+|||||.+.+....     .+.       .+|+...           |+           .+..+..+.
T Consensus       348 g~riaiiG~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~e~~~r~~L~~f~  427 (530)
T COG0488         348 GDRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGDEQEVRAYLGRFG  427 (530)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCccccHHHHHHHHHHcC
Confidence            4568999999999999999984321     010       1222111           11           333333333


Q ss_pred             CCCCCC--ccCCCCHHH-HHHHHHHHhcCCeEEEEecccCCCh---hhHHHHHhhCCCCCCCcEEEEecCChhHH
Q 040913          236 PPSRVT--VIIGEDYKL-KKSILRDFLTNKKYFIALDDVCHNI---EIWDDLEEVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       236 ~~~~~~--~~~~~~~~~-l~~~l~~~l~~kr~LlVLDdvw~~~---~~~~~l~~~l~~~~~gskIivTTR~~~va  304 (425)
                      -+....  .....+..+ ..-.+...+-.+.-++|||.-- |.   +..+.+..+|.+-. |+ ||+.|.+..-.
T Consensus       428 F~~~~~~~~v~~LSGGEk~Rl~La~ll~~~pNvLiLDEPT-NhLDi~s~~aLe~aL~~f~-Gt-vl~VSHDr~Fl  499 (530)
T COG0488         428 FTGEDQEKPVGVLSGGEKARLLLAKLLLQPPNLLLLDEPT-NHLDIESLEALEEALLDFE-GT-VLLVSHDRYFL  499 (530)
T ss_pred             CChHHHhCchhhcCHhHHHHHHHHHHhccCCCEEEEcCCC-ccCCHHHHHHHHHHHHhCC-Ce-EEEEeCCHHHH
Confidence            322211  112223333 3344555556788899999875 43   45555666665433 44 66667665543

>PRK10867 signal recognition particle protein; Provisional

Probab=95.17  E-value=0.041  Score=55.57  Aligned_cols=23  Identities=22%  Similarity=0.209  Sum_probs=18.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .+.+|.++|.+|+||||.+..+.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA  121 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLA  121 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHH
Confidence            47899999999999999655443

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=95.16  E-value=0.012  Score=52.44  Aligned_cols=22  Identities=23%  Similarity=0.123  Sum_probs=20.0

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +|+|.|.+|+||||||+.+...
T Consensus         1 ii~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999883

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=95.15  E-value=0.06  Score=58.23  Aligned_cols=23  Identities=22%  Similarity=0.140  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|+|..|+|||||++.+..
T Consensus       491 G~~iaIvG~sGsGKSTLlklL~g  513 (694)
T TIGR03375       491 GEKVAIIGRIGSGKSTLLKLLLG  513 (694)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46799999999999999998864

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=95.14  E-value=0.016  Score=50.62  Aligned_cols=23  Identities=9%  Similarity=0.037  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.++|++|+||||+|+.+..
T Consensus         4 ~~~i~l~G~~GsGKstla~~La~   26 (175)
T PRK00131          4 GPNIVLIGFMGAGKSTIGRLLAK   26 (175)
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHH
Confidence            45789999999999999999988

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=95.14  E-value=0.13  Score=52.14  Aligned_cols=53  Identities=19%  Similarity=0.147  Sum_probs=38.9

Q ss_pred             CCCCCcccchh---hHHHHHHHHhcCC-------CCcEEEEEEecCCCchHHHHHHhhcCccc
Q 040913          164 QPRLDISEFER---AREEWFDLLIEGP-------IGLSVVAILDSSGFDKTAFAADTYNNNHV  216 (425)
Q Consensus       164 ~~~~~~vGr~~---~~~~l~~~L~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~  216 (425)
                      +.-.++-|-|+   +.++|++.|.++.       .-++=|..+|++|.|||-||++|.-...|
T Consensus       301 v~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~V  363 (752)
T KOG0734|consen  301 VTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGV  363 (752)
T ss_pred             cccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCC
Confidence            33455667664   5566788888763       23566789999999999999999985444

>PRK00625 shikimate kinase; Provisional

Probab=95.13  E-value=0.015  Score=51.32  Aligned_cols=21  Identities=14%  Similarity=0.145  Sum_probs=19.1

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.++||+|+||||+++.+.+
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~   22 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAK   22 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            378999999999999999977

>cd01394 radB RadB

Probab=95.11  E-value=0.034  Score=50.82  Aligned_cols=32  Identities=25%  Similarity=0.195  Sum_probs=24.2

Q ss_pred             HHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          181 DLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       181 ~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|..+=..-.++.|.|.+|+|||||+.++..
T Consensus        10 ~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~   41 (218)
T cd01394          10 ELLGGGVERGTVTQVYGPPGTGKTNIAIQLAV   41 (218)
T ss_pred             HHhcCCccCCeEEEEECCCCCCHHHHHHHHHH
Confidence            33333334568899999999999999988765

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

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.11  E-value=0.046  Score=59.48  Aligned_cols=97  Identities=19%  Similarity=0.162  Sum_probs=56.5

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHH
Q 040913          163 GQPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDII  231 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il  231 (425)
                      ...-.++.|.+..++.|.+.+.-.           -...+-+.++|++|+|||+||+.+.+  +....|-..-  ..+++
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~--e~~~~fi~v~--~~~l~  524 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVAT--ESGANFIAVR--GPEIL  524 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHH--hcCCCEEEEe--hHHHh
Confidence            334456788888888887765421           12345578899999999999999998  4443441100  11111


Q ss_pred             HHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       232 ~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ...         ...+...+...+...-....++|++|++.
T Consensus       525 ~~~---------vGese~~i~~~f~~A~~~~p~iifiDEid  556 (733)
T TIGR01243       525 SKW---------VGESEKAIREIFRKARQAAPAIIFFDEID  556 (733)
T ss_pred             hcc---------cCcHHHHHHHHHHHHHhcCCEEEEEEChh
Confidence            111         11122333333333334577999999984

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.10  E-value=0.013  Score=51.87  Aligned_cols=21  Identities=48%  Similarity=0.526  Sum_probs=19.5

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|.+|+||||||+.+..
T Consensus         1 ii~i~G~sgsGKttla~~l~~   21 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSN   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999887

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=95.07  E-value=0.024  Score=53.07  Aligned_cols=20  Identities=15%  Similarity=0.368  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++|++|+||||+|+.+..
T Consensus         2 Ivl~G~pGSGKST~a~~La~   21 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAK   21 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            67899999999999998876

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.07  E-value=0.033  Score=53.23  Aligned_cols=24  Identities=17%  Similarity=-0.006  Sum_probs=20.9

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhh
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ..+.+|+|.|..|+||||+|+.+.
T Consensus        60 ~~p~IIGIaG~~GSGKSTlar~L~   83 (290)
T TIGR00554        60 KIPYIISIAGSVAVGKSTTARILQ   83 (290)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            457899999999999999997653

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=95.04  E-value=0.083  Score=57.31  Aligned_cols=24  Identities=38%  Similarity=0.302  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|+.|.|||||++.+..
T Consensus       506 ~Ge~vaIvG~SGsGKSTLl~lL~g  529 (711)
T TIGR00958       506 PGEVVALVGPSGSGKSTVAALLQN  529 (711)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            456899999999999999998865

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=95.04  E-value=0.015  Score=49.26  Aligned_cols=21  Identities=24%  Similarity=0.237  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|.|.|.+|+||||+|+.+..
T Consensus         1 ~I~i~G~~GsGKst~a~~la~   21 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAK   21 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999998886

>PRK06217 hypothetical protein; Validated

Probab=95.02  E-value=0.016  Score=51.55  Aligned_cols=22  Identities=23%  Similarity=0.241  Sum_probs=19.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|.|++|+||||||+.+...
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~   24 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAER   24 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4889999999999999999874

>PRK00889 adenylylsulfate kinase; Provisional

Probab=95.01  E-value=0.021  Score=50.30  Aligned_cols=23  Identities=26%  Similarity=0.073  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|+|++|+||||+|+.+..
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~   26 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAE   26 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999887

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=95.01  E-value=0.021  Score=52.42  Aligned_cols=113  Identities=12%  Similarity=0.054  Sum_probs=59.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-------HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--  260 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--  260 (425)
                      ..++.|.|+.|.||||+.+.+....- ..+-.+.+|.       +..|...+...... .....+...=...+...++  
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~-la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~-~~~~StF~~e~~~~~~il~~~  108 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITI-MAQIGSFVPASSATLSIFDSVLTRMGASDSI-QHGMSTFMVELSETSHILSNC  108 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH-HHhCCCEEEcCceEEeccceEEEEecCcccc-ccccchHHHHHHHHHHHHHhC
Confidence            46788999999999999988765211 1111111111       23333333332221 1111122222333344443  


Q ss_pred             CCeEEEEecccCC--C-hh--h-HHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          261 NKKYFIALDDVCH--N-IE--I-WDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       261 ~kr~LlVLDdvw~--~-~~--~-~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      +++-|++||..-.  + .+  . -..+...+... .++.+|++|....++.
T Consensus       109 ~~~sLvllDE~~~gT~~~d~~~i~~~il~~l~~~-~~~~~i~~TH~~~l~~  158 (222)
T cd03287         109 TSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPSLGE  158 (222)
T ss_pred             CCCeEEEEccCCCCCChhhHHHHHHHHHHHHHhc-cCCeEEEEcccHHHHH
Confidence            5789999999741  1 11  1 11223333332 4789999999988765

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>cd03300 ABC_PotA_N PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D

Probab=95.00  E-value=0.063  Score=49.58  Aligned_cols=24  Identities=21%  Similarity=0.127  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||.+.+...
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~g~   49 (232)
T cd03300          26 GEFFTLLGPSGCGKTTLLRLIAGF   49 (232)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999998764

PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.00  E-value=0.017  Score=48.79  Aligned_cols=22  Identities=14%  Similarity=0.321  Sum_probs=19.7

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .|.|+|+.|+|||||++.+...
T Consensus         1 ~i~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHhc
Confidence            3789999999999999999883

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.

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=94.99  E-value=0.02  Score=46.56  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.7

Q ss_pred             EEEEecCCCchHHHHHHhhcCc
Q 040913          193 VAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      |.|+|..|+|||||.+.+.+.+
T Consensus         2 I~V~G~~g~GKTsLi~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDSGVGKTSLIRRLCGGE   23 (119)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECcCCCCHHHHHHHHhcCC
Confidence            6799999999999999998754

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.97  E-value=0.095  Score=47.72  Aligned_cols=26  Identities=23%  Similarity=0.254  Sum_probs=22.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNH  215 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~  215 (425)
                      --+-+|.|+.|+||||||..+.-++.
T Consensus        30 GEvhaiMGPNGsGKSTLa~~i~G~p~   55 (251)
T COG0396          30 GEVHAIMGPNGSGKSTLAYTIMGHPK   55 (251)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45778999999999999999988774

>TIGR01069 mutS2 MutS2 family protein

Probab=94.96  E-value=0.5  Score=51.54  Aligned_cols=114  Identities=15%  Similarity=0.080  Sum_probs=56.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc---cccccccchH--HH--HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN---HVKFYFDCLA--WI--LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--  260 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~---~~~~~F~~~~--wv--~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--  260 (425)
                      ..++.|.|+.|.|||||.+.+....   ....+.++..  .+  +..+...+...... .....+...-+..+...+.  
T Consensus       322 ~~~liItGpNg~GKSTlLK~i~~~~l~aq~G~~Vpa~~~~~~~~~d~i~~~i~~~~si-~~~LStfS~~m~~~~~il~~~  400 (771)
T TIGR01069       322 KRVLAITGPNTGGKTVTLKTLGLLALMFQSGIPIPANEHSEIPYFEEIFADIGDEQSI-EQNLSTFSGHMKNISAILSKT  400 (771)
T ss_pred             ceEEEEECCCCCCchHHHHHHHHHHHHHHhCCCccCCccccccchhheeeecChHhHH-hhhhhHHHHHHHHHHHHHHhc
Confidence            4789999999999999998876521   0010111100  00  22222222111100 0000111111112223332  


Q ss_pred             CCeEEEEecccCC--ChhhHHHH----HhhCCCCCCCcEEEEecCChhHHHH
Q 040913          261 NKKYFIALDDVCH--NIEIWDDL----EEVLPDNQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       261 ~kr~LlVLDdvw~--~~~~~~~l----~~~l~~~~~gskIivTTR~~~va~~  306 (425)
                      ..+-|++||..-.  +...-..+    ...+.  ..|+.+|+||....+...
T Consensus       401 ~~~sLvLlDE~g~GtD~~eg~ala~aiLe~l~--~~g~~viitTH~~eL~~~  450 (771)
T TIGR01069       401 TENSLVLFDELGAGTDPDEGSALAISILEYLL--KQNAQVLITTHYKELKAL  450 (771)
T ss_pred             CCCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--hcCCEEEEECChHHHHHH
Confidence            4789999999862  12222222    22222  357899999999887653

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=94.95  E-value=0.074  Score=57.69  Aligned_cols=24  Identities=25%  Similarity=0.165  Sum_probs=20.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|+|||||++.+..
T Consensus       504 ~Ge~vaIvG~sGsGKSTLlklL~g  527 (710)
T TIGR03796       504 PGQRVALVGGSGSGKSTIAKLVAG  527 (710)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346899999999999999999864

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>PRK13947 shikimate kinase; Provisional

Probab=94.93  E-value=0.018  Score=50.39  Aligned_cols=21  Identities=14%  Similarity=0.184  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|.|+|++|+||||+|+.+.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~   23 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVAT   23 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHH
Confidence            378999999999999999987

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=94.91  E-value=0.069  Score=57.90  Aligned_cols=23  Identities=26%  Similarity=0.176  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|+|..|+|||||++.+..
T Consensus       500 G~~vaIvG~SGsGKSTLlklL~g  522 (708)
T TIGR01193       500 NSKTTIVGMSGSGKSTLAKLLVG  522 (708)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46799999999999999999864

This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.

>PRK05439 pantothenate kinase; Provisional

Probab=94.90  E-value=0.036  Score=53.44  Aligned_cols=25  Identities=16%  Similarity=-0.016  Sum_probs=22.3

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...-+|+|.|.+|+||||+|+.+..
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~  108 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQA  108 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999988765

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=94.88  E-value=0.081  Score=55.26  Aligned_cols=24  Identities=21%  Similarity=0.149  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       347 ~G~~~~ivG~sGsGKSTL~~ll~g  370 (529)
T TIGR02857       347 PGERVALVGPSGAGKSTLLNLLLG  370 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999998865

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=94.87  E-value=0.044  Score=55.07  Aligned_cols=79  Identities=8%  Similarity=0.153  Sum_probs=45.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC------ccCCCCH------H
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT------VIIGEDY------K  249 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~------~~~~~~~------~  249 (425)
                      -..++|+|..|+|||||++.+.+....    +..+.+        ..+++..+.......      ...+...      .
T Consensus       162 GqrigI~G~sG~GKSTLL~~I~~~~~~----dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (444)
T PRK08972        162 GQRMGLFAGSGVGKSVLLGMMTRGTTA----DVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGC  237 (444)
T ss_pred             CCEEEEECCCCCChhHHHHHhccCCCC----CEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHH
Confidence            467899999999999999999873221    222222        555555543332111      0111111      1


Q ss_pred             HHHHHHHHHh--cCCeEEEEecccC
Q 040913          250 LKKSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                      ...-.+.+++  +|+++|+++||+-
T Consensus       238 ~~A~tiAEyfrd~G~~VLl~~DslT  262 (444)
T PRK08972        238 ETATTIAEYFRDQGLNVLLLMDSLT  262 (444)
T ss_pred             HHHHHHHHHHHHcCCCEEEEEcChH
Confidence            1222344444  5899999999994

>PRK14974 cell division protein FtsY; Provisional

Probab=94.87  E-value=0.099  Score=51.07  Aligned_cols=24  Identities=21%  Similarity=0.152  Sum_probs=19.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.++|++|+||||++..+..
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~  162 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAY  162 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH
Confidence            468999999999999996666554

>PRK00300 gmk guanylate kinase; Provisional

Probab=94.86  E-value=0.02  Score=51.79  Aligned_cols=24  Identities=13%  Similarity=0.181  Sum_probs=21.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+|+|+|+.|+|||||++.+...
T Consensus         5 g~~i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          5 GLLIVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999999874

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.83  E-value=0.13  Score=52.01  Aligned_cols=24  Identities=21%  Similarity=0.170  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.+|.++|.+|+||||++..+..
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~  117 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLAR  117 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            478999999999999999887765

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=94.82  E-value=0.046  Score=50.77  Aligned_cols=38  Identities=16%  Similarity=0.149  Sum_probs=29.2

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....+++.+.....+..+|+|.|++|+||+||...+..
T Consensus        14 ~~~~ll~~l~~~~g~a~~iGiTG~PGaGKSTli~~l~~   51 (266)
T PF03308_consen   14 EARELLKRLYPHTGRAHVIGITGPPGAGKSTLIDALIR   51 (266)
T ss_dssp             HHHHHHHHHGGGTT-SEEEEEEE-TTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcCCceEEEeeCCCCCcHHHHHHHHHH
Confidence            45677777776655688999999999999999877655

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>TIGR00959 ffh signal recognition particle protein

Probab=94.81  E-value=0.061  Score=54.27  Aligned_cols=24  Identities=17%  Similarity=0.141  Sum_probs=19.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.++.++|.+|+||||.|..+..
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~  121 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAY  121 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH
Confidence            368999999999999998655543

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=94.81  E-value=0.059  Score=54.30  Aligned_cols=81  Identities=15%  Similarity=0.204  Sum_probs=45.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-------ccCCCCHHH-----H
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-------VIIGEDYKL-----K  251 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-------~~~~~~~~~-----l  251 (425)
                      -..++|+|..|+|||||.+.+.+......  ...+++      ..+.+.+........       ..+......     .
T Consensus       155 GqrigI~G~sG~GKSTLL~~I~~~~~~d~--~vi~~iGeRgrEv~efl~~~~~~~~~~rtv~vv~tsd~p~~~r~~a~~~  232 (433)
T PRK07594        155 GQRVGIFSAPGVGKSTLLAMLCNAPDADS--NVLVLIGERGREVREFIDFTLSEETRKRCVIVVATSDRPALERVRALFV  232 (433)
T ss_pred             CCEEEEECCCCCCccHHHHHhcCCCCCCE--EEEEEECCCchHHHHHHHHhhccCCcceEEEEEECCCCCHHHHHHHHHH
Confidence            45789999999999999999987432211  111122      445555543321111       011111111     1


Q ss_pred             HHHHHHHh--cCCeEEEEecccC
Q 040913          252 KSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       252 ~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                      .-.+.+++  +|+++||++||+-
T Consensus       233 a~tiAEyfrd~G~~VLl~~Dslt  255 (433)
T PRK07594        233 ATTIAEFFRDNGKRVVLLADSLT  255 (433)
T ss_pred             HHHHHHHHHHCCCcEEEEEeCHH
Confidence            22344454  4799999999994

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=94.80  E-value=0.064  Score=46.83  Aligned_cols=21  Identities=10%  Similarity=0.162  Sum_probs=18.5

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|..+||.|+||||+.+++.+
T Consensus         4 ~IvLiG~mGaGKSTIGr~LAk   24 (172)
T COG0703           4 NIVLIGFMGAGKSTIGRALAK   24 (172)
T ss_pred             cEEEEcCCCCCHhHHHHHHHH
Confidence            467899999999999999875

>PRK03846 adenylylsulfate kinase; Provisional

Probab=94.79  E-value=0.025  Score=50.93  Aligned_cols=24  Identities=21%  Similarity=0.055  Sum_probs=22.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..+|.|+|++|+||||||+.+..
T Consensus        23 ~~~~i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         23 KGVVLWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999999877

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.78  E-value=0.019  Score=49.03  Aligned_cols=22  Identities=14%  Similarity=0.309  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +|.+.|++|+||||+|+.+.+.
T Consensus         1 li~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             CEEEEcCCCCCHHHHHHHHHhh
Confidence            3678999999999999998874

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=94.77  E-value=0.071  Score=52.39  Aligned_cols=23  Identities=13%  Similarity=0.151  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        31 Gei~gIiG~sGaGKSTLlr~I~g   53 (343)
T TIGR02314        31 GQIYGVIGASGAGKSTLIRCVNL   53 (343)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999875

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=94.75  E-value=0.1  Score=50.47  Aligned_cols=23  Identities=17%  Similarity=0.109  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        33 Gei~gllGpNGaGKSTLl~~l~G   55 (306)
T PRK13537         33 GECFGLLGPNGAGKTTTLRMLLG   55 (306)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999875

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=94.74  E-value=0.026  Score=50.37  Aligned_cols=22  Identities=23%  Similarity=0.362  Sum_probs=18.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|-+.|.+|+||||+|+++..
T Consensus         2 pLiIlTGyPgsGKTtfakeLak   23 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAK   23 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHH
Confidence            3566789999999999998876

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=94.73  E-value=0.024  Score=50.49  Aligned_cols=23  Identities=17%  Similarity=0.273  Sum_probs=20.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .++.|+|+.|+|||||++.+...
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhcc
Confidence            36889999999999999999774

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

Probab=94.72  E-value=0.04  Score=54.98  Aligned_cols=46  Identities=15%  Similarity=0.089  Sum_probs=36.4

Q ss_pred             CCcccchhhHHHHHHHHhcC------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..+..+..++...            +...+-|.++|++|+||||||+.+..
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk   72 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAK   72 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHH
Confidence            45899999999988777541            11246789999999999999998876

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=94.71  E-value=0.11  Score=49.30  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        30 Ge~~~IvG~nGsGKSTLl~~L~g   52 (275)
T cd03289          30 GQRVGLLGRTGSGKSTLLSAFLR   52 (275)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhh
Confidence            45899999999999999999875

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>cd01878 HflX HflX subfamily

Probab=94.70  E-value=0.067  Score=48.16  Aligned_cols=26  Identities=15%  Similarity=0.279  Sum_probs=22.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ....|+|+|.+|+|||||...+.+..
T Consensus        40 ~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          40 GIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHhcch
Confidence            35689999999999999999988753

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=94.68  E-value=0.039  Score=55.05  Aligned_cols=46  Identities=15%  Similarity=0.101  Sum_probs=35.6

Q ss_pred             CCcccchhhHHHHHHHHhcC------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.++.+..+.-.+...            +...+-|.++|++|+|||++|+.+..
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~   69 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAK   69 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHH
Confidence            45889999988886666532            11346788999999999999998876

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.

>PRK13949 shikimate kinase; Provisional

Probab=94.67  E-value=0.023  Score=49.82  Aligned_cols=21  Identities=14%  Similarity=0.153  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|.|+|++|+||||+++.+.+
T Consensus         3 ~I~liG~~GsGKstl~~~La~   23 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALAR   23 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            488999999999999999887

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=94.65  E-value=0.14  Score=53.33  Aligned_cols=127  Identities=19%  Similarity=0.190  Sum_probs=70.1

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHH-HHHHhhcCcccccc-c----cc---hHHHHHHHHHHhCCCCCCC----
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTA-FAADTYNNNHVKFY-F----DC---LAWILDDIIRSLMPPSRVT----  241 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTt-La~~v~~~~~~~~~-F----~~---~~wv~~~il~~l~~~~~~~----  241 (425)
                      -.++|++.+..    -.||.|||..|+|||| |+|.+|.+---... -    +-   .+-|.+.+...+....+..    
T Consensus       360 ~R~~ll~~ir~----n~vvvivgETGSGKTTQl~QyL~edGY~~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYs  435 (1042)
T KOG0924|consen  360 CRDQLLSVIRE----NQVVVIVGETGSGKTTQLAQYLYEDGYADNGMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYS  435 (1042)
T ss_pred             HHHHHHHHHhh----CcEEEEEecCCCCchhhhHHHHHhcccccCCeeeecCchHHHHHHHHHHHHHHhCCccccccceE
Confidence            34566666655    4589999999999999 89988875321111 1    11   1223566666665544431    


Q ss_pred             ----cc-------CCC-CHHHHHHHHHHHhcCCeEEEEecccCC---Chhh-HHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          242 ----VI-------IGE-DYKLKKSILRDFLTNKKYFIALDDVCH---NIEI-WDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       242 ----~~-------~~~-~~~~l~~~l~~~l~~kr~LlVLDdvw~---~~~~-~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                          +.       .-+ +.--+.+.|.+..-+|=-.||+|..-.   +.+. +..++..+.. ...-|+||||-.-+...
T Consensus       436 IRFEdvT~~~T~IkymTDGiLLrEsL~d~~L~kYSviImDEAHERslNtDilfGllk~~lar-RrdlKliVtSATm~a~k  514 (1042)
T KOG0924|consen  436 IRFEDVTSEDTKIKYMTDGILLRESLKDRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLAR-RRDLKLIVTSATMDAQK  514 (1042)
T ss_pred             EEeeecCCCceeEEEeccchHHHHHhhhhhhhheeEEEechhhhcccchHHHHHHHHHHHHh-hccceEEEeeccccHHH
Confidence                00       111 112233333333334556899998852   1222 2333334332 33689999998776655


Q ss_pred             H
Q 040913          306 S  306 (425)
Q Consensus       306 ~  306 (425)
                      .
T Consensus       515 f  515 (1042)
T KOG0924|consen  515 F  515 (1042)
T ss_pred             H
Confidence            4

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=94.64  E-value=0.086  Score=55.57  Aligned_cols=24  Identities=21%  Similarity=0.145  Sum_probs=20.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       357 ~G~~v~IvG~sGsGKSTLl~lL~g  380 (571)
T TIGR02203       357 PGETVALVGRSGSGKSTLVNLIPR  380 (571)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            356789999999999999998754

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>PRK08149 ATP synthase SpaL; Validated

Probab=94.63  E-value=0.05  Score=54.68  Aligned_cols=25  Identities=20%  Similarity=0.223  Sum_probs=21.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      -..++|+|..|+|||||.+.+.+..
T Consensus       151 Gq~i~I~G~sG~GKTTLl~~i~~~~  175 (428)
T PRK08149        151 GQRMGIFASAGCGKTSLMNMLIEHS  175 (428)
T ss_pred             CCEEEEECCCCCChhHHHHHHhcCC
Confidence            4578999999999999999998744

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=94.63  E-value=0.066  Score=57.32  Aligned_cols=48  Identities=10%  Similarity=0.007  Sum_probs=37.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -+.++|....+.++.+.+..-.....-|-|.|..|+||+++|+.+++.
T Consensus       324 ~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        324 FDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             ccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHh
Confidence            346889888888888777653222334679999999999999999884

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=94.62  E-value=0.093  Score=56.39  Aligned_cols=23  Identities=26%  Similarity=0.183  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..|+|+|..|+|||||++.+..
T Consensus       499 Ge~vaIvG~SGsGKSTL~KLL~g  521 (709)
T COG2274         499 GEKVAIVGRSGSGKSTLLKLLLG  521 (709)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45799999999999999999864

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=94.62  E-value=0.024  Score=49.92  Aligned_cols=23  Identities=13%  Similarity=0.145  Sum_probs=20.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++|.+.|++|+||||+|+.+...
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999998873

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=94.61  E-value=0.084  Score=55.84  Aligned_cols=23  Identities=26%  Similarity=0.199  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|+|..|.|||||++.+..
T Consensus       369 G~~~aIvG~sGsGKSTLl~ll~g  391 (582)
T PRK11176        369 GKTVALVGRSGSGKSTIANLLTR  391 (582)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45799999999999999999875

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=94.61  E-value=0.026  Score=47.51  Aligned_cols=20  Identities=25%  Similarity=0.355  Sum_probs=18.2

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |-++|.+|+|||+||+.+..
T Consensus         2 vlL~G~~G~GKt~l~~~la~   21 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAA   21 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999887

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.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=94.61  E-value=0.072  Score=53.54  Aligned_cols=81  Identities=11%  Similarity=0.197  Sum_probs=45.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-------ccCCCCHH-----HH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-------VIIGEDYK-----LK  251 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-------~~~~~~~~-----~l  251 (425)
                      -..++|+|..|+|||||.+.+....+.  .....+++      ..+++..........       ..+.....     ..
T Consensus       140 Gq~i~I~G~sG~GKTtLl~~I~~~~~~--~~gvi~~iGer~~ev~~~~~~~l~~~~~~~tvvv~atsd~~~~~r~~a~~~  217 (418)
T TIGR03498       140 GQRLGIFAGSGVGKSTLLSMLARNTDA--DVVVIALVGERGREVREFLEDDLGEEGLKRSVVVVATSDESPLMRRQAAYT  217 (418)
T ss_pred             CcEEEEECCCCCChHHHHHHHhCCCCC--CEEEEEEEeeechHHHHHHHHhhhccccceeEEEEECCCCCHHHHHHHHHH
Confidence            457899999999999999998874321  11111222      445554332221111       01111111     12


Q ss_pred             HHHHHHHh--cCCeEEEEecccC
Q 040913          252 KSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       252 ~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                      .-.+.+++  +++++||++||+-
T Consensus       218 a~~iAEyfrd~G~~Vll~~DslT  240 (418)
T TIGR03498       218 ATAIAEYFRDQGKDVLLLMDSVT  240 (418)
T ss_pred             HHHHHHHHHHcCCCEEEeccchh
Confidence            23345555  5799999999994

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=94.60  E-value=0.027  Score=51.66  Aligned_cols=23  Identities=22%  Similarity=0.180  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|+|||||++.+.-
T Consensus        33 Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          33 GETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhc
Confidence            46899999999999999998863

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.59  E-value=0.083  Score=56.72  Aligned_cols=23  Identities=26%  Similarity=0.303  Sum_probs=19.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..||.++|+.|+||||.+..+..
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~  207 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAA  207 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHh
Confidence            57999999999999998776654

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=94.59  E-value=0.051  Score=55.05  Aligned_cols=81  Identities=11%  Similarity=0.224  Sum_probs=46.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC------ccCCC-CH-----HH
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT------VIIGE-DY-----KL  250 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~------~~~~~-~~-----~~  250 (425)
                      .-++|.|.+|+|||||+.++..+...... +.++++        ..+++..+.......      ...+. ..     ..
T Consensus       145 QR~gIfa~~GvGKt~Ll~~i~~~~~~~~~-~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~  223 (463)
T PRK09280        145 GKIGLFGGAGVGKTVLIQELINNIAKEHG-GYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVAL  223 (463)
T ss_pred             CEEEeecCCCCChhHHHHHHHHHHHhcCC-CEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHH
Confidence            45899999999999999887553221110 122333        556666655432211      00111 11     12


Q ss_pred             HHHHHHHHh---cCCeEEEEecccC
Q 040913          251 KKSILRDFL---TNKKYFIALDDVC  272 (425)
Q Consensus       251 l~~~l~~~l---~~kr~LlVLDdvw  272 (425)
                      ..-.+.+++   ++|++||++||+-
T Consensus       224 ~a~tiAEyfrd~~G~~VLll~DslT  248 (463)
T PRK09280        224 TGLTMAEYFRDVEGQDVLLFIDNIF  248 (463)
T ss_pred             HHHHHHHHHHHhcCCceEEEecchH
Confidence            233456666   6799999999994

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

Probab=94.59  E-value=0.0099  Score=56.35  Aligned_cols=129  Identities=18%  Similarity=0.151  Sum_probs=67.5

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCC-C
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIG-E  246 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~-~  246 (425)
                      ++.-.....+.+.+.|...-...+.|.|.|..|+||||++..+..  .+... +.++.++++-..-............ .
T Consensus       105 ~l~~~~~~~~~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~all~--~i~~~-~~~iv~iEd~~E~~l~~~~~~~~~~~~  181 (270)
T PF00437_consen  105 DLGESGSIPEEIAEFLRSAVRGRGNILISGPTGSGKTTLLNALLE--EIPPE-DERIVTIEDPPELRLPGPNQIQIQTRR  181 (270)
T ss_dssp             CCCHTHHCHHHHHHHHHHCHHTTEEEEEEESTTSSHHHHHHHHHH--HCHTT-TSEEEEEESSS-S--SCSSEEEEEEET
T ss_pred             hccCchhhHHHHHHHHhhccccceEEEEECCCccccchHHHHHhh--hcccc-ccceEEeccccceeecccceEEEEeec
Confidence            333333444556666655422367899999999999999988776  22222 1111110000000000000001111 2


Q ss_pred             CHHHHHHHHHHHhcCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEE-EEecCChhHH
Q 040913          247 DYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRV-LITVINPSLL  304 (425)
Q Consensus       247 ~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskI-ivTTR~~~va  304 (425)
                      +.....+.+...|+...=.|+++.+. +.+.+..+...    ..|..+ +-|....++.
T Consensus       182 ~~~~~~~~l~~~LR~~pD~iiigEiR-~~e~~~~~~a~----~tGh~~~~tT~Ha~s~~  235 (270)
T PF00437_consen  182 DEISYEDLLKSALRQDPDVIIIGEIR-DPEAAEAIQAA----NTGHLGSLTTLHANSAE  235 (270)
T ss_dssp             TTBSHHHHHHHHTTS--SEEEESCE--SCHHHHHHHHH----HTT-EEEEEEEE-SSHH
T ss_pred             CcccHHHHHHHHhcCCCCcccccccC-CHhHHHHHHhh----ccCCceeeeeeecCCHH
Confidence            33455666778888888889999999 87777665444    347777 6666655554

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 ....

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=94.58  E-value=0.033  Score=48.06  Aligned_cols=23  Identities=26%  Similarity=0.109  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..||-|.|.+|+||||||+.+..
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~   24 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALER   24 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46888999999999999999987

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=94.58  E-value=0.038  Score=56.12  Aligned_cols=81  Identities=10%  Similarity=0.151  Sum_probs=48.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC------ccCCCC------HH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT------VIIGED------YK  249 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~------~~~~~~------~~  249 (425)
                      -.-++|.|.+|+|||||+.++.++... .+-+.++++        ..+++..+.......      ...+..      ..
T Consensus       143 GQR~gIfa~~G~GKt~Ll~~~~~~~~~-~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~  221 (461)
T PRK12597        143 GGKTGLFGGAGVGKTVLMMELIFNISK-QHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVV  221 (461)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHHh-hCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHH
Confidence            346899999999999999887764322 234555555        555666654432211      011111      12


Q ss_pred             HHHHHHHHHh---cCCeEEEEeccc
Q 040913          250 LKKSILRDFL---TNKKYFIALDDV  271 (425)
Q Consensus       250 ~l~~~l~~~l---~~kr~LlVLDdv  271 (425)
                      ...-.+.+++   +++++|+++||+
T Consensus       222 ~~a~tiAEyfrd~~G~~VLl~~Dsl  246 (461)
T PRK12597        222 LTGLTIAEYLRDEEKEDVLLFIDNI  246 (461)
T ss_pred             HHHHHHHHHHHHhcCCceEEEeccc
Confidence            2334455565   389999999999

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=94.58  E-value=0.022  Score=53.55  Aligned_cols=84  Identities=21%  Similarity=0.202  Sum_probs=45.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCcccccc---c-cchHHH----------HHHHHHHhCCCCCCC-----ccCCCCHH
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFY---F-DCLAWI----------LDDIIRSLMPPSRVT-----VIIGEDYK  249 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~---F-~~~~wv----------~~~il~~l~~~~~~~-----~~~~~~~~  249 (425)
                      .-.+.=|+|.+|+|||.|+.++.-+..+...   . ...+|+          +.+|+..........     -....+.+
T Consensus        37 ~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~~i~~~~~~~~~~~l~~I~v~~~~~~~  116 (256)
T PF08423_consen   37 TGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQQIAERFGLDPEEILDNIFVIRVFDLE  116 (256)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHHHHHHHTTS-HHHHHHTEEEEE-SSHH
T ss_pred             CCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHHHHhhccccccchhhhceeeeecCCHH
Confidence            4568889999999999999776542222111   1 224455          556665443211100     01122344


Q ss_pred             HHHHH---HHHHh-cCCeEEEEecccC
Q 040913          250 LKKSI---LRDFL-TNKKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~---l~~~l-~~kr~LlVLDdvw  272 (425)
                      ++...   +...+ ..+--|||+|.+-
T Consensus       117 ~l~~~L~~l~~~l~~~~ikLIVIDSIa  143 (256)
T PF08423_consen  117 ELLELLEQLPKLLSESKIKLIVIDSIA  143 (256)
T ss_dssp             HHHHHHHHHHHHHHHSCEEEEEEETSS
T ss_pred             HHHHHHHHHHhhccccceEEEEecchH
Confidence            44333   33334 3456699999984

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>PRK00279 adk adenylate kinase; Reviewed

Probab=94.57  E-value=0.16  Score=46.32  Aligned_cols=21  Identities=19%  Similarity=0.110  Sum_probs=18.8

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|++|+||||+|+.+..
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~   22 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAE   22 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            378899999999999998876

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=94.54  E-value=1.3  Score=42.11  Aligned_cols=109  Identities=15%  Similarity=0.078  Sum_probs=63.4

Q ss_pred             CcccchhhHHHHHHHHhcC-----CCCcEEEEEEecCCCchHHHHHHhhcCccccc-cccchHHHHHHHHHHhCCCCCCC
Q 040913          168 DISEFERAREEWFDLLIEG-----PIGLSVVAILDSSGFDKTAFAADTYNNNHVKF-YFDCLAWILDDIIRSLMPPSRVT  241 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~-----~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~il~~l~~~~~~~  241 (425)
                      .++|..-.++.|+..+..-     ..++-|++.+|..|+||.-.++.+.++-.-.. +=+   +| ........      
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~---~V-~~fvat~h------  152 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSP---FV-HHFVATLH------  152 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccch---hH-HHhhhhcc------
Confidence            4677777777787777642     35788999999999999999988877421111 000   00 00000000      


Q ss_pred             ccCCCCH----HHHHHHHHHHhc-CCeEEEEecccCC-ChhhHHHHHhhCC
Q 040913          242 VIIGEDY----KLKKSILRDFLT-NKKYFIALDDVCH-NIEIWDDLEEVLP  286 (425)
Q Consensus       242 ~~~~~~~----~~l~~~l~~~l~-~kr~LlVLDdvw~-~~~~~~~l~~~l~  286 (425)
                      -+.....    +++...++..++ -+|-|+|+|++.- ...-.+.|++.|.
T Consensus       153 FP~~~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp~gLld~lkpfLd  203 (344)
T KOG2170|consen  153 FPHASKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLPPGLLDVLKPFLD  203 (344)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcCHhHHHHHhhhhc
Confidence            0111223    344444444443 3899999999962 1245566666554

>PRK14530 adenylate kinase; Provisional

Probab=94.50  E-value=0.026  Score=51.57  Aligned_cols=21  Identities=14%  Similarity=0.234  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|+|++|+||||+|+.+..
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~   25 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAE   25 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999876

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=94.49  E-value=0.065  Score=49.26  Aligned_cols=111  Identities=11%  Similarity=0.061  Sum_probs=56.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---------HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFL  259 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l  259 (425)
                      ...++.|.|+.|.||||+.+.+.... +  .+....+|         .+.|+..+...... .........-...+...+
T Consensus        29 ~~~~~~l~G~n~~GKstll~~i~~~~-~--la~~g~~vpa~~~~~~~~~~il~~~~l~d~~-~~~lS~~~~e~~~~a~il  104 (222)
T cd03285          29 KSRFLIITGPNMGGKSTYIRQIGVIV-L--MAQIGCFVPCDSADIPIVDCILARVGASDSQ-LKGVSTFMAEMLETAAIL  104 (222)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHH-H--HHHhCCCcCcccEEEeccceeEeeeccccch-hcCcChHHHHHHHHHHHH
Confidence            36789999999999999988765310 0  00111111         23333333222111 001112222222333334


Q ss_pred             --cCCeEEEEecccCC--Chh-----hHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          260 --TNKKYFIALDDVCH--NIE-----IWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       260 --~~kr~LlVLDdvw~--~~~-----~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                        -..+-|++||..-.  +..     .|..+ ..+.. ..|+.+|+||....+..
T Consensus       105 ~~~~~~sLvLLDEp~~gT~~lD~~~~~~~il-~~l~~-~~~~~vlisTH~~el~~  157 (222)
T cd03285         105 KSATENSLIIIDELGRGTSTYDGFGLAWAIA-EYIAT-QIKCFCLFATHFHELTA  157 (222)
T ss_pred             HhCCCCeEEEEecCcCCCChHHHHHHHHHHH-HHHHh-cCCCeEEEEechHHHHH
Confidence              35788999999931  221     22222 22222 24788999998766553

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]

Probab=94.46  E-value=0.028  Score=50.48  Aligned_cols=25  Identities=20%  Similarity=0.153  Sum_probs=22.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ..+|+|-||=|+||||||+.+.++-
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l   28 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHL   28 (216)
T ss_pred             ccEEEEecccccCHHHHHHHHHHHh
Confidence            5689999999999999999998843

>PRK14528 adenylate kinase; Provisional

Probab=94.45  E-value=0.27  Score=43.81  Aligned_cols=23  Identities=13%  Similarity=0.104  Sum_probs=19.9

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.|.|.|++|+||||+|+.+...
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~   24 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCER   24 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            45789999999999999998763

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=94.44  E-value=0.29  Score=47.46  Aligned_cols=45  Identities=9%  Similarity=-0.076  Sum_probs=37.0

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|.+..++.+.+.+..+. -.+..-++|+.|+||+++|..+.+
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r-l~ha~Lf~G~~G~Gk~~~A~~~a~   48 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR-IAPAYLFAGPEGVGRKLAALCFIE   48 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC-CCceEEEECCCCCCHHHHHHHHHH
Confidence            468899999999999988764 347888999999999998876654

>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=94.43  E-value=0.036  Score=46.42  Aligned_cols=24  Identities=21%  Similarity=0.212  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||.+.+...
T Consensus        11 g~~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   11 GEIVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHTTS
T ss_pred             CCEEEEEccCCCccccceeeeccc
Confidence            357899999999999999998873

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 ....

>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family

Probab=94.43  E-value=0.11  Score=56.08  Aligned_cols=24  Identities=17%  Similarity=0.137  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|+|..|.|||||++.+...
T Consensus       483 G~~vaivG~sGsGKSTL~~ll~g~  506 (694)
T TIGR01846       483 GEFIGIVGPSGSGKSTLTKLLQRL  506 (694)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999998753

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>cd00820 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis

Probab=94.43  E-value=0.037  Score=44.50  Aligned_cols=22  Identities=32%  Similarity=0.283  Sum_probs=19.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -..++|+|+.|+|||||+..+.
T Consensus        15 ge~v~I~GpSGsGKSTLl~~l~   36 (107)
T cd00820          15 KVGVLITGDSGIGKTELALELI   36 (107)
T ss_pred             CEEEEEEcCCCCCHHHHHHHhh
Confidence            4678999999999999999976

It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structural

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=94.42  E-value=0.097  Score=55.29  Aligned_cols=24  Identities=21%  Similarity=0.189  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       365 ~G~~~aivG~sGsGKSTL~~ll~g  388 (574)
T PRK11160        365 AGEKVALLGRTGCGKSTLLQLLTR  388 (574)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999999875

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=94.40  E-value=0.029  Score=47.98  Aligned_cols=20  Identities=15%  Similarity=0.170  Sum_probs=18.6

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++|++|+||||+|+.+..
T Consensus         2 i~l~G~~GsGKstla~~la~   21 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAK   21 (154)
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            67899999999999999986

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>TIGR00073 hypB hydrogenase accessory protein HypB

Probab=94.39  E-value=0.035  Score=50.37  Aligned_cols=25  Identities=28%  Similarity=0.418  Sum_probs=22.7

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++++|+++|..|+|||||..++.+
T Consensus        20 ~~~~~i~~~G~~gsGKTTli~~l~~   44 (207)
T TIGR00073        20 HGLVVLNFMSSPGSGKTTLIEKLID   44 (207)
T ss_pred             cCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3699999999999999999988876

HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.38  E-value=0.11  Score=52.76  Aligned_cols=101  Identities=22%  Similarity=0.254  Sum_probs=58.2

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHh----cCCe
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFL----TNKK  263 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l----~~kr  263 (425)
                      ..+..+.+.|++|+|||+||..+...    ..|+.+=-+         .+.   +....++......+.+.+    +..-
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~~----S~FPFvKii---------Spe---~miG~sEsaKc~~i~k~F~DAYkS~l  599 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIALS----SDFPFVKII---------SPE---DMIGLSESAKCAHIKKIFEDAYKSPL  599 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHhh----cCCCeEEEe---------ChH---HccCccHHHHHHHHHHHHHHhhcCcc
Confidence            45677778899999999999998772    334421110         110   223344455555555555    4466


Q ss_pred             EEEEecccCCChhhH------------HHHHhhCCCC-CCCcE--EEEecCChhHHH
Q 040913          264 YFIALDDVCHNIEIW------------DDLEEVLPDN-QNGSR--VLITVINPSLLT  305 (425)
Q Consensus       264 ~LlVLDdvw~~~~~~------------~~l~~~l~~~-~~gsk--IivTTR~~~va~  305 (425)
                      -.||+||+. ..-+|            ..+...|... ..|-|  |+-||....|.+
T Consensus       600 siivvDdiE-rLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~  655 (744)
T KOG0741|consen  600 SIIVVDDIE-RLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQ  655 (744)
T ss_pred             eEEEEcchh-hhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHH
Confidence            789999996 44444            3333333322 23444  555666666655

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.38  E-value=0.24  Score=49.35  Aligned_cols=93  Identities=13%  Similarity=0.068  Sum_probs=49.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCcc---------c----cccccch-HHHHHHHHHHhCCCCCCCccCCCCHHHHHHH
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNH---------V----KFYFDCL-AWILDDIIRSLMPPSRVTVIIGEDYKLKKSI  254 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~---------~----~~~F~~~-~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~  254 (425)
                      ..++|.++|+.|+||||.+..+.....         +    .+.|... .|.++.....+..+..    ...+...+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~----~~~~~~~l~~~  248 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVK----AIESFKDLKEE  248 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceE----eeCcHHHHHHH
Confidence            467999999999999998876654211         1    1223221 2224444444433321    12344555555


Q ss_pred             HHHHhcCCeEEEEecccCCCh---hhHHHHHhhCCC
Q 040913          255 LRDFLTNKKYFIALDDVCHNI---EIWDDLEEVLPD  287 (425)
Q Consensus       255 l~~~l~~kr~LlVLDdvw~~~---~~~~~l~~~l~~  287 (425)
                      +...  .+.=+|++|....+.   ..+..+...+..
T Consensus       249 L~~~--~~~DlVLIDTaGr~~~~~~~l~el~~~l~~  282 (388)
T PRK12723        249 ITQS--KDFDLVLVDTIGKSPKDFMKLAEMKELLNA  282 (388)
T ss_pred             HHHh--CCCCEEEEcCCCCCccCHHHHHHHHHHHHh
Confidence            5443  345588889885222   234555555543

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=94.37  E-value=0.052  Score=52.78  Aligned_cols=47  Identities=13%  Similarity=0.112  Sum_probs=41.2

Q ss_pred             CCCcccchhhHHHHHHHHhcC----CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEG----PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...++|.++.++++++.+...    +..-+|+-.+|+.|.||||||..+.+
T Consensus        60 ~~~~~G~~~~i~~lV~~fk~AA~g~~~~krIl~L~GPvg~GKSsl~~~Lk~  110 (358)
T PF08298_consen   60 EDEFYGMEETIERLVNYFKSAAQGLEERKRILLLLGPVGGGKSSLAELLKR  110 (358)
T ss_pred             cccccCcHHHHHHHHHHHHHHHhccCccceEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999998864    34678999999999999999998876

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

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

Probab=94.37  E-value=0.06  Score=44.45  Aligned_cols=47  Identities=13%  Similarity=-0.005  Sum_probs=35.4

Q ss_pred             CCcccchhhHHHHHHHHhc----C-CCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIE----G-PIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~----~-~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..++|..-..+.+++.+..    + ..++-|++..|.+|+|||.+++.+.++
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~   76 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEH   76 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHH
Confidence            3477877777777666653    2 456899999999999999988777653

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

>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB

Probab=94.37  E-value=0.027  Score=48.72  Aligned_cols=21  Identities=19%  Similarity=0.235  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      |++|+|+.|+|||||+..+..
T Consensus         1 vi~i~G~~gsGKTtl~~~l~~   21 (155)
T TIGR00176         1 VLQIVGPKNSGKTTLIERLVK   21 (155)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999998887

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.

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=94.36  E-value=0.056  Score=52.65  Aligned_cols=37  Identities=19%  Similarity=0.195  Sum_probs=28.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|++.+........+|+|.|.+|+|||||+..+..
T Consensus        42 ~~~l~~~~~~~~~~~~~igi~G~~GaGKSTl~~~l~~   78 (332)
T PRK09435         42 AQELLDALLPHTGNALRIGITGVPGVGKSTFIEALGM   78 (332)
T ss_pred             HHHHHHHHhhcCCCcEEEEEECCCCCCHHHHHHHHHH
Confidence            3456666654445688999999999999999987654

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=94.36  E-value=0.26  Score=47.33  Aligned_cols=23  Identities=17%  Similarity=0.174  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++++.|+.|.|||||.+.+..
T Consensus        31 Gei~gllG~NGAGKTTllk~l~g   53 (293)
T COG1131          31 GEIFGLLGPNGAGKTTLLKILAG   53 (293)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999876

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=94.35  E-value=0.38  Score=42.71  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=19.1

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|.|++|+||||+|+.+...
T Consensus         2 I~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            679999999999999998874

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK13975 thymidylate kinase; Provisional

Probab=94.33  E-value=0.033  Score=49.83  Aligned_cols=23  Identities=17%  Similarity=0.063  Sum_probs=21.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..|.|.|+.|+||||+++.+.+.
T Consensus         3 ~~I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          3 KFIVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            57999999999999999999884

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=94.32  E-value=0.08  Score=54.84  Aligned_cols=95  Identities=18%  Similarity=0.148  Sum_probs=58.2

Q ss_pred             CCCCcccchhhHHHHHHHHhc---C--------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHH
Q 040913          165 PRLDISEFERAREEWFDLLIE---G--------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRS  233 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~---~--------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~  233 (425)
                      .-.++.|.+..++.+.+.+..   .        -...+.+-++|++|.|||.||+++.+  ....+|-...+-  +++..
T Consensus       240 ~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~--~~~~~fi~v~~~--~l~sk  315 (494)
T COG0464         240 TLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVAL--ESRSRFISVKGS--ELLSK  315 (494)
T ss_pred             ceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHh--hCCCeEEEeeCH--HHhcc
Confidence            334556666666665444332   1        13466888999999999999999999  555555321110  11111


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                               ....+...+...+....+...+.|.+|.+.
T Consensus       316 ---------~vGesek~ir~~F~~A~~~~p~iiFiDEiD  345 (494)
T COG0464         316 ---------WVGESEKNIRELFEKARKLAPSIIFIDEID  345 (494)
T ss_pred             ---------ccchHHHHHHHHHHHHHcCCCcEEEEEchh
Confidence                     112334455555555556789999999995

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=94.31  E-value=0.026  Score=49.02  Aligned_cols=20  Identities=15%  Similarity=0.287  Sum_probs=18.0

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++|++|+||||+|+.+.+
T Consensus         1 i~l~G~~GsGKSTla~~l~~   20 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAH   20 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999877

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.31  E-value=0.086  Score=55.23  Aligned_cols=87  Identities=15%  Similarity=0.175  Sum_probs=49.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc------ccchHHHHHHHHHHhCCCCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY------FDCLAWILDDIIRSLMPPSRV  240 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~------F~~~~wv~~~il~~l~~~~~~  240 (425)
                      .+++--...++...+....+--...-|-|.|..|+|||+||+.+++... +++      |+|.                 
T Consensus       408 ~d~i~~~s~kke~~n~~~spv~~~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs-----------------  469 (952)
T KOG0735|consen  408 HDFIQVPSYKKENANQELSPVFRHGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCS-----------------  469 (952)
T ss_pred             CceeecchhhhhhhhhhcccccccccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEech-----------------
Confidence            3444333333333333333322356688999999999999999998433 221      2221                 


Q ss_pred             CccCCCCHHHHH----HHHHHHhcCCeEEEEecccC
Q 040913          241 TVIIGEDYKLKK----SILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       241 ~~~~~~~~~~l~----~~l~~~l~~kr~LlVLDdvw  272 (425)
                       .......+..+    ..+.+++..-.-+|||||+.
T Consensus       470 -~l~~~~~e~iQk~l~~vfse~~~~~PSiIvLDdld  504 (952)
T KOG0735|consen  470 -TLDGSSLEKIQKFLNNVFSEALWYAPSIIVLDDLD  504 (952)
T ss_pred             -hccchhHHHHHHHHHHHHHHHHhhCCcEEEEcchh
Confidence             11112233333    33444555688999999995

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.31  E-value=0.076  Score=52.55  Aligned_cols=23  Identities=26%  Similarity=0.293  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.++|+.|+||||++.++..
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~  159 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAA  159 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999888765

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=94.29  E-value=0.079  Score=53.57  Aligned_cols=83  Identities=7%  Similarity=0.136  Sum_probs=45.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH----HHHHHHHhCCCCCCC-------ccCCCCH-----HHHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI----LDDIIRSLMPPSRVT-------VIIGEDY-----KLKKS  253 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv----~~~il~~l~~~~~~~-------~~~~~~~-----~~l~~  253 (425)
                      -..++|+|..|+|||||++.+.+.....-.+...+..    ..++...+.......       ..+....     ....-
T Consensus       168 GqrigI~G~sG~GKSTLl~~I~g~~~~dv~V~g~Ig~rg~ev~~~~~~~~~~~~l~rsvvv~atsd~~p~~r~~a~~~a~  247 (451)
T PRK05688        168 GQRLGLFAGTGVGKSVLLGMMTRFTEADIIVVGLIGERGREVKEFIEHILGEEGLKRSVVVASPADDAPLMRLRAAMYCT  247 (451)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCCCEEEEEEeCcCcHhHHHHHHHHhhcCCccEEEEEEECCCCCHHHHHHHHHHHH
Confidence            4578999999999999999997732211001111111    455555544332211       0011111     11222


Q ss_pred             HHHHHh--cCCeEEEEecccC
Q 040913          254 ILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       254 ~l~~~l--~~kr~LlVLDdvw  272 (425)
                      .+.+++  +++++||++||+-
T Consensus       248 aiAEyfrd~G~~VLl~~DslT  268 (451)
T PRK05688        248 RIAEYFRDKGKNVLLLMDSLT  268 (451)
T ss_pred             HHHHHHHHCCCCEEEEecchh
Confidence            344444  5899999999994

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.25  E-value=0.064  Score=51.86  Aligned_cols=130  Identities=16%  Similarity=0.163  Sum_probs=76.3

Q ss_pred             CCCCCCCCcccchhhHHHHHHHHhcC----C-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHH
Q 040913          161 SEGQPRLDISEFERAREEWFDLLIEG----P-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDD  229 (425)
Q Consensus       161 ~~~~~~~~~vGr~~~~~~l~~~L~~~----~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~  229 (425)
                      .|.+...++=|.++.+++|.+.+.-+    +       ..++=|..+|++|.|||-||++|.|  +....|=.++=  .+
T Consensus       145 ~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~--~T~AtFIrvvg--SE  220 (406)
T COG1222         145 KPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVAN--QTDATFIRVVG--SE  220 (406)
T ss_pred             CCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCceEEEecc--HH
Confidence            34444556667899888887776432    1       3466678999999999999999999  66666622110  11


Q ss_pred             HHHHhCCCCCCCccCCCCHHHHHHHHHHHhc-CCeEEEEecccCCCh-------------h---hHHHHHhhCC--CCCC
Q 040913          230 IIRSLMPPSRVTVIIGEDYKLKKSILRDFLT-NKKYFIALDDVCHNI-------------E---IWDDLEEVLP--DNQN  290 (425)
Q Consensus       230 il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~-~kr~LlVLDdvw~~~-------------~---~~~~l~~~l~--~~~~  290 (425)
                      +......          +...+...+.+.-+ ...+.|.+|.+. ..             +   ..-+|..-+.  +...
T Consensus       221 lVqKYiG----------EGaRlVRelF~lArekaPsIIFiDEID-AIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~  289 (406)
T COG1222         221 LVQKYIG----------EGARLVRELFELAREKAPSIIFIDEID-AIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRG  289 (406)
T ss_pred             HHHHHhc----------cchHHHHHHHHHHhhcCCeEEEEechh-hhhcccccCCCCchHHHHHHHHHHHHhccCCCCCC
Confidence            1111111          11334444444444 467889999885 21             1   2222333332  2233


Q ss_pred             CcEEEEecCChhHHH
Q 040913          291 GSRVLITVINPSLLT  305 (425)
Q Consensus       291 gskIivTTR~~~va~  305 (425)
                      .-|||..|...++..
T Consensus       290 nvKVI~ATNR~D~LD  304 (406)
T COG1222         290 NVKVIMATNRPDILD  304 (406)
T ss_pred             CeEEEEecCCccccC
Confidence            468998888777655

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=94.25  E-value=0.028  Score=45.26  Aligned_cols=20  Identities=20%  Similarity=0.358  Sum_probs=17.7

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |-|+|.+|+|||+||+.+..
T Consensus         1 I~i~G~~G~GKS~l~~~l~~   20 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAK   20 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999776

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=94.22  E-value=0.031  Score=47.94  Aligned_cols=21  Identities=24%  Similarity=0.211  Sum_probs=19.0

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ||.|+|.+|+||||||+.+..
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~   21 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEE   21 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHH
Confidence            578999999999999998877

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=94.22  E-value=0.036  Score=48.77  Aligned_cols=23  Identities=9%  Similarity=0.128  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|+|+.|+||||+++.+.+
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~   26 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQ   26 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHH
Confidence            34689999999999999999987

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=94.20  E-value=0.14  Score=52.59  Aligned_cols=47  Identities=21%  Similarity=0.082  Sum_probs=37.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..++|......++.+.+..-......+.|.|.+|+|||++|+.+++.
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhc
Confidence            45889888888887777543333455779999999999999999885

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.18  E-value=0.039  Score=56.93  Aligned_cols=93  Identities=15%  Similarity=0.063  Sum_probs=50.6

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH---------HHHHHHHhCCCCCCCccC----
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------LDDIIRSLMPPSRVTVII----  244 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------~~~il~~l~~~~~~~~~~----  244 (425)
                      +++++|..=.. -.-..|+|.+|+|||||++.|.+... ..+=++.++|         ..++.+.+....-....+    
T Consensus       405 RvIDll~PIGk-GQR~LIvgpp~aGKTtLL~~IAn~i~-~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~  482 (672)
T PRK12678        405 RVIDLIMPIGK-GQRGLIVSPPKAGKTTILQNIANAIT-TNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPS  482 (672)
T ss_pred             eeeeeeccccc-CCEeEEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHH
Confidence            44555543221 23468999999999999999988211 1122222223         566666552111000000    


Q ss_pred             -CCCHHHHHHHHHHHh--cCCeEEEEecccC
Q 040913          245 -GEDYKLKKSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       245 -~~~~~~l~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                       ......+.-.+.++|  .++.+||++|++-
T Consensus       483 ~~~~~a~~ai~~Ae~fre~G~dVlillDSlT  513 (672)
T PRK12678        483 DHTTVAELAIERAKRLVELGKDVVVLLDSIT  513 (672)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCEEEEEeCch
Confidence             011223334445555  5899999999984

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=94.17  E-value=0.15  Score=55.15  Aligned_cols=24  Identities=25%  Similarity=0.184  Sum_probs=20.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|+|||||++.+..
T Consensus       478 ~Ge~vaIvG~sGsGKSTLlklL~g  501 (686)
T TIGR03797       478 PGEFVAIVGPSGSGKSTLLRLLLG  501 (686)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            356799999999999999999864

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif

>TIGR00750 lao LAO/AO transport system ATPase

Probab=94.17  E-value=0.057  Score=52.08  Aligned_cols=37  Identities=14%  Similarity=0.100  Sum_probs=27.5

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++-+........+|+|+|.+|+|||||+..+..
T Consensus        20 ~~~~~~~~~~~~~~~~~i~i~G~~G~GKttl~~~l~~   56 (300)
T TIGR00750        20 AKQLLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGM   56 (300)
T ss_pred             HHHHHHhCCcccCCceEEEEECCCCCCHHHHHHHHHH
Confidence            3445554544445689999999999999999988665

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.

>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=94.14  E-value=0.13  Score=48.72  Aligned_cols=33  Identities=24%  Similarity=0.345  Sum_probs=25.1

Q ss_pred             HHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          177 EEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       177 ~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+++.+....   +-+-++|+.|+|||++++...+
T Consensus        23 ~~ll~~l~~~~---~pvLl~G~~GtGKT~li~~~l~   55 (272)
T PF12775_consen   23 SYLLDLLLSNG---RPVLLVGPSGTGKTSLIQNFLS   55 (272)
T ss_dssp             HHHHHHHHHCT---EEEEEESSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---CcEEEECCCCCchhHHHHhhhc
Confidence            44566666543   4457899999999999998775

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.13  E-value=0.15  Score=51.22  Aligned_cols=22  Identities=27%  Similarity=0.292  Sum_probs=19.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ..+++++|..|+||||++..+.
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA  212 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLA  212 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHH
Confidence            5799999999999999887554

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=94.13  E-value=0.085  Score=53.25  Aligned_cols=83  Identities=8%  Similarity=0.091  Sum_probs=46.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH----HHHHHHHhCCCCCCC------ccCCCCH------HHHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI----LDDIIRSLMPPSRVT------VIIGEDY------KLKKS  253 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv----~~~il~~l~~~~~~~------~~~~~~~------~~l~~  253 (425)
                      -..++|+|..|+|||||.+.+.+........-..++.    ..+++..+.......      ...+...      ....-
T Consensus       175 Gqri~I~G~sG~GKTTLL~~Ia~~~~~d~iv~g~Igerg~ev~e~~~~~~~~~~~~~tvVv~~~ad~~~~~r~~~~~~a~  254 (455)
T PRK07960        175 GQRMGLFAGSGVGKSVLLGMMARYTQADVIVVGLIGERGREVKDFIENILGAEGRARSVVIAAPADVSPLLRMQGAAYAT  254 (455)
T ss_pred             CcEEEEECCCCCCccHHHHHHhCCCCCCEEEEEEEEECCeEHHHHHHhhcCcCCCceEEEEEECCCCCHHHHHHHHHHHH
Confidence            4678999999999999999988743221100112222    555555544432211      1111111      11122


Q ss_pred             HHHHHh--cCCeEEEEecccC
Q 040913          254 ILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       254 ~l~~~l--~~kr~LlVLDdvw  272 (425)
                      .+.+++  ++|.+|+++||+-
T Consensus       255 tiAEyfrd~G~~Vll~~DslT  275 (455)
T PRK07960        255 RIAEDFRDRGQHVLLIMDSLT  275 (455)
T ss_pred             HHHHHHHHcCCCeEEEecchh
Confidence            244444  4899999999994

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=94.13  E-value=0.22  Score=53.23  Aligned_cols=93  Identities=18%  Similarity=0.220  Sum_probs=50.7

Q ss_pred             CCcccchhhHHHHHHHH---hcCC-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCC
Q 040913          167 LDISEFERAREEWFDLL---IEGP-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMP  236 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L---~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~  236 (425)
                      .++.|.+..++++.+.+   ....       .-.+-|.++|++|+||||+|+.+.+  +...+|-..-  ..++....  
T Consensus       152 ~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~--~~~~~f~~is--~~~~~~~~--  225 (644)
T PRK10733        152 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG--EAKVPFFTIS--GSDFVEMF--  225 (644)
T ss_pred             HHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHH--HcCCCEEEEe--hHHhHHhh--
Confidence            35667666666554443   2211       1133488999999999999999988  4433431100  00111100  


Q ss_pred             CCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          237 PSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       237 ~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                             .......+...+...-....++|++|++.
T Consensus       226 -------~g~~~~~~~~~f~~a~~~~P~IifIDEiD  254 (644)
T PRK10733        226 -------VGVGASRVRDMFEQAKKAAPCIIFIDEID  254 (644)
T ss_pred             -------hcccHHHHHHHHHHHHhcCCcEEEehhHh
Confidence                   01122333333444444577899999985

>COG3903 Predicted ATPase [General function prediction only]

Probab=94.11  E-value=0.011  Score=58.04  Aligned_cols=108  Identities=15%  Similarity=0.099  Sum_probs=62.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-----------HHHH-HHHhCCCCCCCccCCCCHHHHHHHHH
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----------LDDI-IRSLMPPSRVTVIIGEDYKLKKSILR  256 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-----------~~~i-l~~l~~~~~~~~~~~~~~~~l~~~l~  256 (425)
                      ..+.+.++|.|||||||++-.+-.   +..-|....|.           +--+ ...+.-.       ..+-+.....+.
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~~~v~~~~ag~~gl~-------~~~g~~~~~~~~   82 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDPALVFPTLAGALGLH-------VQPGDSAVDTLV   82 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCchhHhHHHHHhhcccc-------cccchHHHHHHH
Confidence            478899999999999999987766   33344332222           0111 1111111       122244555677


Q ss_pred             HHhcCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH
Q 040913          257 DFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       257 ~~l~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~  306 (425)
                      ..+.++|.++|+||..|-.+.=..+...+-.+.+.-.|+.|+|.......
T Consensus        83 ~~~~~rr~llvldncehl~~~~a~~i~all~~~~~~~~~atsre~~l~~g  132 (414)
T COG3903          83 RRIGDRRALLVLDNCEHLLDACAALIVALLGACPRLAILATSREAILVAG  132 (414)
T ss_pred             HHHhhhhHHHHhcCcHHHHHHHHHHHHHHHccchhhhhHHHhHhhhcccc
Confidence            77889999999999852111112222333344445678888887665544

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.10  E-value=0.082  Score=50.09  Aligned_cols=84  Identities=17%  Similarity=0.037  Sum_probs=46.5

Q ss_pred             cCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH----------HHHHHHHhCCCCCCCccCCCCHH---HH
Q 040913          185 EGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI----------LDDIIRSLMPPSRVTVIIGEDYK---LK  251 (425)
Q Consensus       185 ~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv----------~~~il~~l~~~~~~~~~~~~~~~---~l  251 (425)
                      .+=+.-+++=|+|+.|+||||+|.+++-.  .+..-...+|+          .+.+......+..  -....+.+   .+
T Consensus        55 GGl~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~~l~~~~~d~l~--v~~~~~~e~q~~i  130 (279)
T COG0468          55 GGLPRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAKQLGVDLLDNLL--VSQPDTGEQQLEI  130 (279)
T ss_pred             CCcccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHHHHHHhhhccee--EecCCCHHHHHHH
Confidence            33345788999999999999999887653  22222233444          3334443211111  11112333   33


Q ss_pred             HHHHHHHhcCCeEEEEecccC
Q 040913          252 KSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       252 ~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      .+.+......+--|||+|-|-
T Consensus       131 ~~~~~~~~~~~i~LvVVDSva  151 (279)
T COG0468         131 AEKLARSGAEKIDLLVVDSVA  151 (279)
T ss_pred             HHHHHHhccCCCCEEEEecCc
Confidence            444444444446799999985

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=94.09  E-value=0.048  Score=53.46  Aligned_cols=47  Identities=17%  Similarity=0.131  Sum_probs=37.9

Q ss_pred             CCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          164 QPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+-+.+||.++.+..|+..+.++.  ++-|.|.|..|+||||+|+.+++
T Consensus        14 ~pf~~ivGq~~~k~al~~~~~~p~--~~~vli~G~~GtGKs~~ar~~~~   60 (350)
T CHL00081         14 FPFTAIVGQEEMKLALILNVIDPK--IGGVMIMGDRGTGKSTTIRALVD   60 (350)
T ss_pred             CCHHHHhChHHHHHHHHHhccCCC--CCeEEEEcCCCCCHHHHHHHHHH
Confidence            345678999998888887777654  45566999999999999999865

>PRK14737 gmk guanylate kinase; Provisional

Probab=94.09  E-value=0.046  Score=48.81  Aligned_cols=25  Identities=12%  Similarity=0.120  Sum_probs=22.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+|.|+|++|+|||||++.+.+.
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~   27 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEE   27 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3678999999999999999999873

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=94.05  E-value=0.057  Score=49.19  Aligned_cols=44  Identities=23%  Similarity=0.115  Sum_probs=35.3

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++||-++-.+++--...+++  .+-+.|.||+|+||||-+..+.+
T Consensus        27 ~dIVGNe~tv~rl~via~~gn--mP~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAKEGN--MPNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             HHhhCCHHHHHHHHHHHHcCC--CCceEeeCCCCCchhhHHHHHHH
Confidence            568999999998877766665  66778999999999997666554

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=94.05  E-value=0.074  Score=51.54  Aligned_cols=31  Identities=16%  Similarity=0.199  Sum_probs=23.5

Q ss_pred             HHHhcCCCCcEEEEEEecCCCchHHHHHHhh
Q 040913          181 DLLIEGPIGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       181 ~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ++|..+=..-+++-|+|++|+|||+|+.++.
T Consensus        87 ~lLgGGi~~G~iteI~G~~GsGKTql~lqla  117 (313)
T TIGR02238        87 GILGGGIESMSITEVFGEFRCGKTQLSHTLC  117 (313)
T ss_pred             HHhCCCCcCCeEEEEECCCCCCcCHHHHHHH
Confidence            3444433456888999999999999998765

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK13948 shikimate kinase; Provisional

Probab=94.05  E-value=0.043  Score=48.75  Aligned_cols=24  Identities=17%  Similarity=0.123  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....|.++||.|+||||+++.+.+
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~   32 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSR   32 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            356788999999999999999987

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=94.04  E-value=0.15  Score=54.03  Aligned_cols=24  Identities=25%  Similarity=0.207  Sum_probs=21.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       360 ~G~~~~ivG~sGsGKSTL~~ll~g  383 (585)
T TIGR01192       360 AGQTVAIVGPTGAGKTTLINLLQR  383 (585)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcc
Confidence            456899999999999999998864

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>PRK06936 type III secretion system ATPase; Provisional

Probab=94.02  E-value=0.12  Score=52.10  Aligned_cols=79  Identities=14%  Similarity=0.240  Sum_probs=45.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC------ccCCCCH-H-----
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT------VIIGEDY-K-----  249 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~------~~~~~~~-~-----  249 (425)
                      -..++|.|..|+|||||.+.+.+....    +..+.+        ..+++..........      ...+... .     
T Consensus       162 Gq~~~I~G~sG~GKStLl~~Ia~~~~~----dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~  237 (439)
T PRK06936        162 GQRMGIFAAAGGGKSTLLASLIRSAEV----DVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAG  237 (439)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcCCCC----CEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHH
Confidence            457899999999999999999984332    233333        555554432221111      0111111 1     


Q ss_pred             HHHHHHHHHh--cCCeEEEEecccC
Q 040913          250 LKKSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                      ...-.+.+++  +||++|+++||+-
T Consensus       238 ~~a~tiAEyfrd~G~~Vll~~DslT  262 (439)
T PRK06936        238 FVATSIAEYFRDQGKRVLLLMDSVT  262 (439)
T ss_pred             HHHHHHHHHHHHcCCCEEEeccchh
Confidence            1122344444  5899999999994

>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]

Probab=94.01  E-value=0.047  Score=47.12  Aligned_cols=23  Identities=26%  Similarity=0.237  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++.|+|.+|+||||+.+.+-.
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~   26 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALK   26 (189)
T ss_pred             ceEEEEEcCCCCChHHHHHHHHH
Confidence            58999999999999999887766

>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]

Probab=94.01  E-value=0.042  Score=47.65  Aligned_cols=23  Identities=13%  Similarity=0.234  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|++|+|..|+|||||...+..
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~   24 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVR   24 (161)
T ss_pred             CcEEEEEecCCCChhhHHHHHHH
Confidence            57999999999999999998865

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=94.00  E-value=0.024  Score=46.97  Aligned_cols=27  Identities=22%  Similarity=0.290  Sum_probs=18.0

Q ss_pred             EEEEecCCCchHHHHHHhhcCcccccccc
Q 040913          193 VAILDSSGFDKTAFAADTYNNNHVKFYFD  221 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~~~~~~~F~  221 (425)
                      |-++|.+|+||||+|+.+..  .+...|.
T Consensus         2 vLleg~PG~GKT~la~~lA~--~~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALAR--SLGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHH--HTT--EE
T ss_pred             EeeECCCccHHHHHHHHHHH--HcCCcee
Confidence            56899999999999999987  4555553

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=94.00  E-value=0.039  Score=47.95  Aligned_cols=20  Identities=25%  Similarity=0.305  Sum_probs=18.2

Q ss_pred             EEEEEecCCCchHHHHHHhh
Q 040913          192 VVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .|.|.|.+|+||||++..+-
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH
Confidence            58999999999999999876

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=93.98  E-value=0.078  Score=55.64  Aligned_cols=47  Identities=15%  Similarity=-0.062  Sum_probs=35.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..+.|.+-.+.|.+.......+..+|.|+|+.|+||||+|+.+..
T Consensus       368 pP~~f~rpeV~~iL~~~~~~r~~~g~~Ivl~Gl~GSGKSTia~~La~  414 (568)
T PRK05537        368 IPEWFSFPEVVAELRRTYPPRHKQGFTVFFTGLSGAGKSTIAKALMV  414 (568)
T ss_pred             CChhhcHHHHHHHHHHHhccccCCCeEEEEECCCCChHHHHHHHHHH
Confidence            34456666666655555555455567899999999999999999987

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=93.97  E-value=0.074  Score=50.15  Aligned_cols=82  Identities=12%  Similarity=0.123  Sum_probs=48.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccc--cccccchHHH--------HHHHHHHhCCCCCCC-------ccCCCC-----H
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHV--KFYFDCLAWI--------LDDIIRSLMPPSRVT-------VIIGED-----Y  248 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F~~~~wv--------~~~il~~l~~~~~~~-------~~~~~~-----~  248 (425)
                      .-++|.|-.|+|||+|+..+.++..+  +.+-+.++++        ..+++..+.......       ..+...     .
T Consensus        70 QR~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a  149 (276)
T cd01135          70 QKIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIIT  149 (276)
T ss_pred             CEEEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHH
Confidence            45799999999999999988875431  1223445555        566666665543211       001111     1


Q ss_pred             HHHHHHHHHHh---cCCeEEEEecccC
Q 040913          249 KLKKSILRDFL---TNKKYFIALDDVC  272 (425)
Q Consensus       249 ~~l~~~l~~~l---~~kr~LlVLDdvw  272 (425)
                      ....-.+.+++   +++++|+++||+-
T Consensus       150 ~~~a~aiAEyfrd~~g~~VLl~~D~lt  176 (276)
T cd01135         150 PRMALTTAEYLAYEKGKHVLVILTDMT  176 (276)
T ss_pred             HHHHHHHHHHHHhccCCeEEEEEcChh
Confidence            11233445555   2789999999995

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=93.94  E-value=0.049  Score=46.66  Aligned_cols=23  Identities=17%  Similarity=0.333  Sum_probs=19.8

Q ss_pred             EEEEEecCCCchHHHHHHhhcCc
Q 040913          192 VVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      -|.++|.+|+|||||+..+.++.
T Consensus         2 ki~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           2 KVIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999988643

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=93.93  E-value=1.4  Score=48.13  Aligned_cols=114  Identities=13%  Similarity=0.073  Sum_probs=57.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccc--cccc-cch--HHH--HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHV--KFYF-DCL--AWI--LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--  260 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F-~~~--~wv--~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--  260 (425)
                      .+++.|.|+.+.||||+.+.+.-..-.  ...| ++.  +.+  +..|...++..... .....+...-+..+...+.  
T Consensus       327 ~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si-~~~lStfS~~m~~~~~Il~~~  405 (782)
T PRK00409        327 KTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSI-EQSLSTFSGHMTNIVRILEKA  405 (782)
T ss_pred             ceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccch-hhchhHHHHHHHHHHHHHHhC
Confidence            568889999999999999887531100  0011 110  011  22233333322111 0011111222222233332  


Q ss_pred             CCeEEEEecccCC--ChhhHHHH----HhhCCCCCCCcEEEEecCChhHHHH
Q 040913          261 NKKYFIALDDVCH--NIEIWDDL----EEVLPDNQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       261 ~kr~LlVLDdvw~--~~~~~~~l----~~~l~~~~~gskIivTTR~~~va~~  306 (425)
                      ..+-|++||..-.  +...-..+    ...+.  ..|+.+|+||....++..
T Consensus       406 ~~~sLvLlDE~~~GtDp~eg~ala~aile~l~--~~~~~vIitTH~~el~~~  455 (782)
T PRK00409        406 DKNSLVLFDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKAL  455 (782)
T ss_pred             CcCcEEEecCCCCCCCHHHHHHHHHHHHHHHH--HCCCEEEEECChHHHHHH
Confidence            4778999999862  12222222    22222  247899999999887765

>PHA02774 E1; Provisional

Probab=93.93  E-value=0.17  Score=52.41  Aligned_cols=36  Identities=17%  Similarity=0.153  Sum_probs=26.8

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+..+|. +.++...+.|+|++|.|||.+|..+.+
T Consensus       421 l~~lk~~l~-~~PKknciv~~GPP~TGKS~fa~sL~~  456 (613)
T PHA02774        421 LTALKDFLK-GIPKKNCLVIYGPPDTGKSMFCMSLIK  456 (613)
T ss_pred             HHHHHHHHh-cCCcccEEEEECCCCCCHHHHHHHHHH
Confidence            344455553 434456899999999999999998887

>PRK13946 shikimate kinase; Provisional

Probab=93.93  E-value=0.041  Score=48.93  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.|.++|+.|+||||+++.+.+
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~   32 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLAT   32 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999988

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=93.91  E-value=0.051  Score=44.13  Aligned_cols=21  Identities=19%  Similarity=0.278  Sum_probs=19.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |+|+|+.|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999973

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=93.90  E-value=0.05  Score=49.01  Aligned_cols=24  Identities=17%  Similarity=0.122  Sum_probs=21.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+|.|.|.+|+||||+|+.+...
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~   26 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARH   26 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            568999999999999999998883

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=93.89  E-value=0.049  Score=52.02  Aligned_cols=24  Identities=25%  Similarity=0.270  Sum_probs=20.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.++|++|+||||++..+..
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~  216 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAA  216 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999998877654

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=93.88  E-value=0.069  Score=50.46  Aligned_cols=37  Identities=16%  Similarity=0.132  Sum_probs=30.6

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+|+..+.....+..+|+|.|.||+||+||.-.+-.
T Consensus        37 a~~ll~~l~p~tG~a~viGITG~PGaGKSTli~~L~~   73 (323)
T COG1703          37 ARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGR   73 (323)
T ss_pred             HHHHHHHHhhcCCCCcEEEecCCCCCchHHHHHHHHH
Confidence            3567777777766789999999999999999877655

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=93.87  E-value=0.039  Score=55.70  Aligned_cols=82  Identities=9%  Similarity=0.167  Sum_probs=50.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC------ccCCCC------HH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT------VIIGED------YK  249 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~------~~~~~~------~~  249 (425)
                      -.-++|.|.+|+|||+|+.++.++.. +.+-+.++++        ..+++..+.......      ...+..      ..
T Consensus       138 GQr~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~  216 (449)
T TIGR03305       138 GGKAGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVG  216 (449)
T ss_pred             CCEEEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHH
Confidence            34589999999999999998876532 2223455555        566666665432211      011111      11


Q ss_pred             HHHHHHHHHhc---CCeEEEEecccC
Q 040913          250 LKKSILRDFLT---NKKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~l~~~l~---~kr~LlVLDdvw  272 (425)
                      ...-.+.++++   ++++|+++||+-
T Consensus       217 ~~a~tiAEyfrd~~G~~VLl~~DslT  242 (449)
T TIGR03305       217 HTALTMAEYFRDDEKQDVLLLIDNIF  242 (449)
T ss_pred             HHHHHHHHHHHHhcCCceEEEecChH
Confidence            23344556654   699999999994

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>PLN02348 phosphoribulokinase

Probab=93.87  E-value=0.076  Score=52.57  Aligned_cols=26  Identities=23%  Similarity=0.323  Sum_probs=23.1

Q ss_pred             CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          187 PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       187 ~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....-+|+|.|.+|+||||+|+.+.+
T Consensus        46 ~~~p~IIGIaG~SGSGKSTfA~~L~~   71 (395)
T PLN02348         46 DDGTVVIGLAADSGCGKSTFMRRLTS   71 (395)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34578999999999999999999886

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=93.87  E-value=0.043  Score=49.88  Aligned_cols=24  Identities=17%  Similarity=0.296  Sum_probs=20.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCc
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      .-|.|+|++|+|||||+..+.++.
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEEcCCCccHHHHHHHHhcCc
Confidence            457899999999999999988753

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=93.85  E-value=0.058  Score=48.67  Aligned_cols=24  Identities=25%  Similarity=0.184  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.|++|+|++|+|||||.+.+..=
T Consensus        28 Gevv~iiGpSGSGKSTlLRclN~L   51 (240)
T COG1126          28 GEVVVIIGPSGSGKSTLLRCLNGL   51 (240)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            468999999999999999988753

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=93.85  E-value=0.08  Score=52.55  Aligned_cols=35  Identities=23%  Similarity=0.184  Sum_probs=25.3

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+-+.|..+=..-.++.|.|.+|+|||||+.++..
T Consensus        70 eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~  104 (372)
T cd01121          70 ELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAA  104 (372)
T ss_pred             HHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHH
Confidence            33344433333457899999999999999988765

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PRK04182 cytidylate kinase; Provisional

Probab=93.85  E-value=0.048  Score=47.89  Aligned_cols=21  Identities=24%  Similarity=0.241  Sum_probs=19.9

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|.|.|+.|+||||+|+.+.+
T Consensus         2 ~I~i~G~~GsGKstia~~la~   22 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAE   22 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

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

Probab=93.84  E-value=0.069  Score=53.73  Aligned_cols=46  Identities=17%  Similarity=0.128  Sum_probs=34.1

Q ss_pred             CCcccchhhHHHHHHHHhcC--------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG--------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~--------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.+...+...              ....+-+.++|++|+|||+||+.+.+
T Consensus        71 ~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~  130 (412)
T PRK05342         71 QYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLAR  130 (412)
T ss_pred             hHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHH
Confidence            35899999888875554211              01235688999999999999999986

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

Probab=93.83  E-value=0.1  Score=49.31  Aligned_cols=122  Identities=16%  Similarity=0.145  Sum_probs=62.5

Q ss_pred             ccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchH-HH--HHHHHHHhCCCCCCCccCCC
Q 040913          170 SEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLA-WI--LDDIIRSLMPPSRVTVIIGE  246 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~-wv--~~~il~~l~~~~~~~~~~~~  246 (425)
                      .|...+..+.+..+....  ..+|.|.|..|+||||++..+.+.  +... ...+ .+  ..++.  + ...........
T Consensus        62 lg~~~~~~~~l~~~~~~~--~GlilisG~tGSGKTT~l~all~~--i~~~-~~~iitiEdp~E~~--~-~~~~q~~v~~~  133 (264)
T cd01129          62 LGLKPENLEIFRKLLEKP--HGIILVTGPTGSGKTTTLYSALSE--LNTP-EKNIITVEDPVEYQ--I-PGINQVQVNEK  133 (264)
T ss_pred             cCCCHHHHHHHHHHHhcC--CCEEEEECCCCCcHHHHHHHHHhh--hCCC-CCeEEEECCCceec--C-CCceEEEeCCc
Confidence            454444444444444332  467999999999999999877552  2110 0011 11  00000  0 00000001111


Q ss_pred             CHHHHHHHHHHHhcCCeEEEEecccCCChhhHH-HHHhhCCCCCCCcEEEEecCChhHH
Q 040913          247 DYKLKKSILRDFLTNKKYFIALDDVCHNIEIWD-DLEEVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       247 ~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~~-~l~~~l~~~~~gskIivTTR~~~va  304 (425)
                      ........++..|+...=.|+++.+. +.+... .+....    .|-.++-|....++.
T Consensus       134 ~~~~~~~~l~~~lR~~PD~i~vgEiR-~~e~a~~~~~aa~----tGh~v~tTlHa~~~~  187 (264)
T cd01129         134 AGLTFARGLRAILRQDPDIIMVGEIR-DAETAEIAVQAAL----TGHLVLSTLHTNDAP  187 (264)
T ss_pred             CCcCHHHHHHHHhccCCCEEEeccCC-CHHHHHHHHHHHH----cCCcEEEEeccCCHH
Confidence            11245667777888788889999998 776544 333332    244466555555544

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.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=93.82  E-value=0.09  Score=53.02  Aligned_cols=25  Identities=20%  Similarity=0.193  Sum_probs=21.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-..++|+|..|+|||||++.+.+.
T Consensus       157 ~Gqri~I~G~sG~GKTtLL~~I~~~  181 (442)
T PRK08927        157 RGQRMGIFAGSGVGKSVLLSMLARN  181 (442)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhc
Confidence            3567899999999999999999874

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=93.81  E-value=0.046  Score=48.50  Aligned_cols=23  Identities=17%  Similarity=0.261  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|+|+.|+|||||++.+.+
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~   24 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQ   24 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46788999999999999999987

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]

Probab=93.81  E-value=0.24  Score=49.19  Aligned_cols=23  Identities=22%  Similarity=0.231  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+-|+|||+.|+||+||...+..
T Consensus       613 dSRiaIVGPNGVGKSTlLkLL~G  635 (807)
T KOG0066|consen  613 DSRIAIVGPNGVGKSTLLKLLIG  635 (807)
T ss_pred             cceeEEECCCCccHHHHHHHHhc
Confidence            46789999999999999998874

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=93.80  E-value=0.11  Score=54.75  Aligned_cols=65  Identities=11%  Similarity=0.159  Sum_probs=41.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcC-------
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTN-------  261 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~-------  261 (425)
                      .-++....|++|.||||||.-|..+.-..--             .+  +    -.+.-+...+..+|...++.       
T Consensus       325 ~kKilLL~GppGlGKTTLAHViAkqaGYsVv-------------EI--N----ASDeRt~~~v~~kI~~avq~~s~l~ad  385 (877)
T KOG1969|consen  325 PKKILLLCGPPGLGKTTLAHVIAKQAGYSVV-------------EI--N----ASDERTAPMVKEKIENAVQNHSVLDAD  385 (877)
T ss_pred             ccceEEeecCCCCChhHHHHHHHHhcCceEE-------------Ee--c----ccccccHHHHHHHHHHHHhhccccccC
Confidence            4688999999999999999998874321100             00  0    11223445555666666553       


Q ss_pred             -CeEEEEecccC
Q 040913          262 -KKYFIALDDVC  272 (425)
Q Consensus       262 -kr~LlVLDdvw  272 (425)
                       +..-||+|.+.
T Consensus       386 srP~CLViDEID  397 (877)
T KOG1969|consen  386 SRPVCLVIDEID  397 (877)
T ss_pred             CCcceEEEeccc
Confidence             55559999996

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=93.79  E-value=0.036  Score=51.53  Aligned_cols=20  Identities=20%  Similarity=0.268  Sum_probs=16.8

Q ss_pred             EEecCCCchHHHHHHhhcCc
Q 040913          195 ILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       195 IvG~gGvGKTtLa~~v~~~~  214 (425)
                      |+|++|+||||+++.+.+.-
T Consensus         1 ViGpaGSGKTT~~~~~~~~~   20 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWL   20 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHH
Confidence            68999999999999887743

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=93.79  E-value=0.086  Score=48.83  Aligned_cols=51  Identities=20%  Similarity=0.133  Sum_probs=39.3

Q ss_pred             CCCCCcccchhhHHH---HHHHHhcCC----CCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          164 QPRLDISEFERAREE---WFDLLIEGP----IGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~---l~~~L~~~~----~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ..-++++|.++.+.+   |++.|.+++    -.++-|..+|++|.|||.+|+.+.|..
T Consensus       118 it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~  175 (368)
T COG1223         118 ITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA  175 (368)
T ss_pred             ccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc
Confidence            344678998877654   567776653    247888999999999999999999943

>cd04163 Era Era subfamily

Probab=93.78  E-value=0.058  Score=45.96  Aligned_cols=24  Identities=17%  Similarity=0.212  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+|+++|..|+|||||+..+...
T Consensus         3 ~~~i~~~G~~g~GKttl~~~l~~~   26 (168)
T cd04163           3 SGFVAIVGRPNVGKSTLLNALVGQ   26 (168)
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            467999999999999999998764

Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=93.76  E-value=0.039  Score=47.90  Aligned_cols=21  Identities=14%  Similarity=0.142  Sum_probs=17.3

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |+|.|..|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            789999999999999999873

>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes

Probab=93.76  E-value=0.053  Score=47.06  Aligned_cols=22  Identities=23%  Similarity=0.288  Sum_probs=20.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++++|+|..|+|||||+..+..
T Consensus         2 ~vi~i~G~~gsGKTTli~~L~~   23 (159)
T cd03116           2 KVIGFVGYSGSGKTTLLEKLIP   23 (159)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999998886

In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=93.75  E-value=0.16  Score=53.75  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=21.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       366 ~Ge~iaIvG~SGsGKSTLl~lL~g  389 (592)
T PRK10790        366 SRGFVALVGHTGSGKSTLASLLMG  389 (592)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999999864

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=93.73  E-value=0.05  Score=47.38  Aligned_cols=21  Identities=24%  Similarity=0.248  Sum_probs=19.7

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|.|.|+.|+||||+|+.+.+
T Consensus         2 iI~i~G~~GSGKstia~~la~   22 (171)
T TIGR02173         2 IITISGPPGSGKTTVAKILAE   22 (171)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            789999999999999999977

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=93.72  E-value=0.079  Score=48.36  Aligned_cols=24  Identities=25%  Similarity=0.429  Sum_probs=20.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCc
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      .-++|.|.+|+|||+|++.+.++.
T Consensus        16 qr~~I~g~~g~GKt~Ll~~i~~~~   39 (215)
T PF00006_consen   16 QRIGIFGGAGVGKTVLLQEIANNQ   39 (215)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHC
T ss_pred             CEEEEEcCcccccchhhHHHHhcc
Confidence            357899999999999999988754

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional

Probab=93.72  E-value=0.049  Score=51.66  Aligned_cols=22  Identities=18%  Similarity=0.256  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|+|+|.+|+|||||+..+..
T Consensus         2 ~~i~i~G~~gSGKTTLi~~Li~   23 (274)
T PRK14493          2 KVLSIVGYKATGKTTLVERLVD   23 (274)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999988876

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=93.71  E-value=0.051  Score=48.02  Aligned_cols=22  Identities=14%  Similarity=0.178  Sum_probs=20.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++.|+|..|.|||||++.+..
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~   25 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAA   25 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999887

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=93.71  E-value=0.089  Score=51.53  Aligned_cols=91  Identities=14%  Similarity=0.045  Sum_probs=48.3

Q ss_pred             HHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccc----ccccchHHH----------HHHHHHHhCCCCCCC-----c
Q 040913          182 LLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK----FYFDCLAWI----------LDDIIRSLMPPSRVT-----V  242 (425)
Q Consensus       182 ~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~----~~F~~~~wv----------~~~il~~l~~~~~~~-----~  242 (425)
                      +|..+=..-+++-|.|.+|+|||+|+.+++-.....    ..-...+|+          +.++...+.......     -
T Consensus       118 lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~~g~d~~~~l~~I~~  197 (344)
T PLN03187        118 LLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERFGMDADAVLDNIIY  197 (344)
T ss_pred             hcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHHcCCChhhhcCeEEE
Confidence            343333456788899999999999998875321111    101233455          455555554432110     1


Q ss_pred             cCCCCHHHHHH---HHHHHhc-CCeEEEEecccC
Q 040913          243 IIGEDYKLKKS---ILRDFLT-NKKYFIALDDVC  272 (425)
Q Consensus       243 ~~~~~~~~l~~---~l~~~l~-~kr~LlVLDdvw  272 (425)
                      ....+.+++..   .+...+. .+--|||+|.+-
T Consensus       198 ~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSit  231 (344)
T PLN03187        198 ARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVI  231 (344)
T ss_pred             ecCCCHHHHHHHHHHHHHHHHhcCCCEEEEeCcH
Confidence            12234444333   3333333 345589999984

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=93.70  E-value=0.047  Score=47.86  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=17.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|.|.+|+|||||++.+.+.
T Consensus         2 i~iTG~pG~GKTTll~k~i~~   22 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEE   22 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH
Confidence            678999999999999998873

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]

Probab=93.69  E-value=0.055  Score=48.85  Aligned_cols=23  Identities=13%  Similarity=0.183  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+++|+.|+||||.|+.+-+
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             ceEEEEecCCCCCHHHHHHHHHH
Confidence            46899999999999999998766

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=93.69  E-value=0.072  Score=55.58  Aligned_cols=44  Identities=23%  Similarity=0.075  Sum_probs=35.7

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|.+..++.+...+....  ..-+-|+|++|+|||++|+.+++
T Consensus        65 ~~iiGqs~~i~~l~~al~~~~--~~~vLi~Ge~GtGKt~lAr~i~~  108 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGPN--PQHVIIYGPPGVGKTAAARLVLE  108 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCCC--CceEEEECCCCCCHHHHHHHHHH
Confidence            358999999999988776543  33457899999999999999975

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.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=93.69  E-value=0.099  Score=50.77  Aligned_cols=35  Identities=23%  Similarity=0.046  Sum_probs=26.0

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|-.+|..+=..-.++-|.|.+|+|||||+..+..
T Consensus        84 ~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~  118 (316)
T TIGR02239        84 ELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAV  118 (316)
T ss_pred             HHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHH
Confidence            33344444434578999999999999999988753

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=93.68  E-value=0.35  Score=49.34  Aligned_cols=56  Identities=21%  Similarity=0.084  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHhcCCeEEEEecccCCChhhH---HHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          248 YKLKKSILRDFLTNKKYFIALDDVCHNIEIW---DDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       248 ~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~---~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      .......|.+.|=-+..|+.||+-- +.-+.   .-|...|..-..+ .++|++|+++-..
T Consensus       225 GwrmR~aLAr~Lf~kP~LLLLDEPt-nhLDleA~~wLee~L~k~d~~-~lVi~sh~QDfln  283 (614)
T KOG0927|consen  225 GWRMRAALARALFQKPDLLLLDEPT-NHLDLEAIVWLEEYLAKYDRI-ILVIVSHSQDFLN  283 (614)
T ss_pred             hHHHHHHHHHHHhcCCCEEEecCCc-cCCCHHHHHHHHHHHHhccCc-eEEEEecchhhhh
Confidence            3444556666666788999999975 44222   1233344332322 6899999876443

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=93.68  E-value=0.09  Score=51.45  Aligned_cols=45  Identities=11%  Similarity=0.073  Sum_probs=35.4

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+.+||.+..+..++-.+.++.  ..-+.|.|..|+|||||++.+..
T Consensus         3 f~~ivgq~~~~~al~~~~~~~~--~g~vli~G~~G~gKttl~r~~~~   47 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVIDPK--IGGVMVMGDRGTGKSTAVRALAA   47 (337)
T ss_pred             ccccccHHHHHHHHHHHhcCCC--CCeEEEEcCCCCCHHHHHHHHHH
Confidence            3568899999888766666543  44567999999999999999864

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.

>PLN02200 adenylate kinase family protein

Probab=93.67  E-value=0.056  Score=50.10  Aligned_cols=23  Identities=13%  Similarity=0.117  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|++|+||||+|+.+..
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~   65 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVE   65 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999998876

>TIGR01842 type_I_sec_PrtD type I secretion system ABC transporter, PrtD family

Probab=93.66  E-value=0.23  Score=52.03  Aligned_cols=24  Identities=25%  Similarity=0.249  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       343 ~G~~~~ivG~sGsGKSTL~~ll~g  366 (544)
T TIGR01842       343 AGEALAIIGPSGSGKSTLARLIVG  366 (544)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            356899999999999999999865

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=93.66  E-value=0.13  Score=49.93  Aligned_cols=32  Identities=22%  Similarity=0.139  Sum_probs=24.3

Q ss_pred             HHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          181 DLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       181 ~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|..+=....++-|+|++|+|||+|+.++.-
T Consensus        93 ~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~  124 (317)
T PRK04301         93 ELLGGGIETQSITEFYGEFGSGKTQICHQLAV  124 (317)
T ss_pred             HHhcCCccCCcEEEEECCCCCCHhHHHHHHHH
Confidence            33433334578889999999999999988764

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=93.61  E-value=0.14  Score=48.31  Aligned_cols=92  Identities=14%  Similarity=0.237  Sum_probs=48.8

Q ss_pred             EEEEEEecCCCchHHHH-HHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC-------ccCCCCHHH----
Q 040913          191 SVVAILDSSGFDKTAFA-ADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT-------VIIGEDYKL----  250 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~-------~~~~~~~~~----  250 (425)
                      .-++|.|..|+|||+|| +.+.+..  ...+-+ +++        ..++...+.......       ..+......    
T Consensus        70 Qr~~Ifg~~g~GKt~L~l~~i~~~~--~~~v~~-V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a~  146 (274)
T cd01132          70 QRELIIGDRQTGKTAIAIDTIINQK--GKKVYC-IYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAP  146 (274)
T ss_pred             CEEEeeCCCCCCccHHHHHHHHHhc--CCCeEE-EEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHHH
Confidence            45889999999999995 6665521  111211 222        555666655332111       001111111    


Q ss_pred             -HHHHHHHHh--cCCeEEEEecccCCChhhHHHHHhhC
Q 040913          251 -KKSILRDFL--TNKKYFIALDDVCHNIEIWDDLEEVL  285 (425)
Q Consensus       251 -l~~~l~~~l--~~kr~LlVLDdvw~~~~~~~~l~~~l  285 (425)
                       ..-.+.+++  +++..||++||+-.-...|.++...+
T Consensus       147 ~~a~aiAE~fr~~G~~Vlvl~DslTr~A~A~rEisl~~  184 (274)
T cd01132         147 YTGCAMGEYFMDNGKHALIIYDDLSKQAVAYRQMSLLL  184 (274)
T ss_pred             HHHHHHHHHHHHCCCCEEEEEcChHHHHHHHHHHHHhc
Confidence             122333333  48999999999951235666665444

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.61  E-value=0.1  Score=53.69  Aligned_cols=24  Identities=25%  Similarity=0.256  Sum_probs=20.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|.+|+||||++..+..
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999877654

>PLN02796 D-glycerate 3-kinase

Probab=93.61  E-value=0.059  Score=52.47  Aligned_cols=24  Identities=21%  Similarity=0.156  Sum_probs=22.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+-+|+|.|..|+|||||++.+..
T Consensus        99 ~pliIGI~G~sGSGKSTLa~~L~~  122 (347)
T PLN02796         99 PPLVIGISAPQGCGKTTLVFALVY  122 (347)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH
Confidence            567899999999999999999887

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=93.61  E-value=0.1  Score=50.42  Aligned_cols=82  Identities=16%  Similarity=0.083  Sum_probs=49.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLTN  261 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~~  261 (425)
                      .-+++-|+|..|+||||||.++..  ..+..-..++|+      -...+..++.....- -..+...++....+..+++.
T Consensus        52 ~G~ivEi~G~~ssGKttLaL~~ia--~~q~~g~~~a~ID~e~~ld~~~a~~lGvdl~rllv~~P~~~E~al~~~e~lirs  129 (322)
T PF00154_consen   52 RGRIVEIYGPESSGKTTLALHAIA--EAQKQGGICAFIDAEHALDPEYAESLGVDLDRLLVVQPDTGEQALWIAEQLIRS  129 (322)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHH--HHHHTT-EEEEEESSS---HHHHHHTT--GGGEEEEE-SSHHHHHHHHHHHHHT
T ss_pred             cCceEEEeCCCCCchhhhHHHHHH--hhhcccceeEEecCcccchhhHHHhcCccccceEEecCCcHHHHHHHHHHHhhc
Confidence            467999999999999999998877  333333345566      334455555543321 11123445666666666654


Q ss_pred             -CeEEEEecccC
Q 040913          262 -KKYFIALDDVC  272 (425)
Q Consensus       262 -kr~LlVLDdvw  272 (425)
                       .--++|+|-|-
T Consensus       130 g~~~lVVvDSv~  141 (322)
T PF00154_consen  130 GAVDLVVVDSVA  141 (322)
T ss_dssp             TSESEEEEE-CT
T ss_pred             ccccEEEEecCc
Confidence             44599999986

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=93.60  E-value=0.1  Score=49.53  Aligned_cols=24  Identities=25%  Similarity=0.264  Sum_probs=20.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.++|++|+||||++..+..
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~   94 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLAN   94 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            478999999999999998776654

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=93.56  E-value=1.7  Score=44.65  Aligned_cols=43  Identities=16%  Similarity=0.058  Sum_probs=28.7

Q ss_pred             ccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          170 SEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +|.+..- -|..-|.-+-+.-.-|++||+.|+|||||.+.++-+
T Consensus       397 F~y~~~~-~iy~~l~fgid~~srvAlVGPNG~GKsTLlKl~~gd  439 (614)
T KOG0927|consen  397 FGYSDNP-MIYKKLNFGIDLDSRVALVGPNGAGKSTLLKLITGD  439 (614)
T ss_pred             cCCCCcc-hhhhhhhcccCcccceeEecCCCCchhhhHHHHhhc
Confidence            4555444 344444333223356899999999999999998865

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=93.54  E-value=0.18  Score=53.20  Aligned_cols=24  Identities=21%  Similarity=0.162  Sum_probs=20.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|..|.|||||++.+..
T Consensus       365 ~Ge~i~IvG~sGsGKSTLlklL~g  388 (576)
T TIGR02204       365 PGETVALVGPSGAGKSTLFQLLLR  388 (576)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            345789999999999999998875

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=93.54  E-value=0.057  Score=49.28  Aligned_cols=23  Identities=26%  Similarity=0.164  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus        30 G~~~~l~G~nGsGKSTLl~~i~G   52 (218)
T cd03255          30 GEFVAIVGPSGSGKSTLLNILGG   52 (218)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhC
Confidence            46899999999999999999876

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=93.53  E-value=0.055  Score=48.23  Aligned_cols=21  Identities=14%  Similarity=0.091  Sum_probs=19.5

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|.|.|+.|+||||+++.+.+
T Consensus         2 ~I~ieG~~GsGKtT~~~~L~~   22 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAE   22 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999876

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>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=93.53  E-value=0.11  Score=45.03  Aligned_cols=37  Identities=22%  Similarity=0.261  Sum_probs=29.9

Q ss_pred             hhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          173 ERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       173 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ....++|.+.|..     +++.++|..|+|||||...+..+.
T Consensus        23 ~~g~~~l~~~l~~-----k~~vl~G~SGvGKSSLiN~L~~~~   59 (161)
T PF03193_consen   23 GEGIEELKELLKG-----KTSVLLGQSGVGKSSLINALLPEA   59 (161)
T ss_dssp             TTTHHHHHHHHTT-----SEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CcCHHHHHHHhcC-----CEEEEECCCCCCHHHHHHHHHhhc
Confidence            3556777777754     578899999999999999999853

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.

>cd01862 Rab7 Rab7 subfamily

Probab=93.52  E-value=0.058  Score=46.72  Aligned_cols=21  Identities=38%  Similarity=0.485  Sum_probs=19.0

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||+..+.++
T Consensus         3 i~viG~~~~GKSsl~~~l~~~   23 (172)
T cd01862           3 VIILGDSGVGKTSLMNQYVNK   23 (172)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999988774

Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-

>smart00173 RAS Ras subfamily of RAS small GTPases

Probab=93.51  E-value=0.058  Score=46.41  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=18.8

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||+..+.+.
T Consensus         3 i~v~G~~~~GKTsli~~~~~~   23 (164)
T smart00173        3 LVVLGSGGVGKSALTIQFVQG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999988764

Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=93.49  E-value=0.13  Score=49.80  Aligned_cols=48  Identities=23%  Similarity=0.232  Sum_probs=38.9

Q ss_pred             CCCCcccchhhHHH---HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          165 PRLDISEFERAREE---WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       165 ~~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....+||..+.++.   |++++.++.-.-+.|.|+|++|.|||+||-.+.+
T Consensus        37 ~~dG~VGQ~~AReAaGvIv~mik~gk~aGrgiLi~GppgTGKTAlA~gIa~   87 (450)
T COG1224          37 IGDGLVGQEEAREAAGVIVKMIKQGKMAGRGILIVGPPGTGKTALAMGIAR   87 (450)
T ss_pred             cCCcccchHHHHHhhhHHHHHHHhCcccccEEEEECCCCCcHHHHHHHHHH
Confidence            34568997766554   6788888766678899999999999999999888

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=93.48  E-value=0.059  Score=48.90  Aligned_cols=23  Identities=17%  Similarity=0.124  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||++.+..
T Consensus        27 G~~~~l~G~nGsGKSTLl~~l~G   49 (211)
T cd03225          27 GEFVLIVGPNGSGKSTLLRLLNG   49 (211)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999875

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=93.46  E-value=0.11  Score=52.26  Aligned_cols=24  Identities=17%  Similarity=0.167  Sum_probs=21.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|+|..|+|||||++.+.+.
T Consensus       155 GQ~igI~G~sGaGKSTLl~~I~g~  178 (434)
T PRK07196        155 GQRVGLMAGSGVGKSVLLGMITRY  178 (434)
T ss_pred             ceEEEEECCCCCCccHHHHHHhcc
Confidence            567999999999999999998874

>PRK08356 hypothetical protein; Provisional

Probab=93.46  E-value=0.071  Score=47.89  Aligned_cols=22  Identities=18%  Similarity=0.064  Sum_probs=19.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ..+|.|.|++|+||||+|+.+-
T Consensus         5 ~~~i~~~G~~gsGK~t~a~~l~   26 (195)
T PRK08356          5 KMIVGVVGKIAAGKTTVAKFFE   26 (195)
T ss_pred             cEEEEEECCCCCCHHHHHHHHH
Confidence            3578999999999999999983

>TIGR00231 small_GTP small GTP-binding protein domain

Probab=93.45  E-value=0.063  Score=45.09  Aligned_cols=23  Identities=13%  Similarity=0.264  Sum_probs=20.2

Q ss_pred             EEEEEecCCCchHHHHHHhhcCc
Q 040913          192 VVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      -|+++|.+|+|||||+..+....
T Consensus         3 ki~~~G~~~~GKstl~~~l~~~~   25 (161)
T TIGR00231         3 KIVIVGDPNVGKSTLLNRLLGNK   25 (161)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999988754

This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model.

>cd04119 RJL RJL (RabJ-Like) subfamily

Probab=93.45  E-value=0.061  Score=46.21  Aligned_cols=21  Identities=19%  Similarity=0.275  Sum_probs=18.9

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.+.
T Consensus         3 i~~vG~~~vGKTsli~~l~~~   23 (168)
T cd04119           3 VISMGNSGVGKSCIIKRYCEG   23 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999988764

RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization.

>PRK10463 hydrogenase nickel incorporation protein HypB; Provisional

Probab=93.44  E-value=0.11  Score=49.38  Aligned_cols=25  Identities=24%  Similarity=0.268  Sum_probs=22.8

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..+|.|+|.+|+|||||...+.+
T Consensus       102 ~~~~~v~l~G~pGsGKTTLl~~l~~  126 (290)
T PRK10463        102 RKQLVLNLVSSPGSGKTTLLTETLM  126 (290)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999988877

>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=93.43  E-value=0.2  Score=52.93  Aligned_cols=24  Identities=13%  Similarity=0.109  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-..++|+|+.|.|||||++.+..
T Consensus       340 ~G~~~~ivG~sGsGKSTLl~ll~g  363 (569)
T PRK10789        340 PGQMLGICGPTGSGKSTLLSLIQR  363 (569)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999998865

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=93.43  E-value=0.093  Score=53.32  Aligned_cols=82  Identities=11%  Similarity=0.190  Sum_probs=48.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCcccccccc--chHHH--------HHHHHHHhCCCCCCC------ccCCC-C-----H
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFD--CLAWI--------LDDIIRSLMPPSRVT------VIIGE-D-----Y  248 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~--~~~wv--------~~~il~~l~~~~~~~------~~~~~-~-----~  248 (425)
                      .-++|.|..|+|||||+..+.+.......+.  .++++        ..+++..+.......      ...+. .     .
T Consensus       142 QR~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a  221 (458)
T TIGR01041       142 QKLPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVT  221 (458)
T ss_pred             CEEEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHH
Confidence            4578999999999999999888544331111  22233        556666665433211      00111 1     1


Q ss_pred             HHHHHHHHHHhc---CCeEEEEecccC
Q 040913          249 KLKKSILRDFLT---NKKYFIALDDVC  272 (425)
Q Consensus       249 ~~l~~~l~~~l~---~kr~LlVLDdvw  272 (425)
                      ....-.+.++++   ++++||++||+-
T Consensus       222 ~~~a~tiAEyfr~d~G~~VLli~DslT  248 (458)
T TIGR01041       222 PRMALTAAEYLAFEKDMHVLVILTDMT  248 (458)
T ss_pred             HHHHHHHHHHHHHccCCcEEEEEcChh
Confidence            122333556665   789999999994

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=93.42  E-value=0.062  Score=47.92  Aligned_cols=23  Identities=22%  Similarity=0.287  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||.+.+..
T Consensus        18 Ge~~~i~G~nGsGKSTLl~~i~G   40 (190)
T TIGR01166        18 GEVLALLGANGAGKSTLLLHLNG   40 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999876

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>cd04155 Arl3 Arl3 subfamily

Probab=93.40  E-value=0.059  Score=46.86  Aligned_cols=24  Identities=17%  Similarity=0.101  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|+|+|.+|+|||||.+.+.+.
T Consensus        14 ~~~v~i~G~~g~GKStLl~~l~~~   37 (173)
T cd04155          14 EPRILILGLDNAGKTTILKQLASE   37 (173)
T ss_pred             ccEEEEEccCCCCHHHHHHHHhcC
Confidence            455899999999999999999874

Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation.

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=93.39  E-value=0.13  Score=50.29  Aligned_cols=47  Identities=30%  Similarity=0.332  Sum_probs=34.6

Q ss_pred             CCCcccchhhHHH---HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREE---WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+||..+.++.   +++++..+.-.-+.|.+.|++|.|||+||..+..
T Consensus        23 ~~GlVGQ~~AReAagiiv~mIk~~K~aGr~iLiaGppGtGKTAlA~~ia~   72 (398)
T PF06068_consen   23 ADGLVGQEKAREAAGIIVDMIKEGKIAGRAILIAGPPGTGKTALAMAIAK   72 (398)
T ss_dssp             ETTEES-HHHHHHHHHHHHHHHTT--TT-EEEEEE-TTSSHHHHHHHHHH
T ss_pred             cccccChHHHHHHHHHHHHHHhcccccCcEEEEeCCCCCCchHHHHHHHH
Confidence            4579998776655   5788877765567888999999999999999988

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PRK01184 hypothetical protein; Provisional

Probab=93.39  E-value=0.062  Score=47.63  Aligned_cols=19  Identities=16%  Similarity=0.365  Sum_probs=17.0

Q ss_pred             EEEEEEecCCCchHHHHHH
Q 040913          191 SVVAILDSSGFDKTAFAAD  209 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~  209 (425)
                      .+|.|+|++|+||||+++.
T Consensus         2 ~~i~l~G~~GsGKsT~a~~   20 (184)
T PRK01184          2 KIIGVVGMPGSGKGEFSKI   20 (184)
T ss_pred             cEEEEECCCCCCHHHHHHH
Confidence            4799999999999999873

>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]

Probab=93.39  E-value=0.34  Score=42.73  Aligned_cols=23  Identities=30%  Similarity=0.280  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|++|.||+||...|.-
T Consensus        25 ge~vAi~GpSGaGKSTLLnLIAG   47 (231)
T COG3840          25 GEIVAILGPSGAGKSTLLNLIAG   47 (231)
T ss_pred             CcEEEEECCCCccHHHHHHHHHh
Confidence            45899999999999999988863

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=93.38  E-value=0.062  Score=48.97  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||++.+..
T Consensus        29 Ge~~~i~G~nGsGKSTLl~~l~G   51 (216)
T TIGR00960        29 GEMVFLVGHSGAGKSTFLKLILG   51 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999999876

>COG0410 LivF ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=93.38  E-value=0.17  Score=46.20  Aligned_cols=26  Identities=23%  Similarity=0.238  Sum_probs=22.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNH  215 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~  215 (425)
                      -.+++++|..|+|||||.+.+..-.+
T Consensus        29 Geiv~llG~NGaGKTTlLkti~Gl~~   54 (237)
T COG0410          29 GEIVALLGRNGAGKTTLLKTIMGLVR   54 (237)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            46899999999999999999987443

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=93.37  E-value=0.061  Score=50.23  Aligned_cols=23  Identities=17%  Similarity=0.177  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        28 G~i~~iiGpNG~GKSTLLk~l~g   50 (258)
T COG1120          28 GEITGILGPNGSGKSTLLKCLAG   50 (258)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            57899999999999999999886

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=93.37  E-value=0.19  Score=48.66  Aligned_cols=46  Identities=7%  Similarity=-0.062  Sum_probs=30.7

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          162 EGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      |..++...+.-+ ....++.++..+    +-|.+.|.+|+||||+|+.+..
T Consensus        41 p~~d~~y~f~~~-~~~~vl~~l~~~----~~ilL~G~pGtGKTtla~~lA~   86 (327)
T TIGR01650        41 PDIDPAYLFDKA-TTKAICAGFAYD----RRVMVQGYHGTGKSTHIEQIAA   86 (327)
T ss_pred             CCCCCCccCCHH-HHHHHHHHHhcC----CcEEEEeCCCChHHHHHHHHHH
Confidence            333333333333 345566666543    3588999999999999999876

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.

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=93.37  E-value=0.069  Score=45.25  Aligned_cols=24  Identities=21%  Similarity=0.313  Sum_probs=20.5

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCc
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      +-|-++|..|+|||||++.+...+
T Consensus         2 krimliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    2 KRIMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             ceEEEECCCCCCHHHHHHHHcCCC
Confidence            347789999999999999998743

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=93.36  E-value=0.1  Score=52.67  Aligned_cols=24  Identities=21%  Similarity=0.203  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|+|..|+|||||++.+...
T Consensus       165 Gqri~I~G~SGsGKTTLL~~Ia~l  188 (450)
T PRK06002        165 GQRIGIFAGSGVGKSTLLAMLARA  188 (450)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999988863

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=93.34  E-value=0.066  Score=47.27  Aligned_cols=24  Identities=25%  Similarity=0.210  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (178)
T cd03229          26 GEIVALLGPSGSGKSTLLRCIAGL   49 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999753

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd04159 Arl10_like Arl10-like subfamily

Probab=93.34  E-value=0.077  Score=44.85  Aligned_cols=21  Identities=10%  Similarity=0.120  Sum_probs=19.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |+|+|..|+|||||.+.+.+.
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            689999999999999999875

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>cd04113 Rab4 Rab4 subfamily

Probab=93.32  E-value=0.066  Score=45.93  Aligned_cols=21  Identities=29%  Similarity=0.341  Sum_probs=18.8

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||++.+.+.
T Consensus         3 i~v~G~~~vGKTsli~~l~~~   23 (161)
T cd04113           3 FIIIGSSGTGKSCLLHRFVEN   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            679999999999999998764

Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p

>TIGR03258 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT

Probab=93.30  E-value=0.23  Score=49.22  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        31 Ge~~~llGpsGsGKSTLLr~iaG   53 (362)
T TIGR03258        31 GELLALIGKSGCGKTTLLRAIAG   53 (362)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=93.29  E-value=0.27  Score=49.04  Aligned_cols=23  Identities=22%  Similarity=0.247  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        45 Ge~~~llGpsGsGKSTLLr~IaG   67 (377)
T PRK11607         45 GEIFALLGASGCGKSTLLRMLAG   67 (377)
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999998874

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=93.27  E-value=0.069  Score=50.42  Aligned_cols=34  Identities=21%  Similarity=0.212  Sum_probs=24.7

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++..++..+    .-|-+.|++|+|||+||+.+.+
T Consensus        10 l~~~~l~~l~~g----~~vLL~G~~GtGKT~lA~~la~   43 (262)
T TIGR02640        10 VTSRALRYLKSG----YPVHLRGPAGTGKTTLAMHVAR   43 (262)
T ss_pred             HHHHHHHHHhcC----CeEEEEcCCCCCHHHHHHHHHH
Confidence            344555555543    2455899999999999999986

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).

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=93.26  E-value=0.06  Score=47.06  Aligned_cols=21  Identities=14%  Similarity=0.197  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|+|+.|+||||+|+.+.+
T Consensus         4 ~i~~~G~~GsGKst~~~~la~   24 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQ   24 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            578899999999999999987

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=93.24  E-value=0.068  Score=49.29  Aligned_cols=23  Identities=30%  Similarity=0.254  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      --.++|+|++|+|||||.+.+..
T Consensus        29 GEfvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          29 GEFVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999998863

>PRK13695 putative NTPase; Provisional

Probab=93.24  E-value=0.062  Score=47.26  Aligned_cols=22  Identities=18%  Similarity=0.231  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||++.+++.
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3789999999999999998763

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=93.24  E-value=0.16  Score=46.51  Aligned_cols=21  Identities=10%  Similarity=0.154  Sum_probs=19.4

Q ss_pred             EEEEEEecCCCchHHHHHHhh
Q 040913          191 SVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .++.|.|+.|.||||+.+.+.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~   51 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVA   51 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            788999999999999999874

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=93.23  E-value=0.076  Score=46.78  Aligned_cols=25  Identities=12%  Similarity=0.260  Sum_probs=22.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      -.++.|.|++|+|||||++.++++.
T Consensus         4 G~l~vlsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           4 GLLIVLSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhc
Confidence            4578899999999999999999964

>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=93.23  E-value=0.3  Score=46.55  Aligned_cols=53  Identities=13%  Similarity=0.218  Sum_probs=32.6

Q ss_pred             HHHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCC--CCCCCcEEEEecCChhHHH
Q 040913          253 SILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLP--DNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       253 ~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~--~~~~gskIivTTR~~~va~  305 (425)
                      -.|.+.|....-++..|..-+  +++.=..+...|.  +...|-.|++.|...+|.+
T Consensus       150 VaIARALa~~P~iLL~DEaTSALDP~TT~sIL~LL~~In~~lglTIvlITHEm~Vvk  206 (339)
T COG1135         150 VAIARALANNPKILLCDEATSALDPETTQSILELLKDINRELGLTIVLITHEMEVVK  206 (339)
T ss_pred             HHHHHHHhcCCCEEEecCccccCChHHHHHHHHHHHHHHHHcCCEEEEEechHHHHH
Confidence            356667777777888898752  2233233333333  2344888888888877764

>PRK14532 adenylate kinase; Provisional

Probab=93.22  E-value=0.062  Score=47.83  Aligned_cols=20  Identities=10%  Similarity=0.091  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.+.|++|+||||+|+.+..
T Consensus         3 i~~~G~pGsGKsT~a~~la~   22 (188)
T PRK14532          3 LILFGPPAAGKGTQAKRLVE   22 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999987

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=93.22  E-value=0.075  Score=48.39  Aligned_cols=22  Identities=23%  Similarity=0.271  Sum_probs=20.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|..|+|||||++.+..
T Consensus        24 e~~~i~G~nGsGKSTLl~~l~G   45 (214)
T cd03297          24 EVTGIFGASGAGKSTLLRCIAG   45 (214)
T ss_pred             eeEEEECCCCCCHHHHHHHHhC
Confidence            7999999999999999999876

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>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=93.19  E-value=0.15  Score=45.90  Aligned_cols=42  Identities=19%  Similarity=0.076  Sum_probs=30.4

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++++|.+..+..+.=....    ..-+.++|.+|+|||+||+.+-.
T Consensus         3 ~dI~GQe~aKrAL~iAAaG----~h~lLl~GppGtGKTmlA~~l~~   44 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAAAG----GHHLLLIGPPGTGKTMLARRLPS   44 (206)
T ss_dssp             CCSSSTHHHHHHHHHHHHC----C--EEEES-CCCTHHHHHHHHHH
T ss_pred             hhhcCcHHHHHHHHHHHcC----CCCeEEECCCCCCHHHHHHHHHH
Confidence            5688888887777555444    24578999999999999998764

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.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=93.19  E-value=0.18  Score=49.47  Aligned_cols=94  Identities=12%  Similarity=0.036  Sum_probs=50.5

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc----ccchHHH----------HHHHHHHhCCCCCCC---
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY----FDCLAWI----------LDDIIRSLMPPSRVT---  241 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~----F~~~~wv----------~~~il~~l~~~~~~~---  241 (425)
                      |-++|..+=..-.++-|.|.+|+|||+|+..++-.......    =..++|+          +.+|...+.......   
T Consensus       112 LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~~~~~~~~~~l~~  191 (342)
T PLN03186        112 LDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAERFGLNGADVLEN  191 (342)
T ss_pred             HHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHHHHHcCCChhhhccc
Confidence            33444444345678889999999999999877642221111    1134455          555665554332110   


Q ss_pred             --ccCCCCHHHHHHHHH---HHh-cCCeEEEEecccC
Q 040913          242 --VIIGEDYKLKKSILR---DFL-TNKKYFIALDDVC  272 (425)
Q Consensus       242 --~~~~~~~~~l~~~l~---~~l-~~kr~LlVLDdvw  272 (425)
                        .....+.+.+...+.   ..+ ..+--|||+|-+-
T Consensus       192 i~~~~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~  228 (342)
T PLN03186        192 VAYARAYNTDHQSELLLEAASMMAETRFALMIVDSAT  228 (342)
T ss_pred             eEEEecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcH
Confidence              111233444433332   223 3456699999885

>PRK05922 type III secretion system ATPase; Validated

Probab=93.19  E-value=0.1  Score=52.48  Aligned_cols=24  Identities=8%  Similarity=0.191  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|+|..|+|||||.+.+.+.
T Consensus       157 GqrigI~G~nG~GKSTLL~~Ia~~  180 (434)
T PRK05922        157 GQRIGVFSEPGSGKSSLLSTIAKG  180 (434)
T ss_pred             CcEEEEECCCCCChHHHHHHHhcc
Confidence            345899999999999999999874

>smart00175 RAB Rab subfamily of small GTPases

Probab=93.19  E-value=0.072  Score=45.65  Aligned_cols=21  Identities=14%  Similarity=0.373  Sum_probs=19.0

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||++.+.+.
T Consensus         3 v~v~G~~~~GKTtli~~l~~~   23 (164)
T smart00175        3 IILIGDSGVGKSSLLSRFTDG   23 (164)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999999764

Rab GTPases are implicated in vesicle trafficking.

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

Probab=93.18  E-value=0.079  Score=47.21  Aligned_cols=34  Identities=18%  Similarity=0.224  Sum_probs=24.9

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...++......   -..+.|+|..|+|||||++.+..
T Consensus        14 ~~~~l~~~v~~---g~~i~I~G~tGSGKTTll~aL~~   47 (186)
T cd01130          14 QAAYLWLAVEA---RKNILISGGTGSGKTTLLNALLA   47 (186)
T ss_pred             HHHHHHHHHhC---CCEEEEECCCCCCHHHHHHHHHh
Confidence            34444444332   45789999999999999998876

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.

>cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily

Probab=93.18  E-value=0.07  Score=45.52  Aligned_cols=21  Identities=19%  Similarity=0.438  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.+.
T Consensus         4 i~iiG~~~vGKTsl~~~~~~~   24 (162)
T cd04138           4 LVVVGAGGVGKSALTIQLIQN   24 (162)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999988764

H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=93.15  E-value=0.072  Score=48.33  Aligned_cols=24  Identities=17%  Similarity=0.124  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||++.+...
T Consensus        26 G~~~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          26 GEIFGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999998753

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=93.14  E-value=0.071  Score=49.32  Aligned_cols=23  Identities=22%  Similarity=0.244  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||++.+..
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G   48 (235)
T cd03261          26 GEILAIIGPSGSGKSTLLRLIVG   48 (235)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

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.

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.12  E-value=0.081  Score=51.39  Aligned_cols=24  Identities=17%  Similarity=0.180  Sum_probs=21.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.++|++|+||||++..+..
T Consensus       113 ~~~vi~lvGpnGsGKTTt~~kLA~  136 (318)
T PRK10416        113 KPFVILVVGVNGVGKTTTIGKLAH  136 (318)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            468999999999999998877755

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=93.12  E-value=0.073  Score=48.41  Aligned_cols=23  Identities=22%  Similarity=0.199  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|+|||||++.+..
T Consensus        28 G~~~~l~G~nGsGKSTLl~~i~G   50 (214)
T TIGR02673        28 GEFLFLTGPSGAGKTTLLKLLYG   50 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999876

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=93.09  E-value=0.06  Score=47.63  Aligned_cols=21  Identities=14%  Similarity=0.188  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|+.|+||||+++.+.+
T Consensus         1 ii~itG~~gsGKst~~~~l~~   21 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLKE   21 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999876

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=93.09  E-value=0.065  Score=53.73  Aligned_cols=25  Identities=24%  Similarity=0.185  Sum_probs=22.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+.|+|+|..|+|||||++.+.+.
T Consensus       218 ~~~~IvI~G~~gsGKTTL~~~La~~  242 (399)
T PRK08099        218 FVRTVAILGGESSGKSTLVNKLANI  242 (399)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4788999999999999999998873

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=93.09  E-value=0.12  Score=46.65  Aligned_cols=97  Identities=11%  Similarity=0.107  Sum_probs=46.3

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcCccccccc-----c-chHHH--HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHh
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-----D-CLAWI--LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFL  259 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-----~-~~~wv--~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l  259 (425)
                      ..+.++.+.|.+|.||||++..+..... ...+     | .+...  ...+...-.....  .........+...+.+..
T Consensus        13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~~-~~~~v~i~~D~~r~~~p~~~~~~~~~~~~~~--~~~~~~a~~~~~~~~~~a   89 (199)
T PF06414_consen   13 EKPTLIIIAGQPGSGKSTLARQLLEEFG-GGGIVVIDADEFRQFHPDYDELLKADPDEAS--ELTQKEASRLAEKLIEYA   89 (199)
T ss_dssp             SS-EEEEEES-TTSTTHHHHHHHHHHT--TT-SEEE-GGGGGGGSTTHHHHHHHHCCCTH--HHHHHHHHHHHHHHHHHH
T ss_pred             cCCEEEEEeCCCCCCHHHHHHHhhhhcc-CCCeEEEehHHHHHhccchhhhhhhhhhhhH--HHHHHHHHHHHHHHHHHH
Confidence            4688888999999999999998877311 1111     0 00000  2333332111110  111122334555666666


Q ss_pred             cCCeEEEEecccCCChhhHHHHHhhCCC
Q 040913          260 TNKKYFIALDDVCHNIEIWDDLEEVLPD  287 (425)
Q Consensus       260 ~~kr~LlVLDdvw~~~~~~~~l~~~l~~  287 (425)
                      ..+++=||+|..-.+.+....+...+..
T Consensus        90 ~~~~~nii~E~tl~~~~~~~~~~~~~k~  117 (199)
T PF06414_consen   90 IENRYNIIFEGTLSNPSKLRKLIREAKA  117 (199)
T ss_dssp             HHCT--EEEE--TTSSHHHHHHHHHHHC
T ss_pred             HHcCCCEEEecCCCChhHHHHHHHHHHc
Confidence            6777888889876234444445555543

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=93.09  E-value=0.074  Score=48.35  Aligned_cols=23  Identities=26%  Similarity=0.228  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|.|||||++.+..
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~G   48 (213)
T cd03259          26 GEFLALLGPSGCGKTTLLRLIAG   48 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999998875

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=93.08  E-value=0.072  Score=49.48  Aligned_cols=23  Identities=26%  Similarity=0.236  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|+|||||++.+..
T Consensus        28 Ge~~~l~G~nGsGKSTLl~~l~G   50 (243)
T TIGR02315        28 GEFVAIIGPSGAGKSTLLRCINR   50 (243)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=93.08  E-value=0.95  Score=40.13  Aligned_cols=55  Identities=18%  Similarity=0.196  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCC-CCCCCcEEEEecCChhH
Q 040913          249 KLKKSILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLP-DNQNGSRVLITVINPSL  303 (425)
Q Consensus       249 ~~l~~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~-~~~~gskIivTTR~~~v  303 (425)
                      ++..-.+.+..-.++-|-+||..-.  +.+.-..+...+. ....|.-||.||..+..
T Consensus       135 QqRRvAlArL~ls~~pLWiLDEP~taLDk~g~a~l~~l~~~H~~~GGiVllttHq~l~  192 (209)
T COG4133         135 QQRRVALARLWLSPAPLWILDEPFTALDKEGVALLTALMAAHAAQGGIVLLTTHQPLP  192 (209)
T ss_pred             HHHHHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHHHhcCCCEEEEecCCccC
Confidence            4444556666678999999999852  1222222322222 34668889999877554

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=93.08  E-value=1.3  Score=43.03  Aligned_cols=122  Identities=16%  Similarity=0.046  Sum_probs=62.2

Q ss_pred             hhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccc-----cchHHHHHHHHHHhC---------CCCC
Q 040913          174 RAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-----DCLAWILDDIIRSLM---------PPSR  239 (425)
Q Consensus       174 ~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-----~~~~wv~~~il~~l~---------~~~~  239 (425)
                      ...+.+...+..+. -...+-+.|+.|+||+++|..+.+.--.....     .++-|+     .+-.         .+..
T Consensus        11 ~~~~~l~~~~~~~r-l~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~-----~~g~HPD~~~i~~~p~~   84 (319)
T PRK08769         11 RAYDQTVAALDAGR-LGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLI-----AAGTHPDLQLVSFIPNR   84 (319)
T ss_pred             HHHHHHHHHHHcCC-cceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHH-----hcCCCCCEEEEecCCCc
Confidence            34455565555443 35568899999999999997765421111101     111121     0000         0000


Q ss_pred             CCc--cCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          240 VTV--IIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       240 ~~~--~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ...  ......+++. .+.+.+     .+++-++|+|++.. +...-+.+...+-.-..++.+|++|.+.+
T Consensus        85 ~~~k~~~~I~idqIR-~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~  154 (319)
T PRK08769         85 TGDKLRTEIVIEQVR-EISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPA  154 (319)
T ss_pred             ccccccccccHHHHH-HHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChh
Confidence            000  0011233332 223322     25677999999863 44566666666665555777777766533

>cd00876 Ras Ras family

Probab=93.08  E-value=0.085  Score=44.88  Aligned_cols=21  Identities=24%  Similarity=0.409  Sum_probs=18.8

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|++|+|||||...+.+.
T Consensus         2 i~i~G~~~~GKTsli~~l~~~   22 (160)
T cd00876           2 VVVLGAGGVGKSAITIQFVKG   22 (160)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            689999999999999998764

The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=93.06  E-value=0.075  Score=48.61  Aligned_cols=24  Identities=21%  Similarity=0.158  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||++.+..-
T Consensus        30 G~~~~i~G~nGsGKSTLl~~l~Gl   53 (220)
T cd03293          30 GEFVALVGPSGCGKSTLLRIIAGL   53 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999999998763

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

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

Probab=93.06  E-value=0.081  Score=53.08  Aligned_cols=47  Identities=15%  Similarity=0.029  Sum_probs=35.0

Q ss_pred             CCCcccchhhHHHHHHHHh-------c---CC--C----CcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLI-------E---GP--I----GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~-------~---~~--~----~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..++|.++.++.+...+.       .   ..  .    ..+.|.++|++|+|||+||+.+..
T Consensus        76 ~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~  138 (413)
T TIGR00382        76 DEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLAR  138 (413)
T ss_pred             cceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHH
Confidence            3458899999888865552       1   11  0    135788999999999999999986

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.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=93.04  E-value=0.074  Score=47.06  Aligned_cols=102  Identities=15%  Similarity=0.107  Sum_probs=53.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcccc-c--cccc--hHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVK-F--YFDC--LAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKY  264 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~-~--~F~~--~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~  264 (425)
                      -.+++|+|..|.|||||.+.+..-.... .  .|+.  ..++.+             ...-+.-+...-.+...+..+.-
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q-------------~~~LSgGq~qrv~laral~~~p~   91 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQ-------------YIDLSGGELQRVAIAAALLRNAT   91 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcc-------------cCCCCHHHHHHHHHHHHHhcCCC
Confidence            4589999999999999999988632211 0  1111  001000             00011223334445566667778


Q ss_pred             EEEecccCC--ChhhHHHHHhhCCC--CCCCcEEEEecCChhHH
Q 040913          265 FIALDDVCH--NIEIWDDLEEVLPD--NQNGSRVLITVINPSLL  304 (425)
Q Consensus       265 LlVLDdvw~--~~~~~~~l~~~l~~--~~~gskIivTTR~~~va  304 (425)
                      +++||.--.  +...-..+...+..  ...+..||++|.+....
T Consensus        92 lllLDEPts~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~~~~  135 (177)
T cd03222          92 FYLFDEPSAYLDIEQRLNAARAIRRLSEEGKKTALVVEHDLAVL  135 (177)
T ss_pred             EEEEECCcccCCHHHHHHHHHHHHHHHHcCCCEEEEEECCHHHH
Confidence            999998741  22333333333321  12235677777765543

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=93.03  E-value=0.074  Score=48.35  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||++.+...
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~G~   48 (213)
T cd03235          25 GEFLAIVGPNGAGKSTLLKAILGL   48 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            458999999999999999998763

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>cd00154 Rab Rab family

Probab=93.03  E-value=0.078  Score=44.76  Aligned_cols=21  Identities=19%  Similarity=0.379  Sum_probs=19.0

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.+.
T Consensus         3 i~~~G~~~~GKStl~~~l~~~   23 (159)
T cd00154           3 IVLIGDSGVGKTSLLLRFVDG   23 (159)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999998775

Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di

>smart00072 GuKc Guanylate kinase homologues

Probab=93.02  E-value=0.083  Score=46.96  Aligned_cols=24  Identities=17%  Similarity=0.243  Sum_probs=21.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.|.|+|+.|+|||||+..+.+.
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~   25 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQE   25 (184)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhc
Confidence            467899999999999999999874

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=93.02  E-value=0.078  Score=47.56  Aligned_cols=24  Identities=13%  Similarity=0.108  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|.|||||++.+...
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~   49 (195)
T PRK13541         26 SAITYIKGANGCGKSSLLRMIAGI   49 (195)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998763

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=93.01  E-value=0.076  Score=49.25  Aligned_cols=23  Identities=22%  Similarity=0.211  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|..|+|||||++.+..
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G   49 (241)
T cd03256          27 GEFVALIGPSGAGKSTLLRCLNG   49 (241)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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.

>cd00879 Sar1 Sar1 subfamily

Probab=93.00  E-value=0.13  Score=45.54  Aligned_cols=24  Identities=13%  Similarity=0.065  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|.|+|.+|+|||||...+.++
T Consensus        19 ~~ki~ilG~~~~GKStLi~~l~~~   42 (190)
T cd00879          19 EAKILFLGLDNAGKTTLLHMLKDD   42 (190)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            345699999999999999998764

Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=93.00  E-value=0.25  Score=49.70  Aligned_cols=81  Identities=11%  Similarity=0.241  Sum_probs=45.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC------ccCCC-C-----HHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT------VIIGE-D-----YKLK  251 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~------~~~~~-~-----~~~l  251 (425)
                      -..++|+|..|+|||||.+.+.+.....  ..+.+.+      +.++...+.......      ...+. .     ....
T Consensus       137 Gq~~~I~G~sG~GKTtLl~~I~~~~~~~--~~vi~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~tsd~~~~~r~~a~~~  214 (411)
T TIGR03496       137 GQRMGIFAGSGVGKSTLLGMMARYTEAD--VVVVGLIGERGREVKEFIEDILGEEGLARSVVVAATADESPLMRLRAAFY  214 (411)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCCCCC--EEEEEEEecChHHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHHH
Confidence            4578999999999999999888743221  1111122      455555544332111      00111 1     1112


Q ss_pred             HHHHHHHh--cCCeEEEEecccC
Q 040913          252 KSILRDFL--TNKKYFIALDDVC  272 (425)
Q Consensus       252 ~~~l~~~l--~~kr~LlVLDdvw  272 (425)
                      .-.+.+++  +++++||++||+-
T Consensus       215 a~tiAEyfr~~G~~Vll~~Dslt  237 (411)
T TIGR03496       215 ATAIAEYFRDQGKDVLLLMDSLT  237 (411)
T ss_pred             HHHHHHHHHHCCCCEEEEEeChH
Confidence            23344444  5899999999994

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=92.99  E-value=0.86  Score=44.68  Aligned_cols=44  Identities=18%  Similarity=0.205  Sum_probs=30.5

Q ss_pred             CCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC-hhHH
Q 040913          261 NKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN-PSLL  304 (425)
Q Consensus       261 ~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~-~~va  304 (425)
                      +++-++|+|+... +.+..+.+...+-.-.+++.+|++|.+ ..+.
T Consensus       131 ~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LL  176 (342)
T PRK06964        131 GGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLL  176 (342)
T ss_pred             CCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCc
Confidence            4666888999864 567888888888766667766655555 4443

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=92.99  E-value=0.07  Score=48.43  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=19.8

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +++|+|..|.|||||++.+..
T Consensus        27 ~~~i~G~nGsGKSTLl~~l~G   47 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILAT   47 (211)
T ss_pred             cEEEECCCCCCHHHHHHHHhC
Confidence            899999999999999999885

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=92.98  E-value=0.15  Score=51.61  Aligned_cols=82  Identities=11%  Similarity=0.175  Sum_probs=46.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC------ccCCCC-H-----H
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT------VIIGED-Y-----K  249 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~------~~~~~~-~-----~  249 (425)
                      -.-++|.|.+|+|||||+..+..+... ++=...+++        ..+++.++.......      ...+.. .     .
T Consensus       143 GQr~~If~~~G~GKt~L~~~~~~~~~~-~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~  221 (461)
T TIGR01039       143 GGKIGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVA  221 (461)
T ss_pred             CCEEEeecCCCCChHHHHHHHHHHHHh-cCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHH
Confidence            345899999999999999987653211 111123333        556666664332111      011111 1     1


Q ss_pred             HHHHHHHHHh---cCCeEEEEecccC
Q 040913          250 LKKSILRDFL---TNKKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~l~~~l---~~kr~LlVLDdvw  272 (425)
                      ...-.+.+++   +++++||++||+-
T Consensus       222 ~~a~tiAEyfrd~~G~~VLll~DslT  247 (461)
T TIGR01039       222 LTGLTMAEYFRDEQGQDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEecchh
Confidence            2334556666   4689999999994

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK15453 phosphoribulokinase; Provisional

Probab=92.98  E-value=0.082  Score=50.00  Aligned_cols=24  Identities=21%  Similarity=0.205  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|.|.+|+||||+|+.+.+
T Consensus         4 k~piI~ItG~SGsGKTTva~~l~~   27 (290)
T PRK15453          4 KHPIIAVTGSSGAGTTTVKRAFEK   27 (290)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999997764

>COG4107 PhnK ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=92.97  E-value=0.081  Score=46.06  Aligned_cols=23  Identities=26%  Similarity=0.221  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      --|++|||..|+|||||...+..
T Consensus        32 GeVLgiVGESGSGKtTLL~~is~   54 (258)
T COG4107          32 GEVLGIVGESGSGKTTLLKCISG   54 (258)
T ss_pred             CcEEEEEecCCCcHHhHHHHHhc
Confidence            45899999999999999988765

>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes

Probab=92.97  E-value=0.063  Score=51.01  Aligned_cols=21  Identities=19%  Similarity=0.401  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|..|+|||||++.+..
T Consensus         1 iigI~G~sGsGKSTl~~~L~~   21 (273)
T cd02026           1 IIGVAGDSGCGKSTFLRRLTS   21 (273)
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999875

This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.

>PRK06761 hypothetical protein; Provisional

Probab=92.96  E-value=0.075  Score=50.50  Aligned_cols=23  Identities=22%  Similarity=0.238  Sum_probs=21.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++|.|.|++|+||||+++.+.+.
T Consensus         4 ~lIvI~G~~GsGKTTla~~L~~~   26 (282)
T PRK06761          4 KLIIIEGLPGFGKSTTAKMLNDI   26 (282)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHh
Confidence            57899999999999999999984

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=92.96  E-value=0.079  Score=48.13  Aligned_cols=24  Identities=21%  Similarity=0.270  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||.+.+..-
T Consensus        27 G~~~~i~G~nGsGKSTLl~~l~G~   50 (214)
T cd03292          27 GEFVFLVGPSGAGKSTLLKLIYKE   50 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999998763

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd04124 RabL2 RabL2 subfamily

Probab=92.95  E-value=0.081  Score=45.65  Aligned_cols=21  Identities=14%  Similarity=0.264  Sum_probs=18.1

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||++.+.+.
T Consensus         3 i~vvG~~~vGKTsli~~~~~~   23 (161)
T cd04124           3 IILLGDSAVGKSKLVERFLMD   23 (161)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999887653

RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-b

>PRK13768 GTPase; Provisional

Probab=92.94  E-value=0.081  Score=49.68  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=18.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ..++.|.|.+|+||||++..+.
T Consensus         2 ~~~i~v~G~~G~GKTt~~~~~~   23 (253)
T PRK13768          2 MYIVFFLGTAGSGKTTLTKALS   23 (253)
T ss_pred             cEEEEEECCCCccHHHHHHHHH
Confidence            3578899999999999886654

>PRK06820 type III secretion system ATPase; Validated

Probab=92.94  E-value=0.23  Score=50.26  Aligned_cols=24  Identities=13%  Similarity=0.221  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|+|..|+|||||++.+...
T Consensus       163 Gqri~I~G~sG~GKStLl~~I~~~  186 (440)
T PRK06820        163 GQRIGIFAAAGVGKSTLLGMLCAD  186 (440)
T ss_pred             CCEEEEECCCCCChHHHHHHHhcc
Confidence            347899999999999999998874

>cd01864 Rab19 Rab19 subfamily

Probab=92.92  E-value=0.08  Score=45.70  Aligned_cols=23  Identities=13%  Similarity=0.143  Sum_probs=19.5

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-|.|+|.+|+|||||+..+..+
T Consensus         4 ~kv~vvG~~~~GKTsli~~l~~~   26 (165)
T cd01864           4 FKIILIGDSNVGKTCVVQRFKSG   26 (165)
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            45789999999999999987653

Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=92.91  E-value=0.27  Score=49.62  Aligned_cols=24  Identities=13%  Similarity=0.181  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|.|..|+|||||.+.+.+.
T Consensus       145 Gq~~~I~G~sG~GKStLl~~I~~~  168 (422)
T TIGR02546       145 GQRIGIFAGAGVGKSTLLGMIARG  168 (422)
T ss_pred             CCEEEEECCCCCChHHHHHHHhCC
Confidence            456799999999999999998874

>PF00071 Ras: Ras family; InterPro: IPR001806 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases

Probab=92.91  E-value=0.087  Score=45.19  Aligned_cols=21  Identities=24%  Similarity=0.434  Sum_probs=18.9

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.+.
T Consensus         2 i~vvG~~~vGKtsl~~~~~~~   22 (162)
T PF00071_consen    2 IVVVGDSGVGKTSLINRLING   22 (162)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhh
Confidence            679999999999999988774

This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction; PDB: 1M7B_A 2V55_B 3EG5_C 3LAW_A 1YHN_A 1T91_B 1HE8_B 3SEA_B 3T5G_A 1XTS_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	425
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	4e-29
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-25
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-08
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	3e-20
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	8e-04

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  118 bits (298), Expect = 4e-29
 Identities = 62/431 (14%), Positives = 129/431 (29%), Gaps = 88/431 (20%)

Query: 66  LRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMA---- 121
            R+ + +D+K   I+  +          EE +        +     +      N +    
Sbjct: 12  HREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSF 71

Query: 122 LLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISE-------FER 174
               LH    D+   +    P  +     +    +            + +        ++
Sbjct: 72  YNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVVFVTRKK 131

Query: 175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVK--FYFDCLAWI------ 226
                   L +       V I   +G  K+  AA+   ++ +    +   + W+      
Sbjct: 132 LVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQD 191

Query: 227 -------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNK--KYFIALDDVCHNIEI 277
                  L ++   L      +  +  + +  K  LR  +  K  +  + LDDV      
Sbjct: 192 KSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDV------ 245

Query: 278 WDDLEEVLPDNQNGSRVLIT----------------VINPSLLT---SFELLN------- 311
           WD    VL    +  ++L+T                V   S L      E+L+       
Sbjct: 246 WD--SWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKK 303

Query: 312 ------GEKI--RCDY----VLVEGPLIRIKHSAWQFFVLHYGSAALGNYMDEKM----- 354
                    I   C      V + G L+R   + W++++    +                
Sbjct: 304 ADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEA 363

Query: 355 VLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELY 414
           +   +S   SV  L   +K     L + +  +++ ++ LC LW  E        E  E  
Sbjct: 364 LDEAMS--ISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-------TEEVEDI 414

Query: 415 LKELIHRGFIQ 425
           L+E +++  + 
Sbjct: 415 LQEFVNKSLLF 425

>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 =  108 bits (270), Expect = 2e-25
 Identities = 71/437 (16%), Positives = 135/437 (30%), Gaps = 112/437 (25%)

Query: 62  LFQLLRKKINEDVKRPDILKIL------EDVNQFVHESEEVIDTFFI-NIMQQQNSEE-- 112
           +  +      ++    D+  +       E+++  +   + V  T  +   +  +  E   
Sbjct: 21  ILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQ 80

Query: 113 ---ESESSTNMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDI 169
              E     N   L+   S I   +   +Q  P        EQRD L    ++ Q     
Sbjct: 81  KFVEEVLRINYKFLM---SPI---KTEQRQ--PSMMTRMYIEQRDRL---YNDNQV---F 126

Query: 170 SEFERAREEWFDLLIEGPIGLSV---VAILDSSGFDKTAFAADTYNNNHVKFYFDC-LAW 225
           +++  +R + +  L +  + L     V I    G  KT  A D   +  V+   D  + W
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 226 I--------------LDDIIRSLMPPSRVTVIIGEDYKLK----KSILRDFLTNKKY--- 264
           +              L  ++  + P          + KL+    ++ LR  L +K Y   
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246

Query: 265 FIALDDVCHNIEIWDDLEEVLPDNQNGSRVLIT-----VIN---------------PSLL 304
            + L +V  N + W+             ++L+T     V +                  L
Sbjct: 247 LLVLLNVQ-NAKAWNAFN-------LSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298

Query: 305 TSFELLN--GEKIRCDY------VLVEGPL--------IRIKHSAWQFFVLHYGSAALGN 348
           T  E+ +   + + C        VL   P         IR   + W  +  H     L  
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW-KHVNCDKLTT 357

Query: 349 YMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSE 408
            +  +  L VL         P   +     L VF P   I +  L  +W          +
Sbjct: 358 II--ESSLNVLE--------PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV------IK 401

Query: 409 ETAELYLKELIHRGFIQ 425
               + + +L     ++
Sbjct: 402 SDVMVVVNKLHKYSLVE 418

>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 = 54.5 bits (130), Expect = 5e-08
 Identities = 45/289 (15%), Positives = 86/289 (29%), Gaps = 86/289 (29%)

Query: 34  PLLQNLLAES--------------------EIIASTLLANYEADM-----ALLLFQLLRK 68
           P   +++AES                     II S+L     A+       L +F     
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFP---- 382

Query: 69  KINEDVKRP-DILKIL--EDVNQFVHESEEVIDTFFINIMQQQNSEEES--------ESS 117
                   P  +L ++  + +     +   V++      + ++  +E +        E  
Sbjct: 383 ---PSAHIPTILLSLIWFDVIKS---DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK 436

Query: 118 TNMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELI------HLSSEGQPRLDISE 171
             +     LH  I+D  N  +     D         D+        HL +   P      
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL---DQYFYSHIGHHLKNIEHPE----R 489

Query: 172 FERAREEWFDL-LIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY----------F 220
               R  + D   +E  I        DS+ ++ +    +T     +KFY          +
Sbjct: 490 MTLFRMVFLDFRFLEQKI------RHDSTAWNASGSILNTLQQ--LKFYKPYICDNDPKY 541

Query: 221 DCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALD 269
           + L   ++ I+  L        +I   Y     +LR  L  +   I  +
Sbjct: 542 ERL---VNAILDFLPKIE--ENLICSKY---TDLLRIALMAEDEAIFEE 582

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score = 92.0 bits (228), Expect = 3e-20
 Identities = 63/443 (14%), Positives = 116/443 (26%), Gaps = 96/443 (21%)

Query: 67  RKKINEDVKRPDILKILEDVNQFVHESEEVIDTF---------FINIMQQQNSEEESESS 117
             ++  D +  D L  LE  N F  +  E+I            F+ I ++Q SE      
Sbjct: 14  HTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASELGPLID 73

Query: 118 T----NMALLVGLHSKIIDIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRLDISEFE 173
                N + L       ID       L           ++     L     P+       
Sbjct: 74  FFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQMTC--- 130

Query: 174 RAREEWFDLLIE-----GPIGLSVVAILDSSGFDKTAFAADTYNNN--HVKFYFDCLAWI 226
             RE   D +I+       +    + +   +G  K+  A+   + +   +   +D + W+
Sbjct: 131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWL 190

Query: 227 ---------LDDIIRSLM--------PPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALD 269
                      D+   ++          +  +V       LK+ I    +         D
Sbjct: 191 KDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFD 250

Query: 270 DVCHNIEIWDDLEEVLPDNQNGSRVLIT---------------VINPSLLTSFELLN--- 311
           DV        + E +    +   R L+T                I  + L   E  +   
Sbjct: 251 DV------VQE-ETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLE 303

Query: 312 ---------------GEKI--RCDY----VLVEGPLIRIK-HSAWQFFVLHYGSAALGN- 348
                            K           +++       K             S  L   
Sbjct: 304 AYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLESRGLVGV 363

Query: 349 ----YMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIP 404
                   K +   L R   V  L    +    +  V  PG++I  +    +   +    
Sbjct: 364 ECITPYSYKSLAMALQR--CVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDICSN 421

Query: 405 YN--SEETAELYLKELIHRGFIQ 425
                ++     LK L  RG + 
Sbjct: 422 EEEQLDDEVADRLKRLSKRGALL 444

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 41.0 bits (96), Expect = 8e-04
 Identities = 62/435 (14%), Positives = 134/435 (30%), Gaps = 98/435 (22%)

Query: 66  LRKKINEDVKRPDILKILEDVNQFVHESEEVIDTFFINIMQQQNSEEESESSTNMALLVG 125
            R+ + +D+K   I+  +  ++  V    E        +  Q    + + +   M L   
Sbjct: 12  HREALEKDIKTSYIMDHM--ISNGVLSVIEEE-----KVKSQATQYQRAAALIKMILNKD 64

Query: 126 LHSKII--------DIRNRMQQLPPGDNGFDINEQRDELIHLSSEGQPRL------DISE 171
             + I           ++    L  G      +  +D    ++S  +  L          
Sbjct: 65  NCAYISFYNALLHEGYKDLAALLQSGLPLVSSSSGKDTDGGITSFVRTVLCEGGVPQRPV 124

Query: 172 FERAREEWFDLLIEGPIGLS----VVAILDSSGFDKTAFAADT-YNNNHVKFYF-DCLAW 225
               R++    + +    L+     V I   +G  K+  AA+   +++ ++  F   + W
Sbjct: 125 IFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHW 184

Query: 226 I-------------LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKY--FIALDD 270
           +             L ++   L      +  +  + +  K  LR  +  K     + LDD
Sbjct: 185 VSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDD 244

Query: 271 VCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS-------------FELLNGEKIRC 317
           V            VL    N  ++L+T  + S+  S                  G +I  
Sbjct: 245 VW--------DPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILS 296

Query: 318 DYVLVEGP-------------------------LIRIKHSAWQFFVLHYGSAALGNYMDE 352
            +V ++                           L+R   + W +++    +         
Sbjct: 297 LFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYYLRQLQNKQFKRIRKS 356

Query: 353 -KMVLAVLSRTCSV-FE-LPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEE 409
                  L    S+  E L   +K     L + +  +++ ++ LC LW           E
Sbjct: 357 SSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDL-------ETE 409

Query: 410 TAELYLKELIHRGFI 424
             E  L+E +++  +
Sbjct: 410 EVEDILQEFVNKSLL 424

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	425
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.98
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.96
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.45
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.9
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.72
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.7
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.66
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.66
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.65
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.62
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.59
2fna_A	357	Conserved hypothetical protein; structural genomic	98.51
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.34
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.24
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.17
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.0
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.97
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.93
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.85
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.8
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.79
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.75
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.72
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.72
3co5_A	143	Putative two-component system transcriptional RES	97.66
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.65
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.65
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.65
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.62
3pvs_A	447	Replication-associated recombination protein A; ma	97.61
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.54
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.53
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	97.5
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.5
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.49
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.49
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.47
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.47
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.45
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.4
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.4
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.38
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.34
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.33
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.27
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.27
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.19
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.19
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.13
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.05
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.02
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.99
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.99
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	96.91
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.76
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	96.74
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	96.71
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.66
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.58
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.56
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	96.49
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	96.49
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.46
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.43
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.37
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.27
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.26
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.26
2qgz_A	308	Helicase loader, putative primosome component; str	96.25
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	96.23
3bos_A	242	Putative DNA replication factor; P-loop containing	96.22
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	96.21
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	96.2
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	96.13
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.07
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	96.06
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	96.02
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.99
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.94
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.93
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.92
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.86
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.8
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.72
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.7
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.67
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	95.65
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.63
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.61
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	95.58
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.56
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	95.55
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	95.51
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.48
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.48
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.42
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	95.4
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	95.4
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.32
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.3
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.29
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.28
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	95.26
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.24
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.23
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.22
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.19
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	95.16
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.15
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.14
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	95.11
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.09
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.06
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.06
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.04
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.04
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.03
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.02
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.01
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.01
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.01
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.01
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.99
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.99
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.97
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.97
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	94.96
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	94.95
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.91
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.9
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.89
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	94.87
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.87
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.86
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.85
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	94.84
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.84
1via_A	175	Shikimate kinase; structural genomics, transferase	94.81
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.81
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	94.8
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	94.72
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.71
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.7
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	94.7
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.68
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.68
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.66
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	94.66
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	94.65
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.64
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	94.63
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.63
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	94.63
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.62
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	94.62
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.57
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	94.51
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	94.48
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.44
2vli_A	183	Antibiotic resistance protein; transferase, tunica	94.42
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.41
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	94.4
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	94.4
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.36
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.33
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.33
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	94.32
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	94.31
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.3
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	94.3
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	94.26
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	94.25
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.25
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	94.24
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	94.21
3ice_A	422	Transcription termination factor RHO; transcriptio	94.2
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.18
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.18
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.16
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.14
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.13
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.13
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.12
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	94.11
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.11
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.1
1xp8_A	366	RECA protein, recombinase A; recombination, radior	94.09
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	94.06
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	94.05
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.03
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.02
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	94.0
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	93.97
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.97
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	93.92
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	93.9
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	93.86
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.84
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	93.83
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.81
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	93.79
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.79
3fwy_A	314	Light-independent protochlorophyllide reductase I	93.78
1b0u_A	262	Histidine permease; ABC transporter, transport pro	93.77
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.77
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	93.73
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	93.68
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.68
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	93.67
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	93.66
1g6h_A	257	High-affinity branched-chain amino acid transport	93.65
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	93.63
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	93.62
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.61
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	93.55
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	93.55
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.54
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.52
1sgw_A	214	Putative ABC transporter; structural genomics, P p	93.51
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	93.49
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.49
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.43
2og2_A	359	Putative signal recognition particle receptor; nuc	93.42
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	93.41
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	93.39
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	93.39
2ghi_A	260	Transport protein; multidrug resistance protein, M	93.39
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	93.38
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	93.38
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.37
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.37
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.34
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.28
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.28
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	93.28
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.27
2cvh_A	220	DNA repair and recombination protein RADB; filamen	93.25
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	93.24
2xxa_A	433	Signal recognition particle protein; protein trans	93.24
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.19
2eyu_A	261	Twitching motility protein PILT; pilus retraction	93.18
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.18
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	93.13
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	93.13
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	93.13
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	93.11
3io5_A	333	Recombination and repair protein; storage dimer, i	93.11
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	93.1
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.08
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	93.04
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	93.03
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	93.02
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	92.99
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	92.99
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	92.97
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	92.94
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	92.92
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	92.91
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	92.89
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	92.86
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	92.85
1tue_A	212	Replication protein E1; helicase, replication, E1E	92.85
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	92.85
1u94_A	356	RECA protein, recombinase A; homologous recombinat	92.81
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	92.8
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	92.77
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.77
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	92.75
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	92.75
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	92.73
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	92.69
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	92.68
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	92.67
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	92.64
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	92.63
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.62
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	92.62
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	92.61
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	92.55
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	92.54
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	92.53
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	92.49
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	92.48
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	92.44
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.4
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.4
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.4
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	92.39
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	92.35
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	92.33
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	92.33
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	92.28
3kta_A	182	Chromosome segregation protein SMC; structural mai	92.27
2ged_A	193	SR-beta, signal recognition particle receptor beta	92.25
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.24
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	92.23
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.21
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	92.19
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	92.19
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	92.15
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	92.15
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	92.12
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	92.12
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	92.12
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	92.09
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	92.06
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	92.06
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.05
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	92.01
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	91.97
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	91.95
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	91.94
1h65_A	270	Chloroplast outer envelope protein OEP34; GTPase,	91.93
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	91.93
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	91.89
2r6a_A	454	DNAB helicase, replicative helicase; replication,	91.88
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	91.85
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	91.85
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	91.84
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	91.83
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	91.81
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	91.77
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	91.76
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	91.72
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	91.68
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	91.65
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	91.63
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	91.63
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	91.62
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	91.61
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	91.59
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	91.58
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	91.58
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	91.57
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	91.56
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	91.55
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	91.53
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	91.52
1nrj_B	218	SR-beta, signal recognition particle receptor beta	91.51
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	91.51
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	91.51
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	91.5
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	91.49
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	91.49
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	91.48
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	91.47
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.47
3end_A	307	Light-independent protochlorophyllide reductase ir	91.47
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	91.45
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	91.43
1p9r_A	418	General secretion pathway protein E; bacterial typ	91.42
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	91.41
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	91.4
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	91.3
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	91.27
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	91.25
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	91.24
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	91.2
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.19
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.15
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	91.14
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	91.14
3llu_A	196	RAS-related GTP-binding protein C; structural geno	91.13
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	91.13
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	91.13
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	91.13
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	91.09
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	91.08
2ewv_A	372	Twitching motility protein PILT; pilus retraction	91.07
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	91.06
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	91.04
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	91.02
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	91.02
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	90.97
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	90.96
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	90.95
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	90.94
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	90.93
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	90.92
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	90.85
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	90.85
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	90.83
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	90.82
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	90.8
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	90.78
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	90.77
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	90.74
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	90.74
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	90.73
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	90.72
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	90.71
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	90.7
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	90.69
2fh5_B	214	SR-beta, signal recognition particle receptor beta	90.66
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	90.65
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	90.63
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	90.6
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	90.58
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	90.57
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	90.56
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	90.56
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	90.55
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	90.54
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	90.53
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	90.52
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	90.52
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	90.51
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	90.48
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	90.47
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	90.46
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	90.46
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	90.4
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	90.4
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	90.38
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	90.37
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	90.37
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	90.35
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	90.34
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	90.29
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	90.22
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	90.18
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	90.14
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	90.12
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	90.09
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	90.08
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	90.08
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	90.03
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	90.03
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	89.96
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	89.92
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	89.9
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	89.89
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	89.88
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	89.88
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	89.79
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	89.78
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	89.69
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	89.69
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	89.69
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	89.67
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	89.66
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	89.62
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	89.61
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	89.56
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	89.55
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	89.54
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	89.4
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	89.39
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	89.32
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	89.31
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	89.28
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	89.24
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	89.13
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	89.09
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	88.99
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	88.98
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	88.96
1mky_A	439	Probable GTP-binding protein ENGA; GTPase, DER, KH	88.93
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	88.84
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	88.84
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	88.76
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	88.75
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	88.74
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	88.72
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	88.69
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	88.69
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	88.68
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	88.66
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	88.57
3t5d_A	274	Septin-7; GTP-binding protein, cytoskeleton, signa	88.55
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	88.48
1jwy_B	315	Dynamin A GTPase domain; dynamin, GTPase, GDP, myo	88.47
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	88.35
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	88.34
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	88.25
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	88.2
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	88.15
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	88.11
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	88.11
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	88.1
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	88.1
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	88.07
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	87.99
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	87.92
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	87.81
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	87.76
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	87.73
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	87.73
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	87.71
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	87.58
2qag_A	361	Septin-2, protein NEDD5; cell cycle, cell division	87.55
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	87.5
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	87.45
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	87.34
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	87.31
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	87.27
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	87.23
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	87.21

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=100.00  E-value=1.6e-39  Score=337.37  Aligned_cols=236  Identities=17%  Similarity=0.217  Sum_probs=185.8

Q ss_pred             ccchhhHHHHHHHHhcC-CCCcEEEEEEecCCCchHHHHHHhhc--CccccccccchHHH-------------HHHHHHH
Q 040913          170 SEFERAREEWFDLLIEG-PIGLSVVAILDSSGFDKTAFAADTYN--NNHVKFYFDCLAWI-------------LDDIIRS  233 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~--~~~~~~~F~~~~wv-------------~~~il~~  233 (425)
                      |||+.++++|.++|..+ +...++|+|+||||+||||||+++|+  +.+++.+|++++||             +..|+.+
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~  210 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLM  210 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHH
Confidence            69999999999999865 44689999999999999999999998  77999999999998             5677888


Q ss_pred             hCCCCC---CCccCCCCHHHHHHHHHHHhcCC-eEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH---
Q 040913          234 LMPPSR---VTVIIGEDYKLKKSILRDFLTNK-KYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS---  306 (425)
Q Consensus       234 l~~~~~---~~~~~~~~~~~l~~~l~~~l~~k-r~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~---  306 (425)
                      +.....   .......+...+...+++.|++| |||||||||| +.+.+ .+..     .+||+||||||+..++..   
T Consensus       211 l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~-~~~~~-~~~~-----~~gs~ilvTTR~~~v~~~~~~  283 (549)
T 2a5y_B          211 LKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV-QEETI-RWAQ-----ELRLRCLVTTRDVEISNAASQ  283 (549)
T ss_dssp             HTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEEC-CHHHH-HHHH-----HTTCEEEEEESBGGGGGGCCS
T ss_pred             HhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCC-Cchhh-cccc-----cCCCEEEEEcCCHHHHHHcCC
Confidence            876532   11223446678899999999996 9999999999 77654 2211     169999999999988764   


Q ss_pred             ---------------hcCcC---------------CCCc--ccc-----chhhhccccCCChHHHHHHHHHhchhccCCC
Q 040913          307 ---------------FELLN---------------GEKI--RCD-----YVLVEGPLIRIKHSAWQFFVLHYGSAALGNY  349 (425)
Q Consensus       307 ---------------~~Lf~---------------~~~I--kC~-----i~~~g~~L~~~~~~~w~~~~~~~~~~~~~~~  349 (425)
                                     |+||.               +++|  +|+     ++++|+.|+.+. .+|...+....+...  .
T Consensus       284 ~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~GlPLAl~~~g~~l~~~~-w~~~~~l~~~l~~~~--~  360 (549)
T 2a5y_B          284 TCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKT-FEKMAQLNNKLESRG--L  360 (549)
T ss_dssp             CEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSS-HHHHHHHHHHHHHHC--S
T ss_pred             CCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCCChHHHHHHHHHhccch-HHHHHHhHHHhhccc--H
Confidence                           77773               2344  787     999999998773 233333333322221  1


Q ss_pred             CchHHHHHHhchhhcccCCChhhHHHHh-----------hhhccCCCCcccHHHHHHHHHHc--CCCC-----CCHHHHH
Q 040913          350 MDEKMVLAVLSRTCSVFELPLHLKVCCI-----------YLCVFRPGIEISSRQLCQLWIAE--GFIP-----YNSEETA  411 (425)
Q Consensus       350 ~~~~~~~~~l~~~~sy~~Lp~~lk~cfl-----------y~sifP~~~~i~~~~Li~~Wiae--g~i~-----~~~e~~a  411 (425)
                      .   .+.+++.  +||++||+++|.||+           |||+||+++.|+    +++|+|+  ||+.     .+.++++
T Consensus       361 ~---~i~~~l~--~Sy~~L~~~lk~~f~~Ls~~er~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~~~~~~  431 (549)
T 2a5y_B          361 V---GVECITP--YSYKSLAMALQRCVEVLSDEDRSALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQLDDEVA  431 (549)
T ss_dssp             S---TTCCCSS--SSSSSHHHHHHHHHHTSCHHHHHHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCCTHHHH
T ss_pred             H---HHHHHHh--cccccccHHHHHHHhccchhhhhHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCCHHHHH
Confidence            1   6778899  999999999999999           999999999999    8999999  9997     3478888


Q ss_pred             HHHHHHHHHCcCCC
Q 040913          412 ELYLKELIHRGFIQ  425 (425)
Q Consensus       412 ~~~~~eLv~r~llq  425 (425)
                      + ||++|+++||||
T Consensus       432 ~-~l~~L~~rsLl~  444 (549)
T 2a5y_B          432 D-RLKRLSKRGALL  444 (549)
T ss_dssp             H-HHHHTTTBSSCS
T ss_pred             H-HHHHHHHcCCee
Confidence            8 999999999997

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=100.00  E-value=1.1e-33  Score=318.92  Aligned_cols=246  Identities=20%  Similarity=0.312  Sum_probs=196.8

Q ss_pred             CCCCCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccc-ccccc-chHHH------------
Q 040913          161 SEGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHV-KFYFD-CLAWI------------  226 (425)
Q Consensus       161 ~~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F~-~~~wv------------  226 (425)
                      ..+.....||||+.++++|.++|...+...++|+|+||||+||||||+++|++.++ ..+|. .++||            
T Consensus       118 ~~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~  197 (1249)
T 3sfz_A          118 GVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLM  197 (1249)
T ss_dssp             TCCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHH
T ss_pred             CCCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHH
Confidence            34455677999999999999999877667899999999999999999999997544 55665 45577            


Q ss_pred             -HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCC--eEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhH
Q 040913          227 -LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNK--KYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSL  303 (425)
Q Consensus       227 -~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~k--r~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~v  303 (425)
                       +..++..+............+.+.+...++..+.+|  |+|||||||| +...|..+       .+||+||||||++.+
T Consensus       198 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~-~~~~~~~~-------~~~~~ilvTtR~~~~  269 (1249)
T 3sfz_A          198 KLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVW-DPWVLKAF-------DNQCQILLTTRDKSV  269 (1249)
T ss_dssp             HHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCC-CHHHHTTT-------CSSCEEEEEESSTTT
T ss_pred             HHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCC-CHHHHHhh-------cCCCEEEEEcCCHHH
Confidence             556677776654322334567889999999999887  9999999999 87766543       568999999999988


Q ss_pred             HHH-------------------hcCcC-------------CCCc--ccc-----chhhhccccCCChHHHHHHHHHhchh
Q 040913          304 LTS-------------------FELLN-------------GEKI--RCD-----YVLVEGPLIRIKHSAWQFFVLHYGSA  344 (425)
Q Consensus       304 a~~-------------------~~Lf~-------------~~~I--kC~-----i~~~g~~L~~~~~~~w~~~~~~~~~~  344 (425)
                      +..                   |+||.             +++|  +|+     ++.+|+.|+.++ ..|...++.+...
T Consensus       270 ~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~glPLal~~~~~~l~~~~-~~~~~~l~~l~~~  348 (1249)
T 3sfz_A          270 TDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFP-NRWAYYLRQLQNK  348 (1249)
T ss_dssp             TTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTCHHHHHHHHHHHHHSS-SCHHHHHHHHHSC
T ss_pred             HHhhcCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCCHHHHHHHHHHhhcCh-hHHHHHHHHHhhh
Confidence            742                   55553             3345  787     999999998876 4788888777443


Q ss_pred             ccC------CCCchHHHHHHhchhhcccCCChhhHHHHhhhhccCCCCcccHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Q 040913          345 ALG------NYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKEL  418 (425)
Q Consensus       345 ~~~------~~~~~~~~~~~l~~~~sy~~Lp~~lk~cfly~sifP~~~~i~~~~Li~~Wiaeg~i~~~~e~~a~~~~~eL  418 (425)
                      ...      ....+ .+..+|.  +||+.||+++|.||+|||+||+++.|+++.++.+|.++       ++.++.+|++|
T Consensus       349 ~~~~~~~~~~~~~~-~~~~~l~--~s~~~L~~~~~~~~~~l~~f~~~~~i~~~~~~~~~~~~-------~~~~~~~l~~L  418 (1249)
T 3sfz_A          349 QFKRIRKSSSYDYE-ALDEAMS--ISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE-------TEEVEDILQEF  418 (1249)
T ss_dssp             CCCCSSCTTCTTHH-HHHHHHH--HHHHTSCTTTHHHHHHGGGSCTTCCEEHHHHHHHHTCC-------HHHHHHHHHHH
T ss_pred             hhhhcccccccchH-HHHHHHH--HHHHhCCHHHHHHHHHhCccCCCCeeCHHHHHHHhCCC-------HHHHHHHHHHH
Confidence            211      11223 7999999  99999999999999999999999999999999999765       46789999999


Q ss_pred             HHCcCCC
Q 040913          419 IHRGFIQ  425 (425)
Q Consensus       419 v~r~llq  425 (425)
                      +++||||
T Consensus       419 ~~~sl~~  425 (1249)
T 3sfz_A          419 VNKSLLF  425 (1249)
T ss_dssp             HHTTSCE
T ss_pred             HhccceE
Confidence            9999985

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.98  E-value=8e-33  Score=294.84  Aligned_cols=228  Identities=17%  Similarity=0.195  Sum_probs=178.7

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccc-hHHH-----------HHHHHH---
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDC-LAWI-----------LDDIIR---  232 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~-~~wv-----------~~~il~---  232 (425)
                      ..|||+.++++|.++|...+ ..++|+|+||||+||||||+++|++.+++.+|+. ++|+           +..|+.   
T Consensus       129 ~~VGRe~eLeeL~elL~~~d-~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~  207 (1221)
T 1vt4_I          129 YNVSRLQPYLKLRQALLELR-PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLY  207 (1221)
T ss_dssp             SCCCCHHHHHHHHHHHHHCC-SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHhccC-CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHh
Confidence            35999999999999998643 3789999999999999999999998888999987 7787           233333   


Q ss_pred             HhCCCCCCC-c---cCCCCHHHHHHHHHHHh---cCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          233 SLMPPSRVT-V---IIGEDYKLKKSILRDFL---TNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       233 ~l~~~~~~~-~---~~~~~~~~l~~~l~~~l---~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      .+....... .   ....+.+.+...++..|   .+||+|||||||| +.+.|+.+.       +||+||||||++.++.
T Consensus       208 ~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVw-d~eqLe~f~-------pGSRILVTTRd~~Va~  279 (1221)
T 1vt4_I          208 QIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ-NAKAWNAFN-------LSCKILLTTRFKQVTD  279 (1221)
T ss_dssp             HHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCC-CHHHHHHHH-------SSCCEEEECSCSHHHH
T ss_pred             hcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcC-hHHHHHhhC-------CCeEEEEeccChHHHH
Confidence            332211100 0   01123455677777766   6899999999999 888887652       5999999999999873


Q ss_pred             H-----------------------hcCcC---C---CCc---ccc-----chhhhccccCCChH--HHHHHHHHhchhcc
Q 040913          306 S-----------------------FELLN---G---EKI---RCD-----YVLVEGPLIRIKHS--AWQFFVLHYGSAAL  346 (425)
Q Consensus       306 ~-----------------------~~Lf~---~---~~I---kC~-----i~~~g~~L~~~~~~--~w~~~~~~~~~~~~  346 (425)
                      .                       |+||.   +   .++   -|+     ++++|+.|+.++..  +|...         
T Consensus       280 ~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~~~eeL~~eICgGLPLALkLaGs~Lr~k~~s~eeW~~~---------  350 (1221)
T 1vt4_I          280 FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV---------  350 (1221)
T ss_dssp             HHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCCCTTTHHHHHCCCCHHHHHHHHHHHHHSCSSHHHHHHC---------
T ss_pred             hcCCCeEEEecCccccCCcCHHHHHHHHHHHcCCCHHHHHHHHhCCCHHHHHHHHHHHhCCCCCHHHHhcC---------
Confidence            1                       55553   1   222   476     89999999988533  88753         


Q ss_pred             CCCCchHHHHHHhchhhcccCCChhh-HHHHhhhhccCCCCcccHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCcCCC
Q 040913          347 GNYMDEKMVLAVLSRTCSVFELPLHL-KVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHRGFIQ  425 (425)
Q Consensus       347 ~~~~~~~~~~~~l~~~~sy~~Lp~~l-k~cfly~sifP~~~~i~~~~Li~~Wiaeg~i~~~~e~~a~~~~~eLv~r~llq  425 (425)
                       ..  . .+..+|.  +||+.||++. |.||+|||+||+++.|+++.++.+|+++|      ++.++.+|++|+++||||
T Consensus       351 -~~--~-~I~aaLe--lSYd~Lp~eelK~cFL~LAIFPed~~I~~elLa~LW~aeG------eedAe~~L~eLvdRSLLq  418 (1221)
T 1vt4_I          351 -NC--D-KLTTIIE--SSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVI------KSDVMVVVNKLHKYSLVE  418 (1221)
T ss_dssp             -SC--H-HHHHHHH--HHHHHSCTTHHHHHHHHTTSSCTTSCEEHHHHHHHHCSSC------SHHHHHHHHHHHTSSSSS
T ss_pred             -Ch--h-HHHHHHH--HHHHhCCHHHHHHHHHHHhCCCCCCCCCHHHHHHHhcCCC------HHHHHHHHHHHHhhCCEE
Confidence             11  2 8999999  9999999999 99999999999999999999999999987      245899999999999986

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.96  E-value=1.9e-29  Score=264.13  Aligned_cols=243  Identities=19%  Similarity=0.315  Sum_probs=185.7

Q ss_pred             CCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccc-ccccc-chHHH-------------HH
Q 040913          164 QPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHV-KFYFD-CLAWI-------------LD  228 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-~~~F~-~~~wv-------------~~  228 (425)
                      ...+.+|||+.+.++|.++|.......++|+|+||||+||||||.+++++.++ ..+|+ .++|+             +.
T Consensus       121 ~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~~~~~~~~~l~  200 (591)
T 1z6t_A          121 QRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQ  200 (591)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESCCHHHHHHHHH
T ss_pred             CCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCCchHHHHHHHH
Confidence            34567999999999999999865556899999999999999999999997666 78894 67887             33


Q ss_pred             HHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcC--CeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH
Q 040913          229 DIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTN--KKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       229 ~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~--kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~  306 (425)
                      .+...+............+.+.+...+...+.+  +++|||||||| +...+.    .+   ++|++||||||+..++..
T Consensus       201 ~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~-~~~~l~----~l---~~~~~ilvTsR~~~~~~~  272 (591)
T 1z6t_A          201 NLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVW-DSWVLK----AF---DSQCQILLTTRDKSVTDS  272 (591)
T ss_dssp             HHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEEC-CHHHHH----TT---CSSCEEEEEESCGGGGTT
T ss_pred             HHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCC-CHHHHH----Hh---cCCCeEEEECCCcHHHHh
Confidence            334444421111122345677888888888876  78999999999 765443    23   458999999999987653


Q ss_pred             -------------------hcCcC-------------CCCc--ccc-----chhhhccccCCChHHHHHHHHHhchhccC
Q 040913          307 -------------------FELLN-------------GEKI--RCD-----YVLVEGPLIRIKHSAWQFFVLHYGSAALG  347 (425)
Q Consensus       307 -------------------~~Lf~-------------~~~I--kC~-----i~~~g~~L~~~~~~~w~~~~~~~~~~~~~  347 (425)
                                         ++||.             +++|  +|+     +..+|+.|+.++. .|...++.+......
T Consensus       273 ~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G~PLal~~~a~~l~~~~~-~w~~~l~~l~~~~~~  351 (591)
T 1z6t_A          273 VMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPN-RWEYYLKQLQNKQFK  351 (591)
T ss_dssp             CCSCEEEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTTCHHHHHHHHHHHHHSTT-CHHHHHHHHHSCCCC
T ss_pred             cCCCceEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCCCcHHHHHHHHHHhcCch-hHHHHHHHHHHhHHH
Confidence                               44442             1233  676     8899999987643 788888776533211


Q ss_pred             ------CCCchHHHHHHhchhhcccCCChhhHHHHhhhhccCCCCcccHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHC
Q 040913          348 ------NYMDEKMVLAVLSRTCSVFELPLHLKVCCIYLCVFRPGIEISSRQLCQLWIAEGFIPYNSEETAELYLKELIHR  421 (425)
Q Consensus       348 ------~~~~~~~~~~~l~~~~sy~~Lp~~lk~cfly~sifP~~~~i~~~~Li~~Wiaeg~i~~~~e~~a~~~~~eLv~r  421 (425)
                            ..... .+..++.  .||+.||++.|.||++||+||+|+.|+.+.++.+|.++       .+.++.++++|+++
T Consensus       352 ~~~~~~~~~~~-~l~~~l~--~s~~~L~~~~~~~l~~la~f~~~~~i~~~~l~~l~~~~-------~~~~~~~l~~L~~~  421 (591)
T 1z6t_A          352 RIRKSSSYDYE-ALDEAMS--ISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDME-------TEEVEDILQEFVNK  421 (591)
T ss_dssp             CSSCCCSSCCH-HHHHHHH--HHHHTSCTTTHHHHHHGGGCCTTCCEEHHHHHHHHTCC-------HHHHHHHHHHHHHT
T ss_pred             HhhhccccchH-HHHHHHH--HHHHhCCHHHHHHHHHccccCCCCccCHHHHHHHhccC-------HHHHHHHHHHHHhC
Confidence                  11112 8999999  99999999999999999999999999999999999654       34578999999999


Q ss_pred             cCCC
Q 040913          422 GFIQ  425 (425)
Q Consensus       422 ~llq  425 (425)
                      |||+
T Consensus       422 ~Ll~  425 (591)
T 1z6t_A          422 SLLF  425 (591)
T ss_dssp             TSSE
T ss_pred             cCeE
Confidence            9984

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.45  E-value=7.8e-14  Score=113.31  Aligned_cols=74  Identities=15%  Similarity=0.076  Sum_probs=58.6

Q ss_pred             hHHHHHHHhhhHHHHHHHHHhHHHHHHHHHHH------HHHHhhhh--ccCChhHHHHHHHHHHHhhhhHHHHHHHHHHH
Q 040913           33 TPLLQNLLAESEIIASTLLANYEADMALLLFQ------LLRKKINE--DVKRPDILKILEDVNQFVHESEEVIDTFFINI  104 (425)
Q Consensus        33 ~~ll~~L~~~~~~~~~~~l~~l~~d~~~l~~~------~l~~a~~~--~~~~~~v~~Wl~~lr~layd~eD~lD~~~~~~  104 (425)
                      ++++++|.+-.. ..+.++.++++++++|+.+      +|.+++.+  +..|+.++.|+++||+++||+|||||+|.++.
T Consensus         4 ~~ll~KL~~ll~-~E~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~f~~~~   82 (115)
T 3qfl_A            4 SNLIPKLGELLT-EEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFLVQV   82 (115)
T ss_dssp             CSHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-HHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345555555221 0167888888888888755      78899887  66899999999999999999999999999988


Q ss_pred             hhh
Q 040913          105 MQQ  107 (425)
Q Consensus       105 ~~~  107 (425)
                      ...
T Consensus        83 ~~~   85 (115)
T 3qfl_A           83 DGI   85 (115)
T ss_dssp             HHC
T ss_pred             ccc
Confidence            653

>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=98.90  E-value=1.6e-09  Score=107.36  Aligned_cols=133  Identities=18%  Similarity=0.121  Sum_probs=82.9

Q ss_pred             CCCCcccchhhHHHHHHHH-hc---C-CCCcEEEEE--EecCCCchHHHHHHhhcCccccc-----cccchHHH------
Q 040913          165 PRLDISEFERAREEWFDLL-IE---G-PIGLSVVAI--LDSSGFDKTAFAADTYNNNHVKF-----YFDCLAWI------  226 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L-~~---~-~~~~~vi~I--vG~gGvGKTtLa~~v~~~~~~~~-----~F~~~~wv------  226 (425)
                      .+..++||+.+++.|.++| ..   + ......+.|  +|++|+||||||+.+++......     .|. .+|+      
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~   98 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVK-QAYVNAFNAP   98 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEE-EEEEEGGGCC
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCcee-EEEEECCCCC
Confidence            3477999999999999988 42   2 023455666  99999999999999987421110     111 1122      


Q ss_pred             -----HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccCCCh--------hhHHHHHhhCCCC---
Q 040913          227 -----LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVCHNI--------EIWDDLEEVLPDN---  288 (425)
Q Consensus       227 -----~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~~~--------~~~~~l~~~l~~~---  288 (425)
                           +..++.++.....   ....+...+...+...+.  +++++|||||++ ..        +.+..+...+...   
T Consensus        99 ~~~~~~~~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~-~l~~~~~~~~~~l~~l~~~~~~~~~~  174 (412)
T 1w5s_A           99 NLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQ-SMLSSPRIAAEDLYTLLRVHEEIPSR  174 (412)
T ss_dssp             SHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH-HHHSCTTSCHHHHHHHHTHHHHSCCT
T ss_pred             CHHHHHHHHHHHhCCCCC---CCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHH-HHhhccCcchHHHHHHHHHHHhcccC
Confidence                 6677777755422   112345666777777775  789999999997 32        3333333333211   


Q ss_pred             C--CCcEEEEecCChh
Q 040913          289 Q--NGSRVLITVINPS  302 (425)
Q Consensus       289 ~--~gskIivTTR~~~  302 (425)
                      +  ....+|+||+...
T Consensus       175 ~~~~~v~lI~~~~~~~  190 (412)
T 1w5s_A          175 DGVNRIGFLLVASDVR  190 (412)
T ss_dssp             TSCCBEEEEEEEEETH
T ss_pred             CCCceEEEEEEecccc
Confidence            2  3455888887654

>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=98.72  E-value=1.9e-08  Score=98.55  Aligned_cols=132  Identities=16%  Similarity=0.039  Sum_probs=83.8

Q ss_pred             CCcccchhhHHHHHHHHhc--CCCCcEEEEEEecCCCchHHHHHHhhcCccc---------cccc---cch------HHH
Q 040913          167 LDISEFERAREEWFDLLIE--GPIGLSVVAILDSSGFDKTAFAADTYNNNHV---------KFYF---DCL------AWI  226 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~--~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~---------~~~F---~~~------~wv  226 (425)
                      ..++||+.+++.+.+++..  .....+.+.|+|++|+||||||+.+++...-         ...|   ++.      .-+
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   99 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAV   99 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHH
Confidence            6799999999999988865  2334568999999999999999999873200         1111   111      111


Q ss_pred             HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccCCChh--h-HHH-HHhhCCCCCCCcEEEEecCChh
Q 040913          227 LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIE--I-WDD-LEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       227 ~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~--~-~~~-l~~~l~~~~~gskIivTTR~~~  302 (425)
                      +..++.++.....  .....+...+...+...+..++.+|||||++ ...  . .+. +...+... .+..+|+||+...
T Consensus       100 ~~~l~~~l~~~~~--~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~-~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~~~  175 (384)
T 2qby_B          100 LSSLAGKLTGFSV--PKHGINLGEYIDKIKNGTRNIRAIIYLDEVD-TLVKRRGGDIVLYQLLRSD-ANISVIMISNDIN  175 (384)
T ss_dssp             HHHHHHHHHCSCC--CSSSSCTHHHHHHHHHHHSSSCEEEEEETTH-HHHHSTTSHHHHHHHHTSS-SCEEEEEECSSTT
T ss_pred             HHHHHHHhcCCCC--CCCCCCHHHHHHHHHHHhccCCCEEEEECHH-HhccCCCCceeHHHHhcCC-cceEEEEEECCCc
Confidence            4556666632211  1123345677788888888777799999997 321  1 222 22222222 5788999988753

>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=98.70  E-value=2.8e-08  Score=97.13  Aligned_cols=136  Identities=14%  Similarity=0.079  Sum_probs=82.8

Q ss_pred             CCCCcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCcccccccc---chHHH-------HHHHHH
Q 040913          165 PRLDISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFD---CLAWI-------LDDIIR  232 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~---~~~wv-------~~~il~  232 (425)
                      .+..++||+.+++.+.+++...  ......+.|+|++|+|||||++.+++.  ....+.   ..+|+       ...++.
T Consensus        18 ~p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~~   95 (386)
T 2qby_A           18 IPDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTPYRVLA   95 (386)
T ss_dssp             CCSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSHHHHHH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCHHHHHH
Confidence            3477999999999999988752  234568899999999999999999883  322110   11122       233444


Q ss_pred             HhCCCCCCC-ccCCCCHHHHHHHHHHHhc--CCeEEEEecccCCC------hhhHHHHHhhCCC-CCCCcEEEEecCChh
Q 040913          233 SLMPPSRVT-VIIGEDYKLKKSILRDFLT--NKKYFIALDDVCHN------IEIWDDLEEVLPD-NQNGSRVLITVINPS  302 (425)
Q Consensus       233 ~l~~~~~~~-~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~~------~~~~~~l~~~l~~-~~~gskIivTTR~~~  302 (425)
                      .+....... .....+...+...+.+.+.  +++.+||||+++ .      .+.+..+...+.. ...+..+|+||+...
T Consensus        96 ~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~-~l~~~~~~~~l~~l~~~~~~~~~~~~~~I~~~~~~~  174 (386)
T 2qby_A           96 DLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEID-AFVKKYNDDILYKLSRINSEVNKSKISFIGITNDVK  174 (386)
T ss_dssp             HHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHH-HHHHSSCSTHHHHHHHHHHSCCC--EEEEEEESCGG
T ss_pred             HHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChh-hhhccCcCHHHHHHhhchhhcCCCeEEEEEEECCCC
Confidence            443332211 1122345666667777665  458999999997 3      2334444333321 233566788887764


Q ss_pred             H
Q 040913          303 L  303 (425)
Q Consensus       303 v  303 (425)
                      .
T Consensus       175 ~  175 (386)
T 2qby_A          175 F  175 (386)
T ss_dssp             G
T ss_pred             h
Confidence            3

>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=98.66  E-value=1e-07  Score=93.41  Aligned_cols=135  Identities=18%  Similarity=0.119  Sum_probs=87.6

Q ss_pred             CCCcccchhhHHHHHHHHhcC----CCCcEEEEEEecCCCchHHHHHHhhcCccccccc-----cc-----hHHHHHHHH
Q 040913          166 RLDISEFERAREEWFDLLIEG----PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-----DC-----LAWILDDII  231 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-----~~-----~~wv~~~il  231 (425)
                      +..++||+.+++++.+++...    ....+.+.|+|++|+|||||++.+.+...-...+     ++     ...++..++
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~   95 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIA   95 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCHHHHHHHHH
Confidence            367999999999999988762    2223488999999999999999998732111001     11     112256666


Q ss_pred             HHhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccCC-ChhhHHHHHhhCCCCC----CCcEEEEecCChhH
Q 040913          232 RSLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVCH-NIEIWDDLEEVLPDNQ----NGSRVLITVINPSL  303 (425)
Q Consensus       232 ~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~----~gskIivTTR~~~v  303 (425)
                      ..+.....   ....+...+...+...+.  +++.+||||++.. +......+...+....    .+..||+||+....
T Consensus        96 ~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~~~~  171 (389)
T 1fnn_A           96 RSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAV  171 (389)
T ss_dssp             HHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHHHHHHHTTCHHHHSSCCEEEEEEESSTHH
T ss_pred             HHhCccCC---CCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccchHHHHHHHHHHHhCCCCCcCCEEEEEEECCchH
Confidence            66654322   122355666677776664  5788999999973 3455666666554321    36778888877643

>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=98.66  E-value=4.4e-08  Score=88.83  Aligned_cols=132  Identities=14%  Similarity=0.054  Sum_probs=77.4

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc------ccchHHHHHHHHHHhCCCCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY------FDCLAWILDDIIRSLMPPSRV  240 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~------F~~~~wv~~~il~~l~~~~~~  240 (425)
                      .+++|++..++.+..++..+. ..+.+.|+|++|+||||||+.+++.......      +.+..  ...+..........
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~-~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~   99 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDN--CREIEQGRFVDLIE   99 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC-CCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHH--HHHHHTTCCSSEEE
T ss_pred             HHHhCcHHHHHHHHHHHHcCC-CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHH--HHHHhccCCcceEE
Confidence            468999999999999998754 2347889999999999999999873221111      11100  11111110000000


Q ss_pred             CccCC-CCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          241 TVIIG-EDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       241 ~~~~~-~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ..... .....+ ..+.+.+     .+++.+||+||++. +...++.+...+.....+..+|+||+...
T Consensus       100 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~vlviDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~t~~~~  167 (250)
T 1njg_A          100 IDAASRTKVEDT-RDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ  167 (250)
T ss_dssp             EETTCGGGHHHH-HHHHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGG
T ss_pred             ecCcccccHHHH-HHHHHHhhhchhcCCceEEEEECcccccHHHHHHHHHHHhcCCCceEEEEEeCChH
Confidence            00011 112222 2333332     34679999999962 45677777777765556788888887644

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.65  E-value=6.5e-08  Score=93.26  Aligned_cols=135  Identities=13%  Similarity=0.149  Sum_probs=82.4

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchH---------H--HHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLA---------W--ILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~---------w--v~~~i  230 (425)
                      +...+..++||+.+.+.|.+++..+    +++.|+|++|+|||||++++.+... .-.+++..         +  ++..+
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~~----~~v~i~G~~G~GKT~Ll~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l   81 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLENY----PLTLLLGIRRVGKSSLLRAFLNERP-GILIDCRELYAERGHITREELIKEL   81 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHC----SEEEEECCTTSSHHHHHHHHHHHSS-EEEEEHHHHHHTTTCBCHHHHHHHH
T ss_pred             CCCChHhcCChHHHHHHHHHHHhcC----CeEEEECCCcCCHHHHHHHHHHHcC-cEEEEeecccccccCCCHHHHHHHH
Confidence            3445677999999999999998763    6899999999999999999987421 00112111         0  12333


Q ss_pred             HHHhCCC------------C-CC-CccCCCCHHHHHHHHHHHhcC-CeEEEEecccCCCh---------hhHHHHHhhCC
Q 040913          231 IRSLMPP------------S-RV-TVIIGEDYKLKKSILRDFLTN-KKYFIALDDVCHNI---------EIWDDLEEVLP  286 (425)
Q Consensus       231 l~~l~~~------------~-~~-~~~~~~~~~~l~~~l~~~l~~-kr~LlVLDdvw~~~---------~~~~~l~~~l~  286 (425)
                      ...+...            . .. ......+...+...+....+. ++++|||||++ ..         +.+..+.....
T Consensus        82 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~-~~~~~~~~~~~~~~~~L~~~~~  160 (350)
T 2qen_A           82 QSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQ-YLRFYGSRGGKELLALFAYAYD  160 (350)
T ss_dssp             HHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGG-GGGGBTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHH-HHhccCccchhhHHHHHHHHHH
Confidence            3333220            0 00 011124556677777666653 48999999997 42         22333433322


Q ss_pred             CCCCCcEEEEecCChhH
Q 040913          287 DNQNGSRVLITVINPSL  303 (425)
Q Consensus       287 ~~~~gskIivTTR~~~v  303 (425)
                      . .++.++|+|++....
T Consensus       161 ~-~~~~~~il~g~~~~~  176 (350)
T 2qen_A          161 S-LPNLKIILTGSEVGL  176 (350)
T ss_dssp             H-CTTEEEEEEESSHHH
T ss_pred             h-cCCeEEEEECCcHHH
Confidence            2 247889999887653

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.62  E-value=5.8e-08  Score=94.99  Aligned_cols=132  Identities=14%  Similarity=-0.012  Sum_probs=82.6

Q ss_pred             CCCcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCccc-------cccc---cch-----HHHHH
Q 040913          166 RLDISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHV-------KFYF---DCL-----AWILD  228 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~-------~~~F---~~~-----~wv~~  228 (425)
                      +..++||+.+++.+.+++...  ....+.+.|+|++|+||||||+.+++...-       ...|   ++.     .-++.
T Consensus        18 p~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~   97 (387)
T 2v1u_A           18 PDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVAS   97 (387)
T ss_dssp             CSCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCHHHHHH
Confidence            477999999999999998643  334667889999999999999999873210       1111   110     11156


Q ss_pred             HHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccCCChh----hHHHHHhhC---CCC--CCCcEEEEe
Q 040913          229 DIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVCHNIE----IWDDLEEVL---PDN--QNGSRVLIT  297 (425)
Q Consensus       229 ~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw~~~~----~~~~l~~~l---~~~--~~gskIivT  297 (425)
                      .++.++.....   ....+...+...+...+.  +++.+||||++. ...    ..+.+...+   ...  ..+..+|.|
T Consensus        98 ~l~~~l~~~~~---~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~-~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~I~~  173 (387)
T 2v1u_A           98 AIAEAVGVRVP---FTGLSVGEVYERLVKRLSRLRGIYIIVLDEID-FLPKRPGGQDLLYRITRINQELGDRVWVSLVGI  173 (387)
T ss_dssp             HHHHHHSCCCC---SSCCCHHHHHHHHHHHHTTSCSEEEEEEETTT-HHHHSTTHHHHHHHHHHGGGCC-----CEEEEE
T ss_pred             HHHHHhCCCCC---CCCCCHHHHHHHHHHHHhccCCeEEEEEccHh-hhcccCCCChHHHhHhhchhhcCCCceEEEEEE
Confidence            67777755432   223345666777777773  568999999997 322    222332222   111  345677888


Q ss_pred             cCCh
Q 040913          298 VINP  301 (425)
Q Consensus       298 TR~~  301 (425)
                      |+..
T Consensus       174 t~~~  177 (387)
T 2v1u_A          174 TNSL  177 (387)
T ss_dssp             CSCS
T ss_pred             ECCC
Confidence            7765

>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=98.59  E-value=1.3e-07  Score=84.49  Aligned_cols=121  Identities=11%  Similarity=0.030  Sum_probs=75.6

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      ..+++|++..++.+.+++....  .+.+.|+|++|+|||+||+.+++.  .........++      .+.      ....
T Consensus        16 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~l~~~--~~~~~~~~~~~------~~~------~~~~   79 (226)
T 2chg_A           16 LDEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARD--LFGENWRDNFI------EMN------ASDE   79 (226)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTTC--CCCEEEECSTTSSHHHHHHHHHHH--HHGGGGGGGEE------EEE------TTCT
T ss_pred             HHHHcCcHHHHHHHHHHHhCCC--CCeEEEECCCCCCHHHHHHHHHHH--HhccccccceE------Eec------cccc
Confidence            3468999999999999998764  233889999999999999998872  21110000000      000      0011


Q ss_pred             CCHHHHHHHHHHHh------cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          246 EDYKLKKSILRDFL------TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       246 ~~~~~l~~~l~~~l------~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .....+...+....      .+++.+||+||+.. .....+.+...+.....++++|+||+...
T Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~l~~~l~~~~~~~~~i~~~~~~~  143 (226)
T 2chg_A           80 RGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (226)
T ss_dssp             TCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             cChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence            23334444444443      25789999999972 23455666665554455788888887653

>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=98.51  E-value=1.1e-07  Score=91.82  Aligned_cols=45  Identities=18%  Similarity=0.144  Sum_probs=38.6

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          163 GQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+..++||+.+.+.|.+ +..     +++.|+|++|+|||||++.+.+.
T Consensus         9 ~~~~~~~~gR~~el~~L~~-l~~-----~~v~i~G~~G~GKT~L~~~~~~~   53 (357)
T 2fna_A            9 KDNRKDFFDREKEIEKLKG-LRA-----PITLVLGLRRTGKSSIIKIGINE   53 (357)
T ss_dssp             CCSGGGSCCCHHHHHHHHH-TCS-----SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCHHHhcChHHHHHHHHH-hcC-----CcEEEECCCCCCHHHHHHHHHHh
Confidence            3456779999999999999 654     58999999999999999999874

>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=98.34  E-value=1e-06  Score=83.84  Aligned_cols=118  Identities=13%  Similarity=0.115  Sum_probs=73.5

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc-cccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF-YFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      .+++|++..++.+.+++..+.  .+.+.++|++|+||||+|+.+.+.  ... .+.. .+        +....    ...
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~-~~--------~~~~~----~~~   83 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAHE--LLGRSYAD-GV--------LELNA----SDD   83 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHH-HE--------EEECT----TSC
T ss_pred             HHHHCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHHH--hcCCcccC-CE--------EEecC----ccc
Confidence            568999999999999998765  223889999999999999999873  211 1100 00        00000    011


Q ss_pred             CCHHHHHHHHHHHh-------cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          246 EDYKLKKSILRDFL-------TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       246 ~~~~~l~~~l~~~l-------~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      .....+...+....       .+++.+||+||++. +...++.+...+.....++++|+||+..
T Consensus        84 ~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~~~~  147 (323)
T 1sxj_B           84 RGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  147 (323)
T ss_dssp             CSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             cChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHHHHHHHHHHHhccCCCceEEEEeCCh
Confidence            23344444444433       45689999999972 2345555555554444577888888664

>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=98.24  E-value=1.7e-06  Score=82.57  Aligned_cols=121  Identities=13%  Similarity=0.079  Sum_probs=72.6

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      -.+++|++..++.+.+++..+.  .+.+.++|++|+||||+|+.+++.  +........++      .+  ...    ..
T Consensus        24 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~la~~l~~~--l~~~~~~~~~~------~~--~~~----~~   87 (327)
T 1iqp_A           24 LDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALARE--LFGENWRHNFL------EL--NAS----DE   87 (327)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEE------EE--ETT----CH
T ss_pred             HHHhhCCHHHHHHHHHHHHcCC--CCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCceE------Ee--ecc----cc
Confidence            3468999999999999998764  334889999999999999999873  21110000000      00  000    00


Q ss_pred             CCHHHHHHHHHHHh------cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          246 EDYKLKKSILRDFL------TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       246 ~~~~~l~~~l~~~l------~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .....+...+....      .+++.+||+||+.. +...++.+...+.....++++|+||....
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~  151 (327)
T 1iqp_A           88 RGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSS  151 (327)
T ss_dssp             HHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             CchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCCcc
Confidence            00111112222221      26788999999973 33566666666654455788888887643

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.17  E-value=5.5e-06  Score=71.95  Aligned_cols=46  Identities=11%  Similarity=0.064  Sum_probs=38.9

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|++..++++.+.+....  .+.+.|+|++|+|||+||+.+.+.
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQRRT--KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ccccccchHHHHHHHHHHhcCC--CCceEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999987743  455789999999999999998873

>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=98.00  E-value=4e-05  Score=74.39  Aligned_cols=132  Identities=14%  Similarity=0.059  Sum_probs=73.9

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccchHHHHHHHHHHhCCCCC-
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDCLAWILDDIIRSLMPPSR-  239 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~il~~l~~~~~-  239 (425)
                      .+++|++..++.+.+.+..+. ..+.+.|+|++|+||||+|+.+.+.-....      ++.+...  ..+...-..... 
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~-~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~   92 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNC--REIEQGRFVDLIE   92 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC-CCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHH--HHHHTSCCSSCEE
T ss_pred             hhccCcHHHHHHHHHHHHhCC-CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHH--HHHhccCCCceEE
Confidence            459999999999999997654 234678999999999999999876321111      1111111  111110000000 


Q ss_pred             ---CCccCCCCHHHHHHHHHHH-hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          240 ---VTVIIGEDYKLKKSILRDF-LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       240 ---~~~~~~~~~~~l~~~l~~~-l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                         .......+...+...+... ..+++.+||+||+.. +....+.+...+.....+..+|++|...
T Consensus        93 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~Ll~~le~~~~~~~~Il~~~~~  159 (373)
T 1jr3_A           93 IDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDP  159 (373)
T ss_dssp             EETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHHHHHHHHHHHHSCCSSEEEEEEESCG
T ss_pred             ecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHHHHHHHHHHHhcCCCceEEEEEeCCh
Confidence               0001112233333222211 135678999999962 3456666766665545567777777654

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.97  E-value=1.2e-05  Score=75.28  Aligned_cols=50  Identities=16%  Similarity=0.081  Sum_probs=39.5

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          163 GQPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...-.+++|.+..++.|.+.+...           -....-+.|+|++|+|||+||+.+.+
T Consensus        13 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~   73 (285)
T 3h4m_A           13 NVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVAT   73 (285)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            344567999999999998877532           12345688999999999999999988

>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=97.93  E-value=1.9e-05  Score=75.36  Aligned_cols=116  Identities=15%  Similarity=0.112  Sum_probs=74.1

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      -.+++|.+..++.+.+++..+. ..+++-+.|++|+|||++|+.+.+  .....|-.           +       ....
T Consensus        25 ~~~ivg~~~~~~~l~~~l~~~~-~~~~~L~~G~~G~GKT~la~~la~--~l~~~~~~-----------i-------~~~~   83 (324)
T 3u61_B           25 IDECILPAFDKETFKSITSKGK-IPHIILHSPSPGTGKTTVAKALCH--DVNADMMF-----------V-------NGSD   83 (324)
T ss_dssp             TTTSCCCHHHHHHHHHHHHTTC-CCSEEEECSSTTSSHHHHHHHHHH--HTTEEEEE-----------E-------ETTT
T ss_pred             HHHHhCcHHHHHHHHHHHHcCC-CCeEEEeeCcCCCCHHHHHHHHHH--HhCCCEEE-----------E-------cccc
Confidence            4578999999999999998654 345677889999999999999987  33222210           0       1111


Q ss_pred             CCHHHHHHHHHHHhc-----CCeEEEEecccCC-C-hhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          246 EDYKLKKSILRDFLT-----NKKYFIALDDVCH-N-IEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       246 ~~~~~l~~~l~~~l~-----~kr~LlVLDdvw~-~-~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .....+...+.+...     +++.+|++||+.. . .+..+.+...+.....+.++|+||....
T Consensus        84 ~~~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~n~~~  147 (324)
T 3u61_B           84 CKIDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITANNID  147 (324)
T ss_dssp             CCHHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEESSGG
T ss_pred             cCHHHHHHHHHHHHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEeCCcc
Confidence            224444444444433     3788999999973 2 3345555554433334567888876644

>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=97.85  E-value=1.7e-05  Score=75.10  Aligned_cols=123  Identities=11%  Similarity=0.017  Sum_probs=71.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGE  246 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~  246 (425)
                      .+++|++..++.+.+++..+.  .+.+.++|++|+||||+|+.+.+.-. ...+... ++      .+.....   ....
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~~--~~~~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~-~~------~~~~~~~---~~~~   83 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERKN--IPHLLFSGPPGTGKTATAIALARDLF-GENWRDN-FI------EMNASDE---RGID   83 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTTC--CCCEEEESSSSSSHHHHHHHHHHHHH-TTCHHHH-CE------EEETTST---TCTT
T ss_pred             HHHhCCHHHHHHHHHHHhCCC--CCeEEEECcCCcCHHHHHHHHHHHhc-CCcccCC-eE------EEeCccc---cChH
Confidence            458999999999998887654  23388999999999999999887310 1110000 00      0000000   0011


Q ss_pred             CHHHHHHHHHHH--h-cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          247 DYKLKKSILRDF--L-TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       247 ~~~~l~~~l~~~--l-~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ........+...  + .+++.+||+|++.. +....+.+...+.....++++|+||....
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~~~L~~~le~~~~~~~~i~~~~~~~  143 (319)
T 2chq_A           84 VVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQAALRRTMEMYSKSCRFILSCNYVS  143 (319)
T ss_dssp             TSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHHHTTGGGTSSSSSSEEEEEEESCGG
T ss_pred             HHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence            112222222211  1 25688999999962 33455666666655556778888876643

>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=97.80  E-value=7.3e-05  Score=68.74  Aligned_cols=48  Identities=17%  Similarity=0.104  Sum_probs=36.1

Q ss_pred             CCCCcccchhhHHHHHHHHh---cCC-------CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          165 PRLDISEFERAREEWFDLLI---EGP-------IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|.+..++.|.+++.   ..+       ...+-+.++|++|+|||+||+.+.+
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~   61 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT   61 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            34678999988888766543   221       2345577999999999999999988

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.79  E-value=8.6e-06  Score=68.41  Aligned_cols=110  Identities=10%  Similarity=-0.060  Sum_probs=62.5

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcc-ccccc--cchHHHHHHHHHHhCCCCCCCccC
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNH-VKFYF--DCLAWILDDIIRSLMPPSRVTVII  244 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~-~~~~F--~~~~wv~~~il~~l~~~~~~~~~~  244 (425)
                      .++|+...+.++.+.+..-.....-|-|+|.+|+|||++|+.+++... ....|  ++..                 ...
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v~~~~~-----------------~~~   64 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT-----------------PDN   64 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCEEEECC-----------------TTT
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEEEECCC-----------------CCc
Confidence            578999999999888764222223467999999999999999988421 12222  1100                 000


Q ss_pred             CCCHHHHHHHHHHHhcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCC
Q 040913          245 GEDYKLKKSILRDFLTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVIN  300 (425)
Q Consensus       245 ~~~~~~l~~~l~~~l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~  300 (425)
                      .....   ..+..   ...-.|+||++.. +......+...+.......++|.||..
T Consensus        65 ~~~~~---~~~~~---a~~g~l~ldei~~l~~~~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           65 APQLN---DFIAL---AQGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             SSCHH---HHHHH---HTTSCEEEECGGGSCHHHHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             chhhh---cHHHH---cCCcEEEEcChHHCCHHHHHHHHHHHhhcCCCEEEEEECCc
Confidence            11111   11111   1335789999963 234445555555443445677777754

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.75  E-value=4.9e-05  Score=72.37  Aligned_cols=102  Identities=10%  Similarity=0.031  Sum_probs=65.0

Q ss_pred             CcccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccc---hH-------HHHHH
Q 040913          168 DISEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDC---LA-------WILDD  229 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~---~~-------wv~~~  229 (425)
                      .+.||+++.++|...|...  ....+.+-|+|++|+|||++++.+.+.-....      .|..   -+       -++..
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~  100 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEK  100 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHH
Confidence            3789999999998887753  33567788999999999999999988421100      1221   00       11677


Q ss_pred             HHHHhCCCCCCCccCCCCHHHHHHHHHHH--hcCCeEEEEecccC
Q 040913          230 IIRSLMPPSRVTVIIGEDYKLKKSILRDF--LTNKKYFIALDDVC  272 (425)
Q Consensus       230 il~~l~~~~~~~~~~~~~~~~l~~~l~~~--l~~kr~LlVLDdvw  272 (425)
                      |.+++.....   ......+.+...+...  -.++.++|+||++.
T Consensus       101 I~~~L~g~~~---~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d  142 (318)
T 3te6_A          101 IWFAISKENL---CGDISLEALNFYITNVPKAKKRKTLILIQNPE  142 (318)
T ss_dssp             HHHHHSCCC-----CCCCHHHHHHHHHHSCGGGSCEEEEEEECCS
T ss_pred             HHHHhcCCCC---CchHHHHHHHHHHHHhhhccCCceEEEEecHH
Confidence            8888854321   1122333444333332  24678999999996

>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=97.72  E-value=0.00016  Score=68.96  Aligned_cols=55  Identities=18%  Similarity=0.166  Sum_probs=41.2

Q ss_pred             CCCCCcccchhhHHHHHHHHhc----------CCCCcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          164 QPRLDISEFERAREEWFDLLIE----------GPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      ..-.+++|.+..++.|.+.+..          .....+-+.++|++|+|||+||+.+.+  .....|
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~--~~~~~~   79 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVAT--EANSTF   79 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHH--HHTCEE
T ss_pred             CCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHH--HHCCCE
Confidence            4446789999999999887731          112345688999999999999999988  444343

>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=97.72  E-value=2e-05  Score=75.14  Aligned_cols=47  Identities=17%  Similarity=0.116  Sum_probs=37.7

Q ss_pred             CCCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|++..++.+..++...   ......+.|+|++|+|||+||+.+++
T Consensus        11 ~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~   60 (324)
T 1hqc_A           11 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAH   60 (324)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHH
T ss_pred             HHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHH
Confidence            457999999999988877631   12345678999999999999999987

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.66  E-value=4.7e-05  Score=63.67  Aligned_cols=47  Identities=17%  Similarity=-0.027  Sum_probs=33.4

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+++|.+..++++.+.+..-.....-|-|+|.+|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHh
Confidence            35789999998888877642111233678999999999999999984

>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=97.65  E-value=0.00025  Score=65.85  Aligned_cols=46  Identities=20%  Similarity=0.099  Sum_probs=34.9

Q ss_pred             CCcccchhhHHHHHH-------HHhcC-CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFD-------LLIEG-PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~-------~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.....++++.       .+... ....+.+.|+|++|+|||+||+.+.+
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~   86 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE   86 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            457888777776666       33322 34567888999999999999999988

>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=97.65  E-value=0.00012  Score=69.30  Aligned_cols=96  Identities=16%  Similarity=0.117  Sum_probs=58.6

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIR  232 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~  232 (425)
                      ..-.+++|.+..++.|.+.+...           -...+.+.++|++|+|||+||+.+.+  .....|-..-  ..++..
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~--~~~~~~i~v~--~~~l~~   87 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQANFISIK--GPELLT   87 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHH--HTTCEEEEEC--HHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHH--HhCCCEEEEE--hHHHHh
Confidence            34456899999998888776531           12356788999999999999999998  4433331100  112222


Q ss_pred             HhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          233 SLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       233 ~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ......         ...+...+.........+|+||++.
T Consensus        88 ~~~g~~---------~~~~~~~f~~a~~~~p~il~iDEid  118 (301)
T 3cf0_A           88 MWFGES---------EANVREIFDKARQAAPCVLFFDELD  118 (301)
T ss_dssp             HHHTTC---------TTHHHHHHHHHHHTCSEEEEECSTT
T ss_pred             hhcCch---------HHHHHHHHHHHHhcCCeEEEEEChH
Confidence            221111         1222333333334577999999995

>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=97.65  E-value=0.00013  Score=70.11  Aligned_cols=46  Identities=11%  Similarity=0.045  Sum_probs=38.5

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|++..++.+..++..+..  +.+.++|++|+||||+|+.+.+.
T Consensus        36 ~~~i~g~~~~~~~l~~~l~~~~~--~~~ll~G~~G~GKT~la~~la~~   81 (353)
T 1sxj_D           36 LDEVTAQDHAVTVLKKTLKSANL--PHMLFYGPPGTGKTSTILALTKE   81 (353)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTTC--CCEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhhCCHHHHHHHHHHHhcCCC--CEEEEECCCCCCHHHHHHHHHHH
Confidence            45689999999999999887642  23789999999999999998873

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.62  E-value=0.00047  Score=65.86  Aligned_cols=49  Identities=16%  Similarity=0.164  Sum_probs=38.1

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC----------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          164 QPRLDISEFERAREEWFDLLIEG----------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.-.+++|.+..++.|.+.+...          ....+-|.++|++|+|||+||+.+.+
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~   67 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVAT   67 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHH
Confidence            44467899999999888776421          12346788999999999999999998

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.61  E-value=0.00015  Score=72.44  Aligned_cols=114  Identities=14%  Similarity=0.089  Sum_probs=64.6

Q ss_pred             CCCcccchhhH---HHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCc
Q 040913          166 RLDISEFERAR---EEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTV  242 (425)
Q Consensus       166 ~~~~vGr~~~~---~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~  242 (425)
                      -.+++|.+..+   ..+...+..+.  .+.+.++|++|+||||||+.+.+  .....|...                  .
T Consensus        25 l~~ivGq~~~~~~~~~L~~~i~~~~--~~~vLL~GppGtGKTtlAr~ia~--~~~~~f~~l------------------~   82 (447)
T 3pvs_A           25 LAQYIGQQHLLAAGKPLPRAIEAGH--LHSMILWGPPGTGKTTLAEVIAR--YANADVERI------------------S   82 (447)
T ss_dssp             TTTCCSCHHHHSTTSHHHHHHHHTC--CCEEEEECSTTSSHHHHHHHHHH--HTTCEEEEE------------------E
T ss_pred             HHHhCCcHHHHhchHHHHHHHHcCC--CcEEEEECCCCCcHHHHHHHHHH--HhCCCeEEE------------------E
Confidence            45689988887   67777777765  46788999999999999999998  444444210                  0


Q ss_pred             cCCCCHHHHHHHHHHH----hcCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          243 IIGEDYKLKKSILRDF----LTNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       243 ~~~~~~~~l~~~l~~~----l~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ........+...+...    ..+++.+|++|++.. +....+.+...+.. +.-.-|..||.+..
T Consensus        83 a~~~~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~LL~~le~-~~v~lI~att~n~~  146 (447)
T 3pvs_A           83 AVTSGVKEIREAIERARQNRNAGRRTILFVDEVHRFNKSQQDAFLPHIED-GTITFIGATTENPS  146 (447)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC------CCHHHHHT-TSCEEEEEESSCGG
T ss_pred             eccCCHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHHHHHHHHHHHhc-CceEEEecCCCCcc
Confidence            0111222222222221    246789999999962 22334444444433 11222334555543

>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=97.54  E-value=8.6e-05  Score=64.40  Aligned_cols=42  Identities=19%  Similarity=0.038  Sum_probs=29.1

Q ss_pred             chhhHHHHHHHHhcCC-CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          172 FERAREEWFDLLIEGP-IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       172 r~~~~~~l~~~L~~~~-~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .....+.+.+++..-. .....+.|+|++|+|||||++.+++.
T Consensus        19 ~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~   61 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKA   61 (180)
T ss_dssp             HHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3344444455554322 23567899999999999999999873

>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=97.53  E-value=0.00019  Score=69.14  Aligned_cols=44  Identities=11%  Similarity=-0.034  Sum_probs=35.5

Q ss_pred             CCcccchhhHHHHHHHH-hcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLL-IEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L-~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|.+...+.+.+++ ..+. ... +.|+|+.|+||||+++.+.+
T Consensus        14 ~~~vg~~~~~~~l~~~~~~~~~-~~~-~ll~Gp~G~GKTtl~~~la~   58 (354)
T 1sxj_E           14 NALSHNEELTNFLKSLSDQPRD-LPH-LLLYGPNGTGKKTRCMALLE   58 (354)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTTC-CCC-EEEECSTTSSHHHHHHTHHH
T ss_pred             HHhcCCHHHHHHHHHHHhhCCC-CCe-EEEECCCCCCHHHHHHHHHH
Confidence            45889999998888888 4433 233 89999999999999998776

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=97.50  E-value=0.0001  Score=70.76  Aligned_cols=47  Identities=13%  Similarity=0.023  Sum_probs=38.8

Q ss_pred             CCCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|++..++.+..++...   ......+.|+|++|+|||+||+.+.+
T Consensus        28 ~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~   77 (338)
T 3pfi_A           28 FDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISY   77 (338)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHH
Confidence            456999999999998888752   23345678999999999999999987

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.50  E-value=0.00034  Score=66.01  Aligned_cols=45  Identities=9%  Similarity=0.034  Sum_probs=34.6

Q ss_pred             CcccchhhHHHHHHHHhcC-------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIEG-------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~-------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +++|.+..++.|.+.+...             ......+.|+|++|+|||+||+.+.+
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~   89 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAG   89 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHH
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            4889998888887765421             23355688999999999999987766

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=97.49  E-value=9.8e-05  Score=73.79  Aligned_cols=117  Identities=15%  Similarity=0.162  Sum_probs=61.1

Q ss_pred             Ccc-cchhh--HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccc--hHHH-----HHHHHHHhCCC
Q 040913          168 DIS-EFERA--REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDC--LAWI-----LDDIIRSLMPP  237 (425)
Q Consensus       168 ~~v-Gr~~~--~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~--~~wv-----~~~il~~l~~~  237 (425)
                      +++ |....  ...+......+.. ...+.|+|++|+||||||+.+.+  .....|..  .+++     ..++...+...
T Consensus       106 ~fv~g~~n~~a~~~~~~~a~~~~~-~~~lll~Gp~G~GKTtLa~aia~--~l~~~~~~~~v~~v~~~~~~~~~~~~~~~~  182 (440)
T 2z4s_A          106 NFVVGPGNSFAYHAALEVAKHPGR-YNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITSEKFLNDLVDSMKEG  182 (440)
T ss_dssp             GCCCCTTTHHHHHHHHHHHHSTTS-SCCEEEECSSSSSHHHHHHHHHH--HHHHHCCSSCEEEEEHHHHHHHHHHHHHTT
T ss_pred             hcCCCCchHHHHHHHHHHHhCCCC-CCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeHHHHHHHHHHHHHcc
Confidence            344 64433  3334444444332 66788999999999999999988  33222110  0111     22233322211


Q ss_pred             CCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccCC-Ch--hhHHHHHhhCCC-CCCCcEEEEecCC
Q 040913          238 SRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCH-NI--EIWDDLEEVLPD-NQNGSRVLITVIN  300 (425)
Q Consensus       238 ~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~-~~--~~~~~l~~~l~~-~~~gskIivTTR~  300 (425)
                               ..    ..+...+..+.-+|+|||+.. ..  ..-+.+...+.. ...|..||+||.+
T Consensus       183 ---------~~----~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          183 ---------KL----NEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             ---------CH----HHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             ---------cH----HHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence                     11    122333333677999999962 11  223334333321 1346788888876

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.49  E-value=0.00047  Score=66.75  Aligned_cols=48  Identities=25%  Similarity=0.239  Sum_probs=37.6

Q ss_pred             CCCcccchhhHHH---HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREE---WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~---l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|++..++.   +.+.+..+....+.+.|+|++|+|||+||+.+.+.
T Consensus        43 ~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           43 SQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             hhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999988776   45556655444467889999999999999999873

>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=97.47  E-value=0.00018  Score=69.78  Aligned_cols=48  Identities=15%  Similarity=0.063  Sum_probs=38.1

Q ss_pred             CCCCcccchhhHHHHHHHHhc----C------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          165 PRLDISEFERAREEWFDLLIE----G------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~----~------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|.+..++.|.+.+..    .      ....+.+.|+|++|+|||+||+.+.+
T Consensus        82 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~  139 (357)
T 3d8b_A           82 NWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIAS  139 (357)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            345689999999999887753    1      12356788999999999999999987

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.47  E-value=0.00051  Score=67.33  Aligned_cols=49  Identities=16%  Similarity=0.112  Sum_probs=38.5

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC----------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          164 QPRLDISEFERAREEWFDLLIEG----------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-.+++|.+..++.|.+++...          ....+-+.|+|++|+|||+||+.+.+
T Consensus       112 ~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~  170 (389)
T 3vfd_A          112 VKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAA  170 (389)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHH
T ss_pred             CChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            34467999999999998887321          11245688999999999999999987

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.45  E-value=7.8e-05  Score=64.33  Aligned_cols=44  Identities=14%  Similarity=0.062  Sum_probs=37.8

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|++.+.+.+.+.+....  .+.+.|+|++|+||||||+.+.+
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~~--~~~vll~G~~G~GKT~la~~~~~   65 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRRT--KNNPILLGDPGVGKTAIVEGLAI   65 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEESCGGGCHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCCC--CCceEEECCCCCCHHHHHHHHHH
Confidence            468999999999999997643  44568999999999999999887

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.40  E-value=9.2e-05  Score=65.41  Aligned_cols=39  Identities=23%  Similarity=0.083  Sum_probs=28.6

Q ss_pred             hHHHHHHHHhcCCCC--cEEEEEEecCCCchHHHHHHhhcC
Q 040913          175 AREEWFDLLIEGPIG--LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~--~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+.+.+++......  ...+.|+|++|+||||||+.+++.
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~   77 (202)
T 2w58_A           37 AIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANE   77 (202)
T ss_dssp             HHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            445556666554322  267889999999999999999983

>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=97.40  E-value=0.00022  Score=67.97  Aligned_cols=37  Identities=22%  Similarity=0.010  Sum_probs=27.4

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+..++..+......+.|+|++|+||||||+.+.+
T Consensus        23 ~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~   59 (324)
T 1l8q_A           23 YEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGN   59 (324)
T ss_dssp             HHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHH
T ss_pred             HHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            3445555554433456688999999999999999988

>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=97.38  E-value=0.00062  Score=65.92  Aligned_cols=96  Identities=22%  Similarity=0.222  Sum_probs=56.9

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFDLLIEG----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRS  233 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~  233 (425)
                      ..-.+++|.+..++.|.+.+...          ....+-|.++|++|+|||+||+.+.+  .....|-..-  ..++...
T Consensus        48 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~--~~~~~~~~v~--~~~l~~~  123 (355)
T 2qp9_X           48 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVAT--EANSTFFSVS--SSDLVSK  123 (355)
T ss_dssp             CCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHH--HHTCEEEEEE--HHHHHSC
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHH--HhCCCEEEee--HHHHhhh
Confidence            34457899999999998876321          12234578899999999999999998  4433331110  1111111


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      .         .......+...+...-..+..+|+||++.
T Consensus       124 ~---------~g~~~~~~~~~f~~a~~~~~~vl~iDEid  153 (355)
T 2qp9_X          124 W---------MGESEKLVKQLFAMARENKPSIIFIDQVD  153 (355)
T ss_dssp             C------------CHHHHHHHHHHHHHTSSEEEEEECGG
T ss_pred             h---------cchHHHHHHHHHHHHHHcCCeEEEEechH
Confidence            0         01122223333333334678999999996

>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=97.34  E-value=0.00065  Score=67.85  Aligned_cols=50  Identities=16%  Similarity=0.163  Sum_probs=38.8

Q ss_pred             CCCCCCcccchhhHHHHHHHHhc----C------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          163 GQPRLDISEFERAREEWFDLLIE----G------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~----~------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...-.+++|.+..++.|.+.+..    +      ....+-|.++|++|+|||+||+.+.+
T Consensus       130 ~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~  189 (444)
T 2zan_A          130 NVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVAT  189 (444)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            34446789999999999887631    1      12346788999999999999999998

>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=97.33  E-value=0.00013  Score=67.52  Aligned_cols=47  Identities=13%  Similarity=-0.074  Sum_probs=33.9

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..++|.+..+.++.+.+..-......|.|+|.+|+|||+||+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHh
Confidence            45789999999888777642222345679999999999999999874

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.27  E-value=0.00044  Score=64.89  Aligned_cols=48  Identities=17%  Similarity=0.159  Sum_probs=38.1

Q ss_pred             CCCCcccchhhHHHHHHHHhcC----------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          165 PRLDISEFERAREEWFDLLIEG----------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~----------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|.+..++.+.+.+..+          ....+.+.|+|++|+||||||+.+.+
T Consensus        19 ~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~   76 (297)
T 3b9p_A           19 EWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVAT   76 (297)
T ss_dssp             CGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHH
T ss_pred             CHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHH
Confidence            3456999999999998877431          11245788999999999999999988

>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=97.27  E-value=0.0002  Score=66.16  Aligned_cols=49  Identities=22%  Similarity=0.162  Sum_probs=35.9

Q ss_pred             CCCCCcccchhhHHHHHHHHhc----------CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          164 QPRLDISEFERAREEWFDLLIE----------GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~----------~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-.+++|.+..++.+.+.+..          +....+-+.++|++|+|||+||+.+.+
T Consensus         8 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   66 (268)
T 2r62_A            8 VRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAG   66 (268)
T ss_dssp             CCSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHH
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            3446799999888888776541          111123367999999999999999988

>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=97.19  E-value=0.0011  Score=63.53  Aligned_cols=118  Identities=13%  Similarity=0.117  Sum_probs=67.6

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc-cccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF-YFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~-~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      .+++|.+..++.|...+..+.  .+.+.++|++|+||||+|+.+.+.  +.. .+..  .     ...+..      ...
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g~--~~~~ll~Gp~G~GKTtla~~la~~--l~~~~~~~--~-----~~~~~~------~~~   87 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALARE--IYGKNYSN--M-----VLELNA------SDD   87 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHH--HHTTSHHH--H-----EEEECT------TSC
T ss_pred             HHhcCcHHHHHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHH--HcCCCccc--e-----EEEEcC------ccc
Confidence            457888888888888888764  223789999999999999998872  211 0000  0     000000      011


Q ss_pred             CCHHHHHHHHHHHh------cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          246 EDYKLKKSILRDFL------TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       246 ~~~~~l~~~l~~~l------~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      .....+.+.+....      .+.+-++|+|++.. +....+.+...+......+++|++|...
T Consensus        88 ~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~~~~~L~~~le~~~~~~~~il~~n~~  150 (340)
T 1sxj_C           88 RGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYA  150 (340)
T ss_dssp             CSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCG
T ss_pred             ccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHHHHHHHHHHHhcCCCCeEEEEEecCc
Confidence            12333333333332      23467899999852 3345555555544334456777776543

>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=97.19  E-value=0.0011  Score=66.92  Aligned_cols=93  Identities=16%  Similarity=0.145  Sum_probs=58.3

Q ss_pred             CCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHh
Q 040913          166 RLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSL  234 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l  234 (425)
                      -.+++|.+..+++|.+++...           .....-+.|+|++|+|||+||+.+.+  +....|-..-  ..++...+
T Consensus       203 ~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~--~~~~~fv~vn--~~~l~~~~  278 (489)
T 3hu3_A          203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAFFFLIN--GPEIMSKL  278 (489)
T ss_dssp             GGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHH--HCSSEEEEEE--HHHHHTSC
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHH--HhCCCEEEEE--chHhhhhh
Confidence            346899999999998877532           22345688999999999999999988  4444441100  11111110


Q ss_pred             CCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEeccc
Q 040913          235 MPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDV  271 (425)
Q Consensus       235 ~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdv  271 (425)
                               .......+...+.....++..+|+||++
T Consensus       279 ---------~g~~~~~~~~~f~~A~~~~p~iLfLDEI  306 (489)
T 3hu3_A          279 ---------AGESESNLRKAFEEAEKNAPAIIFIDEL  306 (489)
T ss_dssp             ---------TTHHHHHHHHHHHHHHHTCSEEEEEESH
T ss_pred             ---------cchhHHHHHHHHHHHHhcCCcEEEecch
Confidence                     1112233444444555567889999999

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.13  E-value=0.0013  Score=60.28  Aligned_cols=96  Identities=18%  Similarity=0.182  Sum_probs=54.1

Q ss_pred             CCCCCcccchhhHHHHHHHH---hcCC-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFDLL---IEGP-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRS  233 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L---~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~  233 (425)
                      ..-.+++|.+..++.+.+.+   ....       ...+-+.|+|++|+||||||+.+.+.  ....|-.           
T Consensus         9 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~--~~~~~~~-----------   75 (257)
T 1lv7_A            9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE--AKVPFFT-----------   75 (257)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHH--HTCCEEE-----------
T ss_pred             CCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHH--cCCCEEE-----------
Confidence            34457899988887776543   2211       12334789999999999999999873  2222210           


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      +....-...........+...+.........++++|++.
T Consensus        76 i~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~il~iDeid  114 (257)
T 1lv7_A           76 ISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEID  114 (257)
T ss_dssp             ECSCSSTTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHH
T ss_pred             EeHHHHHHHhhhhhHHHHHHHHHHHHHcCCeeehhhhhh
Confidence            000000000111223344444444445567899999983

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.05  E-value=0.00057  Score=64.44  Aligned_cols=45  Identities=16%  Similarity=0.133  Sum_probs=36.4

Q ss_pred             CcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.+..++.+...+...       ......+.++|++|+||||+|+.+.+
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~   69 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA   69 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHH
Confidence            4789999988888777653       12246899999999999999999887

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=97.02  E-value=0.0014  Score=65.78  Aligned_cols=96  Identities=13%  Similarity=0.127  Sum_probs=54.7

Q ss_pred             CCCCCcccchhhHHHHHHHHh---cC-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFDLLI---EG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRS  233 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~---~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~  233 (425)
                      ..-.+++|.+..++++.+.+.   ..       -...+-|.++|++|+||||||+.+.+  +....|-..-  .    ..
T Consensus        13 ~~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~--~~~~~f~~is--~----~~   84 (476)
T 2ce7_A           13 VTFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAG--EANVPFFHIS--G----SD   84 (476)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHH--HHTCCEEEEE--G----GG
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH--HcCCCeeeCC--H----HH
Confidence            344578999988777766543   21       01123477999999999999999988  3333331100  0    00


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      +...     ........+...+.....+...+|+||++.
T Consensus        85 ~~~~-----~~g~~~~~~r~lf~~A~~~~p~ILfIDEid  118 (476)
T 2ce7_A           85 FVEL-----FVGVGAARVRDLFAQAKAHAPCIVFIDEID  118 (476)
T ss_dssp             TTTC-----CTTHHHHHHHHHHHHHHHTCSEEEEEETGG
T ss_pred             HHHH-----HhcccHHHHHHHHHHHHhcCCCEEEEechh
Confidence            0000     001112233344444445678999999995

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.99  E-value=0.0012  Score=70.49  Aligned_cols=45  Identities=13%  Similarity=0.109  Sum_probs=37.9

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|++.++++++..|....  ..-+.++|++|+|||++|+.+.+
T Consensus       179 ld~iiG~~~~i~~l~~~l~~~~--~~~vLL~G~pGtGKT~la~~la~  223 (758)
T 3pxi_A          179 LDPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQ  223 (758)
T ss_dssp             SCCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHH
T ss_pred             CCCccCchHHHHHHHHHHhCCC--CCCeEEECCCCCCHHHHHHHHHH
Confidence            3469999999999999998754  23367999999999999999887

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.99  E-value=0.0011  Score=62.32  Aligned_cols=24  Identities=13%  Similarity=0.105  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..+.++|++|+|||+||+.+.+
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~   58 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFR   58 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356788899999999999999998

>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=96.91  E-value=0.0037  Score=66.74  Aligned_cols=44  Identities=20%  Similarity=0.108  Sum_probs=37.6

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++||+.++.++++.|....  ..-+.++|.+|+||||+|+.+.+
T Consensus       186 d~~iGr~~~i~~l~~~l~~~~--~~~vlL~G~~GtGKT~la~~la~  229 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRRR--KNNPLLVGESGVGKTAIAEGLAW  229 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhccC--CCCeEEEcCCCCCHHHHHHHHHH
Confidence            468999999999999998654  33457899999999999999887

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.76  E-value=0.0023  Score=54.93  Aligned_cols=22  Identities=41%  Similarity=0.684  Sum_probs=19.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -.+++|+|+.|+|||||++..+
T Consensus         9 gei~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHc
Confidence            4689999999999999999644

>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=96.74  E-value=0.0079  Score=56.78  Aligned_cols=115  Identities=7%  Similarity=-0.065  Sum_probs=66.4

Q ss_pred             cchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc-ccc-ccccchHHHHHHHHHHhCCCCCCCccCCCCH
Q 040913          171 EFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN-HVK-FYFDCLAWILDDIIRSLMPPSRVTVIIGEDY  248 (425)
Q Consensus       171 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~-~~~-~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~  248 (425)
                      |-++..+.|.+.+..+.  .+..-++|+.|+||||+|..+.+.. ... .|.+.. .        +..     .......
T Consensus         1 g~~~~~~~L~~~i~~~~--~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~-~--------l~~-----~~~~~~i   64 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVL-E--------IDP-----EGENIGI   64 (305)
T ss_dssp             ---CHHHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEE-E--------ECC-----SSSCBCH
T ss_pred             ChHHHHHHHHHHHHCCC--CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEE-E--------EcC-----CcCCCCH
Confidence            34555677777777665  6788899999999999999987621 010 111110 0        000     0012334


Q ss_pred             HHHHHHHHHHh----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          249 KLKKSILRDFL----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       249 ~~l~~~l~~~l----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      +++.+.+...-    .+++-++|+|++.. +....+.+...+....+.+.+|++|.+.
T Consensus        65 d~ir~li~~~~~~p~~~~~kvviIdead~lt~~a~naLLk~LEep~~~t~fIl~t~~~  122 (305)
T 2gno_A           65 DDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRW  122 (305)
T ss_dssp             HHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             HHHHHHHHHHhhccccCCceEEEeccHHHhCHHHHHHHHHHHhCCCCCeEEEEEECCh
Confidence            44433322221    24677999999963 4466677777766555677877776553

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=96.71  E-value=0.0012  Score=66.43  Aligned_cols=44  Identities=14%  Similarity=0.128  Sum_probs=37.3

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.++|++.+++.+++.|....  ..-+.++|++|+|||++|+.+.+
T Consensus       180 d~iiGr~~~i~~l~~~l~r~~--~~~~LL~G~pG~GKT~la~~la~  223 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRRT--KNNPVLIGEPGVGKTAIAEGLAQ  223 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCSS--SCEEEEESCTTTTTHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhccC--CCCeEEECCCCCCHHHHHHHHHH
Confidence            469999999999999998744  23356899999999999999887

>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=96.66  E-value=0.0097  Score=56.85  Aligned_cols=125  Identities=10%  Similarity=0.041  Sum_probs=66.5

Q ss_pred             hhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccc------cccchHHHHHHHHHHhCCCCCCCc----
Q 040913          173 ERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKF------YFDCLAWILDDIIRSLMPPSRVTV----  242 (425)
Q Consensus       173 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~------~F~~~~wv~~~il~~l~~~~~~~~----  242 (425)
                      ++..+.+.+.+..+. -.+.+-++|+.|+||||+|+.+.+.-....      +-.|..  -+.+...-......-.    
T Consensus         8 ~~~~~~l~~~i~~~~-~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~--c~~~~~~~~~d~~~~~~~~~   84 (334)
T 1a5t_A            8 RPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRG--CQLMQAGTHPDYYTLAPEKG   84 (334)
T ss_dssp             HHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHH--HHHHHHTCCTTEEEECCCTT
T ss_pred             HHHHHHHHHHHHcCC-cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHH--HHHHhcCCCCCEEEEecccc
Confidence            455666677666543 345688999999999999988765211100      001111  0011110000000000    


Q ss_pred             cCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          243 IIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       243 ~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      ......+++.+ +.+.+     .+++-++|+|++.. +.+..+.+...+.....++.+|++|.+.
T Consensus        85 ~~~~~i~~ir~-l~~~~~~~~~~~~~kvviIdead~l~~~a~naLLk~lEep~~~~~~Il~t~~~  148 (334)
T 1a5t_A           85 KNTLGVDAVRE-VTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREP  148 (334)
T ss_dssp             CSSBCHHHHHH-HHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             CCCCCHHHHHH-HHHHHhhccccCCcEEEEECchhhcCHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence            11233444433 33333     35678999999963 3456667777776555567777777664

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.58  E-value=0.0037  Score=61.93  Aligned_cols=98  Identities=14%  Similarity=0.087  Sum_probs=58.4

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhc----C-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLIE----G-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~i  230 (425)
                      |.+.-.++.|.++.++.|.+.+.-    +       -..++=|.++|++|+|||+||+++.+  +...+|-..--     
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~--e~~~~~~~v~~-----  248 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAA--TIGANFIFSPA-----  248 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH--HHTCEEEEEEG-----
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHH--HhCCCEEEEeh-----
Confidence            444556788999988888776542    1       13456678999999999999999998  44444421000     


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                       ..+...     ....+...+...+...-....++|++|++.
T Consensus       249 -s~l~sk-----~~Gese~~ir~~F~~A~~~~P~IifiDEiD  284 (437)
T 4b4t_L          249 -SGIVDK-----YIGESARIIREMFAYAKEHEPCIIFMDEVD  284 (437)
T ss_dssp             -GGTCCS-----SSSHHHHHHHHHHHHHHHSCSEEEEEECCC
T ss_pred             -hhhccc-----cchHHHHHHHHHHHHHHhcCCceeeeeccc
Confidence             001110     111122222333333334678999999996

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.56  E-value=0.0033  Score=62.12  Aligned_cols=98  Identities=16%  Similarity=0.140  Sum_probs=58.8

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhc----C-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLIE----G-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~i  230 (425)
                      |.+.-.++.|.++.++.|.+.+.-    +       -...+=|.++|++|+|||+||+++.+  ....+|-..-.     
T Consensus       167 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~--~~~~~~~~v~~-----  239 (428)
T 4b4t_K          167 PDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVAN--STKAAFIRVNG-----  239 (428)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHH--HHTCEEEEEEG-----
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHH--HhCCCeEEEec-----
Confidence            445556788999999988776542    1       13355678999999999999999998  44444421000     


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                       ..+..     .....+...+...+...-....++|++|++.
T Consensus       240 -~~l~~-----~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD  275 (428)
T 4b4t_K          240 -SEFVH-----KYLGEGPRMVRDVFRLARENAPSIIFIDEVD  275 (428)
T ss_dssp             -GGTCC-----SSCSHHHHHHHHHHHHHHHTCSEEEEEECTH
T ss_pred             -chhhc-----cccchhHHHHHHHHHHHHHcCCCeeechhhh
Confidence             00000     0111122233333333334678999999985

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=96.49  E-value=0.0075  Score=60.89  Aligned_cols=52  Identities=19%  Similarity=0.154  Sum_probs=36.5

Q ss_pred             CCCCCCCcccchhhHHHHHHHHh---cCC-------CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          162 EGQPRLDISEFERAREEWFDLLI---EGP-------IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~---~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +...-.+++|.+..+.++.+...   ...       .-.+-+.|+|++|+||||||+.+.+.
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~   87 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE   87 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHH
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            34445679999888777765543   211       11223889999999999999999883

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.49  E-value=0.0029  Score=61.88  Aligned_cols=98  Identities=14%  Similarity=0.121  Sum_probs=58.1

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhc----C-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLIE----G-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~i  230 (425)
                      |.+.-.++.|.++.+++|.+.+.-    +       -..++=|.++|++|.|||.||+++.+  +...+|-..--     
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~--e~~~~f~~v~~-----  215 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH--HTDCKFIRVSG-----  215 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHH--HHTCEEEEEEG-----
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHH--hhCCCceEEEh-----
Confidence            444556788999998888766542    1       12345677999999999999999998  55444421000     


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                       ..+..     .....+...+...+...-+...++|++|++.
T Consensus       216 -s~l~s-----k~vGese~~vr~lF~~Ar~~aP~IIFiDEiD  251 (405)
T 4b4t_J          216 -AELVQ-----KYIGEGSRMVRELFVMAREHAPSIIFMDEID  251 (405)
T ss_dssp             -GGGSC-----SSTTHHHHHHHHHHHHHHHTCSEEEEEESSS
T ss_pred             -HHhhc-----cccchHHHHHHHHHHHHHHhCCceEeeecch
Confidence             00000     0111122223333333334678999999996

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.46  E-value=0.0023  Score=56.72  Aligned_cols=38  Identities=16%  Similarity=0.136  Sum_probs=28.7

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++|.+.+........+|+|+|+.|+|||||++.+..
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~   44 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAA   44 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            34455555554334578999999999999999998876

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.43  E-value=0.0041  Score=61.74  Aligned_cols=97  Identities=15%  Similarity=0.124  Sum_probs=58.1

Q ss_pred             CCCCCCcccchhhHHHHHHHHhc----C-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHH
Q 040913          163 GQPRLDISEFERAREEWFDLLIE----G-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDII  231 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il  231 (425)
                      .+.-.++.|.++.+++|.+.+.-    +       -...+=|.++|++|+|||+||+++.+  +...+|-..--      
T Consensus       205 ~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~--e~~~~fi~vs~------  276 (467)
T 4b4t_H          205 DVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVAN--RTDATFIRVIG------  276 (467)
T ss_dssp             SCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHH--HHTCEEEEEEG------
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCCCeEEEEh------
Confidence            34446788999999888775432    1       13456678999999999999999998  55444421000      


Q ss_pred             HHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       232 ~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ..+...     ....+...+...+...-....++|++|++.
T Consensus       277 s~L~sk-----~vGesek~ir~lF~~Ar~~aP~IIfiDEiD  312 (467)
T 4b4t_H          277 SELVQK-----YVGEGARMVRELFEMARTKKACIIFFDEID  312 (467)
T ss_dssp             GGGCCC-----SSSHHHHHHHHHHHHHHHTCSEEEEEECCT
T ss_pred             HHhhcc-----cCCHHHHHHHHHHHHHHhcCCceEeecccc
Confidence            001111     111122233333333334678999999996

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.37  E-value=0.0036  Score=61.97  Aligned_cols=58  Identities=14%  Similarity=0.175  Sum_probs=42.5

Q ss_pred             CCCCCCCCcccchhhHHHHHHHHh----cC-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          161 SEGQPRLDISEFERAREEWFDLLI----EG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       161 ~~~~~~~~~vGr~~~~~~l~~~L~----~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      .|.+.-.++.|.++.+++|.+.+.    .+       -..++=|.++|++|+|||+||+++.+  +...+|
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~--e~~~~f  243 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAA--QTNATF  243 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH--HHTCEE
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHH--HhCCCE
Confidence            344555678899999998877643    22       13456678999999999999999998  444444

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=96.27  E-value=0.011  Score=62.87  Aligned_cols=98  Identities=14%  Similarity=0.130  Sum_probs=60.7

Q ss_pred             CCCCCCCcccchhhHHHHHHHHh----cCC-------CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLI----EGP-------IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~----~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~i  230 (425)
                      +.+.-.++.|.++.+++|.+.+.    .++       ..++-|.++|++|+|||+||+.+.+  +...+|-.+-  ..++
T Consensus       199 ~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~--elg~~~~~v~--~~~l  274 (806)
T 3cf2_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAFFFLIN--GPEI  274 (806)
T ss_dssp             SSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHT--TTTCEEEEEE--HHHH
T ss_pred             CCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH--HhCCeEEEEE--hHHh
Confidence            34445568899988888877653    221       2456788999999999999999999  5554442100  0111


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      .    ..     ........+...+....+...++|++|++.
T Consensus       275 ~----sk-----~~gese~~lr~lF~~A~~~~PsIIfIDEiD  307 (806)
T 3cf2_A          275 M----SK-----LAGESESNLRKAFEEAEKNAPAIIFIDELD  307 (806)
T ss_dssp             H----SS-----CTTHHHHHHHHHHHHHTTSCSEEEEEESGG
T ss_pred             h----cc-----cchHHHHHHHHHHHHHHHcCCeEEEEehhc
Confidence            1    11     111223344444444556678999999996

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.26  E-value=0.0046  Score=54.42  Aligned_cols=41  Identities=17%  Similarity=0.078  Sum_probs=32.4

Q ss_pred             chhhHHHHHHHHhcC-CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          172 FERAREEWFDLLIEG-PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       172 r~~~~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      |++..+.|.+.+... .....+|+|.|..|+|||||++.+..
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            3 LRDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             HHHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            455667788777754 23568999999999999999998865

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.25  E-value=0.0018  Score=61.39  Aligned_cols=40  Identities=15%  Similarity=0.150  Sum_probs=28.7

Q ss_pred             hhHHHHHHHHhcCCC-CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          174 RAREEWFDLLIEGPI-GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       174 ~~~~~l~~~L~~~~~-~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+.+.+++..... ....+.++|++|+|||+||+.+++.
T Consensus       135 ~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          135 EAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             HHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHH
Confidence            344455566665322 2456789999999999999999883

>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=96.23  E-value=0.0038  Score=63.55  Aligned_cols=48  Identities=10%  Similarity=-0.012  Sum_probs=39.6

Q ss_pred             CCCcccchhhHHHHHHHHhcCC---------------CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIEGP---------------IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~---------------~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|++..++.+.++|....               ...+.+.|+|++|+||||+|+.+.+.
T Consensus        38 ~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~  100 (516)
T 1sxj_A           38 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE  100 (516)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            3569999999999999997510               13468889999999999999999873

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.22  E-value=0.0055  Score=54.87  Aligned_cols=44  Identities=5%  Similarity=-0.029  Sum_probs=31.1

Q ss_pred             CCcccc---hhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEF---ERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr---~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|.   +...+.+..++..+  ..+.+.|+|++|+||||||+.+.+
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~   74 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACA   74 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHH
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHH
Confidence            456663   34455555555543  356788999999999999999887

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=96.21  E-value=0.0057  Score=65.24  Aligned_cols=46  Identities=13%  Similarity=0.066  Sum_probs=37.1

Q ss_pred             CCcccchhhHHHHHHHHhcCC-------CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGP-------IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~-------~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.+.+.+....       .....+.++|++|+|||+||+.+.+
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~  543 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAE  543 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHH
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            468999999998888876421       2344789999999999999999887

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=96.20  E-value=0.0023  Score=60.04  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=36.5

Q ss_pred             CCcccchhhHHHHHHHHhcC------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.+...+...            ......+.++|++|+|||++|+.+.+
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   72 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   72 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            45899999999998877641            11244577999999999999999987

>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=96.13  E-value=0.0028  Score=60.66  Aligned_cols=46  Identities=17%  Similarity=0.069  Sum_probs=35.2

Q ss_pred             CCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.+-..+...   ......+.++|++|+||||||+.+.+
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~   73 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS   73 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            45788877777776665532   22346789999999999999999988

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=96.07  E-value=0.0055  Score=58.01  Aligned_cols=69  Identities=12%  Similarity=0.073  Sum_probs=42.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccc-cchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEe
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYF-DCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIAL  268 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVL  268 (425)
                      .+++.|+|++|+||||||.++......+-.| +..          .....   .....+.+.....+.+.+...+ +||+
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~----------~eE~v---~~~~~~le~~l~~i~~~l~~~~-LLVI  188 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVR----------FGEPL---SGYNTDFNVFVDDIARAMLQHR-VIVI  188 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEE----------BSCSS---TTCBCCHHHHHHHHHHHHHHCS-EEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEec----------chhhh---hhhhcCHHHHHHHHHHHHhhCC-EEEE
Confidence            4667899999999999999987631111111 110          00000   0011356777777777777666 9999


Q ss_pred             cccC
Q 040913          269 DDVC  272 (425)
Q Consensus       269 Ddvw  272 (425)
                      |++.
T Consensus       189 DsI~  192 (331)
T 2vhj_A          189 DSLK  192 (331)
T ss_dssp             ECCT
T ss_pred             eccc
Confidence            9996

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=96.06  E-value=0.0032  Score=59.47  Aligned_cols=47  Identities=15%  Similarity=-0.000  Sum_probs=37.1

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..++|....+.++.+.+..-......|.|+|.+|+|||++|+.+++.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHh
Confidence            45899999999998887653222345679999999999999999873

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.02  E-value=0.0091  Score=58.69  Aligned_cols=58  Identities=21%  Similarity=0.111  Sum_probs=42.0

Q ss_pred             CCCCCCCCcccchhhHHHHHHHHhc----C-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          161 SEGQPRLDISEFERAREEWFDLLIE----G-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       161 ~~~~~~~~~vGr~~~~~~l~~~L~~----~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      .|.+.-.++.|.++.++.|.+.+.-    +       -...+=|.++|++|.|||.||+++.+  +...+|
T Consensus       176 ~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~--e~~~~f  244 (437)
T 4b4t_I          176 SPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVAN--QTSATF  244 (437)
T ss_dssp             SCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHH--HHTCEE
T ss_pred             CCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHH--HhCCCE
Confidence            3445556788999988888766532    2       12356688999999999999999998  444444

>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=95.99  E-value=0.0038  Score=67.55  Aligned_cols=45  Identities=11%  Similarity=0.112  Sum_probs=38.0

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++||+.++.++++.|....  ..-+.++|.+|+||||||+.+.+
T Consensus       169 ld~viGr~~~i~~l~~~l~~~~--~~~vlL~G~pG~GKT~la~~la~  213 (854)
T 1qvr_A          169 LDPVIGRDEEIRRVIQILLRRT--KNNPVLIGEPGVGKTAIVEGLAQ  213 (854)
T ss_dssp             SCCCCSCHHHHHHHHHHHHCSS--CCCCEEEECTTSCHHHHHHHHHH
T ss_pred             CcccCCcHHHHHHHHHHHhcCC--CCceEEEcCCCCCHHHHHHHHHH
Confidence            3568999999999999998754  23457899999999999999887

>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=95.94  E-value=0.0074  Score=65.29  Aligned_cols=45  Identities=16%  Similarity=0.133  Sum_probs=36.1

Q ss_pred             CcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.+..++.+...+...       ......+.|+|++|+|||++|+.+.+
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~  610 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA  610 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHH
Confidence            4789999888887777542       12346788999999999999999887

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.93  E-value=0.0075  Score=56.53  Aligned_cols=26  Identities=15%  Similarity=0.097  Sum_probs=22.6

Q ss_pred             CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          187 PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       187 ~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....+|+|+|..|+||||||+.+..
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~   53 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYN   53 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            44678999999999999999988765

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=95.92  E-value=0.0038  Score=52.94  Aligned_cols=20  Identities=30%  Similarity=0.327  Sum_probs=18.7

Q ss_pred             EEEEEEecCCCchHHHHHHh
Q 040913          191 SVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v  210 (425)
                      .+|.|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            47899999999999999999

>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=95.86  E-value=0.006  Score=58.99  Aligned_cols=44  Identities=18%  Similarity=0.191  Sum_probs=35.0

Q ss_pred             cccchhhHHHHHHHHhc-------------CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          169 ISEFERAREEWFDLLIE-------------GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~-------------~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.+..++.+...+..             .......+.++|++|+|||++|+.+.+
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~   73 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLAR   73 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            68999999988887731             111345688999999999999999988

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=95.80  E-value=0.0058  Score=52.96  Aligned_cols=24  Identities=17%  Similarity=0.152  Sum_probs=21.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+|+|+|++|+|||||++.+...
T Consensus         9 g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            9 GNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhc
Confidence            468999999999999999999874

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.72  E-value=0.02  Score=57.76  Aligned_cols=42  Identities=19%  Similarity=0.143  Sum_probs=35.7

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .++|.+..++.+...+..+.    -|.++|++|+|||+||+.+.+.
T Consensus        23 ~ivGq~~~i~~l~~al~~~~----~VLL~GpPGtGKT~LAraLa~~   64 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSGE----SVFLLGPPGIAKSLIARRLKFA   64 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHTC----EEEEECCSSSSHHHHHHHGGGG
T ss_pred             hhHHHHHHHHHHHHHHhcCC----eeEeecCchHHHHHHHHHHHHH
Confidence            38899999988888777643    5778999999999999999984

>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=95.70  E-value=0.0095  Score=59.54  Aligned_cols=48  Identities=23%  Similarity=0.194  Sum_probs=36.4

Q ss_pred             CCCcccchhhHHHHH---HHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWF---DLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~---~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+++|.+..++.+.   +++..+....+-+.++|++|+|||+||+.+.+.
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~iLl~GppGtGKT~la~ala~~   86 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQE   86 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCCCeEEEECCCcCCHHHHHHHHHHH
Confidence            367999998887654   444444434456789999999999999999883

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=95.67  E-value=0.005  Score=52.69  Aligned_cols=22  Identities=9%  Similarity=0.075  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|++|+||||+|+.+.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5788999999999999999887

>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=95.65  E-value=0.0079  Score=54.86  Aligned_cols=49  Identities=22%  Similarity=0.235  Sum_probs=34.0

Q ss_pred             CCCCCcccchhhHHHHHHHHhc--C---------CCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          164 QPRLDISEFERAREEWFDLLIE--G---------PIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~--~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-.+++|.+..+.++.+....  .         ....+ +.|+|++|+|||||++.+.+.
T Consensus        13 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g-~ll~G~~G~GKTtl~~~i~~~   72 (254)
T 1ixz_A           13 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   72 (254)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCCCCHHHHHHHHHHH
Confidence            3345688988777666554321  1         11223 889999999999999999883

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.63  E-value=0.0062  Score=52.06  Aligned_cols=22  Identities=14%  Similarity=0.335  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            5789999999999999999887

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.61  E-value=0.0075  Score=56.00  Aligned_cols=48  Identities=25%  Similarity=0.237  Sum_probs=32.9

Q ss_pred             CCCCCcccchhhHHHHHHHHhcC------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          164 QPRLDISEFERAREEWFDLLIEG------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.-.++.|.++.++.|.+.+...            ....+ +.++|++|+||||||+.+..
T Consensus         7 ~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~G-vlL~Gp~GtGKTtLakala~   66 (274)
T 2x8a_A            7 VTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAG-VLLAGPPGCGKTLLAKAVAN   66 (274)
T ss_dssp             -----CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSE-EEEESSTTSCHHHHHHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCe-EEEECCCCCcHHHHHHHHHH
Confidence            44456888888888877654311            11233 89999999999999999987

>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=95.58  E-value=0.0055  Score=51.95  Aligned_cols=22  Identities=14%  Similarity=0.117  Sum_probs=20.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|+.|+||||+|+.+..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999876

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.56  E-value=0.0057  Score=52.80  Aligned_cols=23  Identities=9%  Similarity=0.218  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~   27 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLIT   27 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35899999999999999999876

>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=95.55  E-value=0.0023  Score=61.84  Aligned_cols=110  Identities=15%  Similarity=0.097  Sum_probs=62.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCC----ccCCCCHHHHHHHHHHHhcCCeEE
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVT----VIIGEDYKLKKSILRDFLTNKKYF  265 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~----~~~~~~~~~l~~~l~~~l~~kr~L  265 (425)
                      -.+++|+|+.|+|||||.+.+...  +.......+....+-. .+.......    .....+.......+...|....=+
T Consensus       123 ~g~i~I~GptGSGKTTlL~~l~g~--~~~~~~~~i~t~ed~~-e~~~~~~~~~v~q~~~~~~~~~~~~~La~aL~~~Pdv  199 (356)
T 3jvv_A          123 RGLVLVTGPTGSGKSTTLAAMLDY--LNNTKYHHILTIEDPI-EFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDI  199 (356)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHH--HHHHCCCEEEEEESSC-CSCCCCSSSEEEEEEBTTTBSCHHHHHHHHTTSCCSE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc--ccCCCCcEEEEccCcH-HhhhhccccceeeeeeccccCCHHHHHHHHhhhCcCE
Confidence            459999999999999999987652  1100000000000000 000000000    000111133455788889888999


Q ss_pred             EEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH
Q 040913          266 IALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       266 lVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~  306 (425)
                      |++|.+. +.+.++.+....   ..|..||+||...+.+..
T Consensus       200 illDEp~-d~e~~~~~~~~~---~~G~~vl~t~H~~~~~~~  236 (356)
T 3jvv_A          200 ILVGEMR-DLETIRLALTAA---ETGHLVFGTLHTTSAAKT  236 (356)
T ss_dssp             EEESCCC-SHHHHHHHHHHH---HTTCEEEEEESCSSHHHH
T ss_pred             EecCCCC-CHHHHHHHHHHH---hcCCEEEEEEccChHHHH
Confidence            9999998 777776654442   236679999988776643

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=95.51  E-value=0.0057  Score=51.26  Aligned_cols=23  Identities=9%  Similarity=0.052  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..+.|+|..|+|||||++.+++
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~   58 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVA   58 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999987

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.48  E-value=0.0065  Score=53.28  Aligned_cols=23  Identities=13%  Similarity=0.108  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|+|+.|+||||+++.+..
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999886

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=95.48  E-value=0.0094  Score=50.87  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|+|+.|+||||+++.+..
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999998875

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=95.42  E-value=0.0086  Score=52.55  Aligned_cols=23  Identities=22%  Similarity=0.182  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|+|+.|+|||||++.+..
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~   47 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQ   47 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999999877

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=95.40  E-value=0.0061  Score=51.89  Aligned_cols=22  Identities=9%  Similarity=0.166  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|+|+|+.|+|||||++.+..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999877

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=95.40  E-value=0.0099  Score=55.09  Aligned_cols=50  Identities=22%  Similarity=0.223  Sum_probs=35.2

Q ss_pred             CCCCCCcccchhhHHHHHHHHhc--C---------CCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          163 GQPRLDISEFERAREEWFDLLIE--G---------PIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~--~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-.+++|.+..+.++.+....  .         ..... +.|+|++|+|||||++.+.+.
T Consensus        36 ~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~g-vll~Gp~GtGKTtl~~~i~~~   96 (278)
T 1iy2_A           36 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKG-VLLVGPPGVGKTHLARAVAGE   96 (278)
T ss_dssp             CCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCE-EEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCe-EEEECCCcChHHHHHHHHHHH
Confidence            34456789988777776554331  1         11123 889999999999999999883

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.32  E-value=0.01  Score=52.39  Aligned_cols=24  Identities=21%  Similarity=0.147  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|+.|+|||||++.+..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~   28 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALAR   28 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999998876

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.30  E-value=0.0087  Score=52.42  Aligned_cols=23  Identities=22%  Similarity=0.231  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~   29 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVK   29 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECcCCCCHHHHHHHHHh
Confidence            35899999999999999998875

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.29  E-value=0.0094  Score=51.45  Aligned_cols=22  Identities=14%  Similarity=0.188  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|+.|+||||+|+.+.+
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999877

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.28  E-value=0.0098  Score=56.52  Aligned_cols=42  Identities=10%  Similarity=-0.017  Sum_probs=35.5

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|++..++.+...+..+.    -+.++|++|+|||+||+.+.+
T Consensus        27 ~~i~g~~~~~~~l~~~l~~~~----~vll~G~pGtGKT~la~~la~   68 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICTGG----HILLEGVPGLAKTLSVNTLAK   68 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHHTC----CEEEESCCCHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHcCC----eEEEECCCCCcHHHHHHHHHH
Confidence            358899999999888877642    477899999999999999987

>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=95.26  E-value=0.011  Score=51.18  Aligned_cols=23  Identities=9%  Similarity=0.137  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|++|+||||+++.+..
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999876

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.24  E-value=0.0079  Score=51.83  Aligned_cols=23  Identities=17%  Similarity=0.255  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.|.|+|+.|+||||+|+.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45788999999999999999876

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=95.23  E-value=0.03  Score=54.05  Aligned_cols=23  Identities=13%  Similarity=0.151  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~G   76 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNL   76 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHhc
Confidence            46899999999999999998864

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=95.22  E-value=0.013  Score=56.38  Aligned_cols=82  Identities=15%  Similarity=0.104  Sum_probs=47.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhc-
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLT-  260 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~-  260 (425)
                      .-.++.|.|++|+|||||+.++........  ..++|+      -......++...... .....+.++....+...++ 
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~~~~~g--g~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~~  137 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAEAQKMG--GVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDELVRS  137 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhcC--CeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhhh
Confidence            457999999999999999988875311100  011122      111344444332211 1123456677666666664 


Q ss_pred             CCeEEEEecccC
Q 040913          261 NKKYFIALDDVC  272 (425)
Q Consensus       261 ~kr~LlVLDdvw  272 (425)
                      .+.-++|+|.+-
T Consensus       138 ~~~dlvVIDSi~  149 (356)
T 3hr8_A          138 GVVDLIVVDSVA  149 (356)
T ss_dssp             SCCSEEEEECTT
T ss_pred             cCCCeEEehHhh
Confidence            455689999884

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.19  E-value=0.012  Score=51.68  Aligned_cols=25  Identities=16%  Similarity=0.178  Sum_probs=22.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+|+|+|+.|+||||+++.+...
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHh
Confidence            3678999999999999999998773

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=95.16  E-value=0.011  Score=51.18  Aligned_cols=22  Identities=14%  Similarity=0.157  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999975

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=95.15  E-value=0.016  Score=56.23  Aligned_cols=45  Identities=16%  Similarity=0.147  Sum_probs=34.3

Q ss_pred             CcccchhhHHHHHHHHhc----------------------------CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIE----------------------------GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~----------------------------~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.+..++.|...+..                            .......+.++|++|+|||++|+.+.+
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~   94 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   94 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHH
Confidence            478988888888777621                            011234578999999999999999987

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.14  E-value=0.0097  Score=52.19  Aligned_cols=23  Identities=26%  Similarity=0.293  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|+|+.|+|||||++.+..
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999876

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=95.11  E-value=0.013  Score=51.15  Aligned_cols=25  Identities=20%  Similarity=0.101  Sum_probs=22.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+|+|+|+.|+||||+++.+...
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHC
Confidence            4689999999999999999999873

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.09  E-value=0.022  Score=53.13  Aligned_cols=38  Identities=16%  Similarity=0.238  Sum_probs=27.3

Q ss_pred             hHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          175 AREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       175 ~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++++..+...   .....+|.|.|++|+||||+|+.+..
T Consensus        15 ~~~~~~~~~l~~~~~~~~~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           15 RLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             HHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            334444444433   23467899999999999999999876

>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=95.06  E-value=0.011  Score=52.26  Aligned_cols=24  Identities=13%  Similarity=0.261  Sum_probs=21.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+|+|+|+.|+|||||++.+...
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhh
Confidence            568999999999999999998763

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=95.06  E-value=0.011  Score=52.80  Aligned_cols=22  Identities=23%  Similarity=0.262  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|+|+|+.|+||||+++.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999876

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.04  E-value=0.011  Score=51.77  Aligned_cols=23  Identities=13%  Similarity=0.228  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|+|+.|+||||+++.+..
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~   28 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFE   28 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999876

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.04  E-value=0.022  Score=50.54  Aligned_cols=36  Identities=19%  Similarity=0.248  Sum_probs=26.2

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.+-..+...  ....|.|+|.+|+|||||+..+...
T Consensus        26 a~~~r~~~~~~--~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           26 ADKNRKLLNKH--GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             HHHHHHHHHHT--TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC--CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            34444444332  4788999999999999999887763

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=95.03  E-value=0.012  Score=51.69  Aligned_cols=22  Identities=14%  Similarity=0.151  Sum_probs=19.9

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|+|+|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3699999999999999999876

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.02  E-value=0.011  Score=51.50  Aligned_cols=21  Identities=24%  Similarity=0.408  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|+.|+||||+++.+.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            589999999999999999877

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.01  E-value=0.0092  Score=52.32  Aligned_cols=23  Identities=13%  Similarity=0.228  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~   40 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAE   40 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999998876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.01  E-value=0.022  Score=54.11  Aligned_cols=39  Identities=10%  Similarity=0.024  Sum_probs=27.4

Q ss_pred             hhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          174 RAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       174 ~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....+...+...  .....+|+|.|..|+|||||++.+..
T Consensus        74 ~~l~~~~~~~l~~~~~~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           74 QTLQQATYQFLGKPEPKVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             HHHHHHHHHHHTCCCCCCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3334444334333  34577999999999999999988754

>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=95.01  E-value=0.011  Score=53.10  Aligned_cols=108  Identities=16%  Similarity=0.034  Sum_probs=56.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccc----cccchHHHHHHHHHHhCCCCCCC--ccCCCCHHHHHHHHHHHhcCCe
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKF----YFDCLAWILDDIIRSLMPPSRVT--VIIGEDYKLKKSILRDFLTNKK  263 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~----~F~~~~wv~~~il~~l~~~~~~~--~~~~~~~~~l~~~l~~~l~~kr  263 (425)
                      -.++.|.|..|+||||++..+.+......    .|..... .+ -..++.......  ........++.+.+.+.+.+.+
T Consensus        12 G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d-~r-~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~   89 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKID-TR-SIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDE   89 (223)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-GG-GCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTT
T ss_pred             cEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccC-ch-HHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCC
Confidence            57888999999999998876654221110    1110000 00 001122221110  1112234556666666555555


Q ss_pred             E-EEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          264 Y-FIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       264 ~-LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      + +||+|.+.+ +.+..+.+...- +  .|-.||+|-+..+
T Consensus        90 ~dvViIDEaQ~l~~~~ve~l~~L~-~--~gi~Vil~Gl~~d  127 (223)
T 2b8t_A           90 TKVIGIDEVQFFDDRICEVANILA-E--NGFVVIISGLDKN  127 (223)
T ss_dssp             CCEEEECSGGGSCTHHHHHHHHHH-H--TTCEEEEECCSBC
T ss_pred             CCEEEEecCccCcHHHHHHHHHHH-h--CCCeEEEEecccc
Confidence            5 999999963 234444443322 2  2788999998544

>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=95.01  E-value=0.011  Score=50.86  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|++|+||||+++.+.+
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999877

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.99  E-value=0.013  Score=50.64  Aligned_cols=23  Identities=26%  Similarity=0.211  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998876

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=94.99  E-value=0.013  Score=50.70  Aligned_cols=22  Identities=18%  Similarity=0.286  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .++|+|+.|+|||||++.+...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5789999999999999988763

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=94.97  E-value=0.014  Score=51.33  Aligned_cols=22  Identities=23%  Similarity=0.194  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|+|+|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999866

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=94.96  E-value=0.024  Score=54.41  Aligned_cols=43  Identities=16%  Similarity=0.188  Sum_probs=31.5

Q ss_pred             ccchhhHHHHHHHHhcC--CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          170 SEFERAREEWFDLLIEG--PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~--~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      |+.+.-.+++++.+...  ......|.++|++|+||||+++.+..
T Consensus         2 ~~~~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A            2 VDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             CCHHHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHH
Confidence            44555666677666432  23456789999999999999998877

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=94.95  E-value=0.013  Score=55.89  Aligned_cols=45  Identities=11%  Similarity=0.035  Sum_probs=32.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.+..+..+...+....  ..-+-++|.+|+|||+||+.+.+
T Consensus        23 f~~i~G~~~~~~~l~~~~~~~~--~~~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           23 FSAIVGQEDMKLALLLTAVDPG--IGGVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGG--GCCEEEECCGGGCTTHHHHHHHH
T ss_pred             chhccChHHHHHHHHHHhhCCC--CceEEEECCCCccHHHHHHHHHH
Confidence            3458998886666544444322  22378999999999999999987

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.91  E-value=0.019  Score=52.38  Aligned_cols=40  Identities=18%  Similarity=0.091  Sum_probs=29.0

Q ss_pred             hhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          173 ERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       173 ~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +...+.++..+..+   .....+|.++|++|+||||+|+.+..
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~i~l~G~~GsGKSTla~~L~~   54 (253)
T 2p5t_B           12 KHALARNLRSLTRGKKSSKQPIAILLGGQSGAGKTTIHRIKQK   54 (253)
T ss_dssp             HHHHHHHHHHHHTTCCCCSSCEEEEEESCGGGTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCcccCCeEEEEECCCCCCHHHHHHHHHH
Confidence            33445555555543   23467899999999999999999876

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.90  E-value=0.013  Score=53.58  Aligned_cols=22  Identities=18%  Similarity=0.081  Sum_probs=20.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|+.|+||||||+.+..
T Consensus         2 ~li~I~G~~GSGKSTla~~La~   23 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4789999999999999999876

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.89  E-value=0.01  Score=52.21  Aligned_cols=24  Identities=13%  Similarity=0.256  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|+|++|+|||||++.+..
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLS   34 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999999876

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=94.87  E-value=0.021  Score=51.87  Aligned_cols=37  Identities=11%  Similarity=-0.115  Sum_probs=26.7

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++...+.........|.|.|++|+||||+|+.+.+
T Consensus        15 ~~~~~~~~~~~~~~~~~I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           15 LNELKRRYACLSKPDGRYIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             HHHHHHHHHHHTSCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3344433333333567899999999999999999876

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.87  E-value=0.01  Score=52.04  Aligned_cols=23  Identities=17%  Similarity=0.258  Sum_probs=19.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++++|+|+.|+|||||++.+..
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35789999999999999999875

>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=94.86  E-value=0.011  Score=50.78  Aligned_cols=23  Identities=17%  Similarity=0.333  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|.|++|+||||+++.+..
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~   33 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELAS   33 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHH
Confidence            45788999999999999999886

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.85  E-value=0.014  Score=50.54  Aligned_cols=23  Identities=9%  Similarity=0.195  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=94.84  E-value=0.015  Score=53.07  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998866

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.84  E-value=0.019  Score=50.80  Aligned_cols=41  Identities=29%  Similarity=0.292  Sum_probs=29.1

Q ss_pred             cchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          171 EFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       171 Gr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.++..+.+...+...  ...+|.|+|.+|+|||||+..+...
T Consensus        13 ~~~~~~~~~~~~~~~~--~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           13 ENKRLAEKNREALRES--GTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             HHHHHHHHHHHHHHHH--TCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             hcHHHHHHHHHhhccc--CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            3344455555554433  3789999999999999999887653

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.81  E-value=0.011  Score=50.61  Aligned_cols=21  Identities=14%  Similarity=0.172  Sum_probs=19.5

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|++|+||||+|+.+..
T Consensus         6 ~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            588999999999999999876

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=94.81  E-value=0.016  Score=54.76  Aligned_cols=25  Identities=12%  Similarity=-0.020  Sum_probs=22.1

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....+|+|+|..|+|||||++.+..
T Consensus        88 ~~g~ivgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           88 PVPFIIGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCchHHHHHHHHHh
Confidence            3468999999999999999998875

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=94.80  E-value=0.017  Score=50.59  Aligned_cols=24  Identities=21%  Similarity=0.267  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|.|+.|+||||+++.+.+
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~   37 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVK   37 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999999876

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=94.72  E-value=0.016  Score=49.75  Aligned_cols=23  Identities=22%  Similarity=0.137  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.+.|+.|+||||+++.+.+
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999999876

>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=94.71  E-value=0.016  Score=51.13  Aligned_cols=23  Identities=17%  Similarity=0.088  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45899999999999999998865

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=94.70  E-value=0.016  Score=52.66  Aligned_cols=23  Identities=22%  Similarity=0.199  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|+|+.|+|||||++.+.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999984

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=94.70  E-value=0.01  Score=51.75  Aligned_cols=22  Identities=18%  Similarity=0.305  Sum_probs=19.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|.|+|++|+|||||++.+..
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            3477999999999999999876

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.68  E-value=0.017  Score=49.83  Aligned_cols=24  Identities=25%  Similarity=0.119  Sum_probs=21.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|.|++|+||||+++.+..
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~   35 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLAD   35 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999999877

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=94.68  E-value=0.017  Score=49.97  Aligned_cols=23  Identities=22%  Similarity=0.109  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|+|+.|+||||+++.+.+
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46799999999999999999877

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.66  E-value=0.019  Score=52.04  Aligned_cols=24  Identities=4%  Similarity=0.094  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|.|+.|+|||||++.+..
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999998865

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=94.66  E-value=0.018  Score=50.47  Aligned_cols=23  Identities=17%  Similarity=0.058  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+.+
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~   26 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKD   26 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH
Confidence            36899999999999999999876

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=94.65  E-value=0.018  Score=49.59  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.64  E-value=0.016  Score=48.99  Aligned_cols=23  Identities=13%  Similarity=0.186  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999877

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=94.63  E-value=0.018  Score=52.87  Aligned_cols=23  Identities=13%  Similarity=0.359  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|++|+||||+|+.+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            56899999999999999999876

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=94.63  E-value=0.027  Score=53.65  Aligned_cols=24  Identities=25%  Similarity=0.167  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++|+|+.|+||||+++.+..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag  151 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLAN  151 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999988764

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=94.63  E-value=0.012  Score=50.74  Aligned_cols=22  Identities=9%  Similarity=0.139  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3589999999999999999876

>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=94.62  E-value=0.016  Score=49.56  Aligned_cols=23  Identities=13%  Similarity=0.098  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++.|+|..|+|||||+..+..
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~   26 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVA   26 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999988876

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=94.62  E-value=0.016  Score=50.31  Aligned_cols=23  Identities=13%  Similarity=0.200  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999877

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=94.57  E-value=0.034  Score=53.56  Aligned_cols=37  Identities=14%  Similarity=0.043  Sum_probs=28.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+.+.+........+|+|+|.+|+|||||+..+..
T Consensus        65 ~~~~~~~~~~~~~~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           65 AQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhHhhcCCceEEEEECCCCCCHHHHHHHHHH
Confidence            4455555654445678999999999999999988753

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=94.51  E-value=0.018  Score=52.54  Aligned_cols=23  Identities=17%  Similarity=0.211  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|+|+.|+||||+++.+..
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999985

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=94.48  E-value=0.014  Score=49.48  Aligned_cols=22  Identities=9%  Similarity=0.178  Sum_probs=19.9

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|+.|+||||+|+.+.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4689999999999999999877

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=94.44  E-value=0.023  Score=48.01  Aligned_cols=24  Identities=17%  Similarity=0.140  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++++|+.|.|||||.+.+..
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g   55 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999999877

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=94.42  E-value=0.014  Score=50.04  Aligned_cols=23  Identities=22%  Similarity=0.120  Sum_probs=16.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999999876

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.41  E-value=0.017  Score=51.57  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g   45 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLN   45 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45799999999999999998865

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=94.40  E-value=0.02  Score=49.43  Aligned_cols=21  Identities=29%  Similarity=0.347  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|+.|+||||+++.+.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=94.40  E-value=0.02  Score=48.29  Aligned_cols=21  Identities=5%  Similarity=-0.064  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999877

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=94.36  E-value=0.1  Score=51.33  Aligned_cols=24  Identities=21%  Similarity=0.277  Sum_probs=21.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|+|++|+||||+|+.+..
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999999877

>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=94.33  E-value=0.021  Score=50.15  Aligned_cols=24  Identities=13%  Similarity=0.351  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.|+|+.|+|||||++.+..
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~   41 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLS   41 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHh
Confidence            357899999999999999999876

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=94.33  E-value=0.028  Score=54.09  Aligned_cols=82  Identities=17%  Similarity=0.098  Sum_probs=44.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLTN  261 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~~  261 (425)
                      .-.++.|.|.+|+||||||.++........  ..++|+      -......++.....- -....+.++....+....+.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~g--~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~~  137 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAAG--GIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVRS  137 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCC--CeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHhc
Confidence            356899999999999999988764211000  011122      011233333221110 11223556666666555543


Q ss_pred             -CeEEEEecccC
Q 040913          262 -KKYFIALDDVC  272 (425)
Q Consensus       262 -kr~LlVLDdvw  272 (425)
                       +.-+||+|.+-
T Consensus       138 ~~~~lIVIDsl~  149 (349)
T 2zr9_A          138 GALDIIVIDSVA  149 (349)
T ss_dssp             TCCSEEEEECGG
T ss_pred             CCCCEEEEcChH
Confidence             55699999985

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=94.32  E-value=0.021  Score=49.92  Aligned_cols=23  Identities=22%  Similarity=0.140  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+|+.+..
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45799999999999999999876

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=94.31  E-value=0.023  Score=50.01  Aligned_cols=23  Identities=4%  Similarity=0.007  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+++.+.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.30  E-value=0.049  Score=51.28  Aligned_cols=24  Identities=17%  Similarity=0.032  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|..|+|||||++.+..
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999998876

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=94.30  E-value=0.032  Score=48.81  Aligned_cols=113  Identities=13%  Similarity=0.100  Sum_probs=58.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc-----Ccccc-ccccchHHH--HHHHHHHhCCCCC---CC-ccCC-------CCHHH
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN-----NNHVK-FYFDCLAWI--LDDIIRSLMPPSR---VT-VIIG-------EDYKL  250 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~-----~~~~~-~~F~~~~wv--~~~il~~l~~~~~---~~-~~~~-------~~~~~  250 (425)
                      ...|-|++..|.||||+|-...-     ..+|. -.|....|-  -.+++..+.....   .. ....       .....
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~  107 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMA  107 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHH
Confidence            35667777788999998854432     12221 123222122  3445555520000   00 0000       11123


Q ss_pred             HHHHHHHHhcCCeE-EEEecccCC----ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          251 KKSILRDFLTNKKY-FIALDDVCH----NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       251 l~~~l~~~l~~kr~-LlVLDdvw~----~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ......+.+.+.+| |||||++-.    .--..+.+...+.......-||+|+|+..
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap  164 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCH  164 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCC
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCc
Confidence            34445555655555 999999841    11344555556655555778999999953

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=94.26  E-value=0.011  Score=52.08  Aligned_cols=21  Identities=19%  Similarity=0.254  Sum_probs=19.2

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|..|+||||+++.+..
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            689999999999999998865

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=94.25  E-value=0.025  Score=49.52  Aligned_cols=24  Identities=17%  Similarity=0.134  Sum_probs=21.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|.|+.|+||||+++.+..
T Consensus        11 ~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           11 HHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999876

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=94.25  E-value=0.026  Score=50.16  Aligned_cols=24  Identities=17%  Similarity=0.160  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|+|+.|+|||||++.+..
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g   47 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAV   47 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999864

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=94.24  E-value=0.027  Score=50.30  Aligned_cols=26  Identities=15%  Similarity=0.173  Sum_probs=23.1

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+||.|.|++|+||||.|+.+.+.
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35789999999999999999998873

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=94.21  E-value=0.023  Score=49.87  Aligned_cols=23  Identities=4%  Similarity=-0.143  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+++.+.+
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=94.20  E-value=0.012  Score=57.14  Aligned_cols=34  Identities=15%  Similarity=-0.037  Sum_probs=25.4

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++++.+..-. .-..++|+|.+|+|||||++.+.+
T Consensus       163 raID~~~pi~-rGQr~~IvG~sG~GKTtLl~~Iar  196 (422)
T 3ice_A          163 RVLDLASPIG-RGQRGLIVAPPKAGKTMLLQNIAQ  196 (422)
T ss_dssp             HHHHHHSCCB-TTCEEEEECCSSSSHHHHHHHHHH
T ss_pred             eeeeeeeeec-CCcEEEEecCCCCChhHHHHHHHH
Confidence            4556555432 234789999999999999998876

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=94.18  E-value=0.03  Score=55.47  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=34.9

Q ss_pred             CCcccchhhHHHHHHHHhcC------------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG------------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~------------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.|...+...            +...+-|.++|++|+||||+|+.+..
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~   72 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   72 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHH
Confidence            45889998888887666321            11245588999999999999999876

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=94.18  E-value=0.026  Score=53.18  Aligned_cols=24  Identities=25%  Similarity=0.180  Sum_probs=20.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++|+|++|+|||||+..+..
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            357999999999999999988763

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=94.16  E-value=0.029  Score=49.66  Aligned_cols=23  Identities=22%  Similarity=0.203  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999865

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.14  E-value=0.045  Score=48.46  Aligned_cols=22  Identities=27%  Similarity=0.203  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|+.|+|||||.+.+..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~G   44 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAV   44 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            4799999999999999998874

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.13  E-value=0.052  Score=51.49  Aligned_cols=24  Identities=25%  Similarity=0.303  Sum_probs=21.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|.+|+||||++..+..
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~  127 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMAN  127 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999887754

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=94.13  E-value=0.025  Score=51.13  Aligned_cols=23  Identities=22%  Similarity=0.133  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            45899999999999999998864

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.12  E-value=0.026  Score=50.58  Aligned_cols=23  Identities=22%  Similarity=0.094  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~G   52 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGL   52 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999998874

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=94.11  E-value=0.03  Score=52.07  Aligned_cols=24  Identities=33%  Similarity=0.397  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|.|+.|+||||+|+.+..
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999999998873

>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=94.10  E-value=0.026  Score=50.46  Aligned_cols=24  Identities=13%  Similarity=0.137  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|+|+.|+|||||.+.+..
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g   38 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLK   38 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999998875

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=94.09  E-value=0.034  Score=53.82  Aligned_cols=81  Identities=15%  Similarity=0.058  Sum_probs=45.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhcC-
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLTN-  261 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~~-  261 (425)
                      -.++.|.|.+|+||||||.++........  ..++|+      -......+......- -....+.+++...+...++. 
T Consensus        74 G~li~I~G~pGsGKTtlal~la~~~~~~g--~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~~~  151 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVRSG  151 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTTT
T ss_pred             CcEEEEEcCCCCChHHHHHHHHHHHHHCC--CeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHhcC
Confidence            45788899999999999988765211110  122233      111233333321100 01223567777777766653 


Q ss_pred             CeEEEEecccC
Q 040913          262 KKYFIALDDVC  272 (425)
Q Consensus       262 kr~LlVLDdvw  272 (425)
                      +--+||+|.+-
T Consensus       152 ~~~lVVIDsl~  162 (366)
T 1xp8_A          152 AIDVVVVDSVA  162 (366)
T ss_dssp             CCSEEEEECTT
T ss_pred             CCCEEEEeChH
Confidence            45599999984

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=94.06  E-value=0.025  Score=50.58  Aligned_cols=23  Identities=17%  Similarity=0.221  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|.|+.|+||||+|+.+..
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46799999999999999999876

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=94.05  E-value=0.015  Score=49.92  Aligned_cols=22  Identities=18%  Similarity=0.259  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|..|+|||||++.+..
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~   24 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMP   24 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999998876

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=94.02  E-value=0.029  Score=47.98  Aligned_cols=23  Identities=22%  Similarity=0.075  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+++.+..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46889999999999999999876

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=94.00  E-value=0.032  Score=49.27  Aligned_cols=23  Identities=13%  Similarity=0.034  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|+.|+||||+++.+..
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~   47 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEH   47 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999876

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=93.97  E-value=0.032  Score=52.46  Aligned_cols=23  Identities=22%  Similarity=0.189  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+++|+|+.|+||||+++.+..
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHH
Confidence            57999999999999999988764

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.97  E-value=0.023  Score=49.51  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=19.2

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +++|+|+.|+|||||++.+..
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g   23 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHh
Confidence            689999999999999998876

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=93.92  E-value=0.028  Score=49.97  Aligned_cols=23  Identities=13%  Similarity=0.141  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|.|+.|+||||+|+.+.+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999877

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=93.90  E-value=0.029  Score=50.91  Aligned_cols=22  Identities=18%  Similarity=0.258  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|+.|+|||||.+.+..
T Consensus        25 e~~~liG~nGsGKSTLl~~l~G   46 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAG   46 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            6899999999999999998864

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=93.86  E-value=0.026  Score=50.25  Aligned_cols=23  Identities=13%  Similarity=-0.109  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|.|+.|+||||+++.+.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45688999999999999999887

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.84  E-value=0.03  Score=49.47  Aligned_cols=21  Identities=14%  Similarity=0.199  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999866

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=93.83  E-value=0.031  Score=50.58  Aligned_cols=23  Identities=17%  Similarity=0.294  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999875

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.81  E-value=0.021  Score=51.24  Aligned_cols=22  Identities=23%  Similarity=0.259  Sum_probs=16.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -.+++|+|+.|+|||||++.+.
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHH
Confidence            4689999999999999999988

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=93.79  E-value=0.058  Score=54.05  Aligned_cols=24  Identities=17%  Similarity=0.181  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++|+|..|+|||||++.+..
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHH
Confidence            467999999999999999988765

>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=93.79  E-value=0.031  Score=48.73  Aligned_cols=24  Identities=8%  Similarity=0.021  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|.|.|+.|+||||+++.+.+.
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHT
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH
Confidence            357999999999999999998873

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=93.78  E-value=0.035  Score=52.55  Aligned_cols=22  Identities=23%  Similarity=0.441  Sum_probs=19.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHh
Q 040913          189 GLSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      +.+||+|.|=|||||||.+-.+
T Consensus        47 ~aKVIAIaGKGGVGKTTtavNL   68 (314)
T 3fwy_A           47 GAKVFAVYGKGGIGKSTTSSNL   68 (314)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHH
T ss_pred             CceEEEEECCCccCHHHHHHHH
Confidence            5899999999999999987554

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=93.77  E-value=0.032  Score=51.35  Aligned_cols=23  Identities=30%  Similarity=0.307  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999864

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=93.77  E-value=0.032  Score=51.76  Aligned_cols=23  Identities=26%  Similarity=0.315  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        34 Ge~~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           34 GEVTAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHc
Confidence            35899999999999999998863

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=93.73  E-value=0.032  Score=48.73  Aligned_cols=21  Identities=24%  Similarity=0.200  Sum_probs=19.8

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +|+|.|+.|+||||+++.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            899999999999999999876

>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=93.68  E-value=0.032  Score=47.92  Aligned_cols=23  Identities=22%  Similarity=0.239  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++.|+|..|+|||||+..+..
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~   28 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIP   28 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHH
Confidence            57899999999999999988876

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.68  E-value=0.034  Score=50.39  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999874

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=93.67  E-value=0.033  Score=49.19  Aligned_cols=21  Identities=10%  Similarity=0.123  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999876

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=93.66  E-value=0.13  Score=53.03  Aligned_cols=23  Identities=26%  Similarity=0.186  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||++.+..
T Consensus       369 G~~~~ivG~sGsGKSTll~~l~g  391 (582)
T 3b5x_A          369 GKTVALVGRSGSGKSTIANLFTR  391 (582)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999864

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=93.65  E-value=0.034  Score=50.93  Aligned_cols=23  Identities=17%  Similarity=0.170  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999864

>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=93.63  E-value=0.035  Score=52.05  Aligned_cols=24  Identities=21%  Similarity=0.192  Sum_probs=20.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++++|.+|+||||++..+..
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~  127 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAA  127 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            356999999999999999887754

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=93.62  E-value=0.038  Score=50.16  Aligned_cols=23  Identities=22%  Similarity=0.135  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            56899999999999999999864

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=93.61  E-value=0.035  Score=51.19  Aligned_cols=23  Identities=22%  Similarity=0.212  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46899999999999999999874

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=93.55  E-value=0.037  Score=49.75  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~G   56 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMG   56 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=93.55  E-value=0.037  Score=50.97  Aligned_cols=23  Identities=26%  Similarity=0.245  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~G   72 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNL   72 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHc
Confidence            46899999999999999998874

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=93.54  E-value=0.037  Score=50.48  Aligned_cols=23  Identities=17%  Similarity=0.169  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999876

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=93.52  E-value=0.038  Score=50.37  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999865

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=93.51  E-value=0.032  Score=49.71  Aligned_cols=23  Identities=22%  Similarity=0.232  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~G   57 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTIST   57 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35789999999999999999865

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=93.49  E-value=0.028  Score=51.36  Aligned_cols=23  Identities=13%  Similarity=-0.000  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+|.|+|+.|+||||+++.+..
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            34799999999999999999977

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=93.49  E-value=0.12  Score=49.37  Aligned_cols=25  Identities=8%  Similarity=0.057  Sum_probs=21.6

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-.++.|+|.+|+||||||.++..
T Consensus       120 ~~G~i~~I~G~~GsGKTtla~~la~  144 (343)
T 1v5w_A          120 ESMAITEAFGEFRTGKTQLSHTLCV  144 (343)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999988765

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.43  E-value=0.04  Score=50.53  Aligned_cols=23  Identities=13%  Similarity=0.109  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~G   63 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIIST   63 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999874

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=93.42  E-value=0.045  Score=52.73  Aligned_cols=24  Identities=21%  Similarity=0.166  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++|+|..|+|||||+..+..
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHh
Confidence            367999999999999999988764

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=93.41  E-value=0.062  Score=45.89  Aligned_cols=26  Identities=12%  Similarity=0.012  Sum_probs=22.2

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....-|.|+|.+|+|||||...+.+.
T Consensus        14 ~~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           14 DQEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCceEEEEECCCCCCHHHHHHHHhcC
Confidence            34567889999999999999998874

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=93.39  E-value=0.041  Score=52.52  Aligned_cols=22  Identities=14%  Similarity=0.261  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|+|.|+.|+||||||..+..
T Consensus         8 ~lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHH
Confidence            5899999999999999998876

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=93.39  E-value=0.059  Score=53.62  Aligned_cols=34  Identities=21%  Similarity=0.235  Sum_probs=24.1

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .++.|..--. -..++|+|.+|+|||||++.+..+
T Consensus       141 ~ID~L~pi~k-Gq~~~i~G~sGvGKTtL~~~l~~~  174 (473)
T 1sky_E          141 VVDLLAPYIK-GGKIGLFGGAGVGKTVLIQELIHN  174 (473)
T ss_dssp             HHHHHSCEET-TCEEEEECCSSSCHHHHHHHHHHH
T ss_pred             HHHHHhhhcc-CCEEEEECCCCCCccHHHHHHHhh
Confidence            4555543211 235789999999999999988763

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=93.39  E-value=0.041  Score=50.57  Aligned_cols=23  Identities=22%  Similarity=0.299  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            45899999999999999999875

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=93.38  E-value=0.042  Score=47.54  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+|+|..|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            567899999999999999998764

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=93.38  E-value=0.047  Score=51.40  Aligned_cols=24  Identities=17%  Similarity=0.152  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|+|.+|+||||++..+..
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~  126 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAK  126 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHH
Confidence            468999999999999999988764

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=93.37  E-value=0.041  Score=50.77  Aligned_cols=23  Identities=26%  Similarity=0.283  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999998876

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.37  E-value=0.041  Score=50.90  Aligned_cols=23  Identities=30%  Similarity=0.268  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~G   67 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQN   67 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999999875

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=93.34  E-value=0.059  Score=45.20  Aligned_cols=23  Identities=9%  Similarity=0.159  Sum_probs=20.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..|+|+|.+|+|||||...+.+.
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            56899999999999999998764

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.28  E-value=0.043  Score=50.58  Aligned_cols=23  Identities=9%  Similarity=0.075  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~G   55 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAG   55 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999999864

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.28  E-value=0.043  Score=50.04  Aligned_cols=23  Identities=13%  Similarity=0.235  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            35899999999999999999875

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=93.28  E-value=0.047  Score=48.92  Aligned_cols=25  Identities=20%  Similarity=0.072  Sum_probs=22.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+|+|.|+.|+|||||++.+...
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhc
Confidence            4579999999999999999998873

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.27  E-value=0.042  Score=47.08  Aligned_cols=22  Identities=18%  Similarity=0.292  Sum_probs=19.5

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||...+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999998873

>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=93.25  E-value=0.045  Score=48.20  Aligned_cols=24  Identities=17%  Similarity=0.003  Sum_probs=20.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.++.|+|.+|+|||||+..+..
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL   42 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999998865

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=93.24  E-value=0.044  Score=49.43  Aligned_cols=23  Identities=22%  Similarity=0.198  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|.|++|+||||+++.+..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999999876

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.24  E-value=0.077  Score=52.50  Aligned_cols=37  Identities=22%  Similarity=0.123  Sum_probs=26.7

Q ss_pred             HHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++.++|...       ....++|.++|.+|+||||++..+..
T Consensus        79 ~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~  122 (433)
T 2xxa_A           79 RNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGK  122 (433)
T ss_dssp             HHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            44555555432       13478999999999999999877763

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.19  E-value=0.045  Score=50.07  Aligned_cols=23  Identities=17%  Similarity=0.270  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~G   53 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLG   53 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999875

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=93.18  E-value=0.047  Score=50.20  Aligned_cols=110  Identities=15%  Similarity=0.166  Sum_probs=56.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHH-HHHHHHhCCCCCC---CccCCCCHHHHHHHHHHHhcCCeE
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWIL-DDIIRSLMPPSRV---TVIIGEDYKLKKSILRDFLTNKKY  264 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~-~~il~~l~~~~~~---~~~~~~~~~~l~~~l~~~l~~kr~  264 (425)
                      .-.+++|+|+.|+|||||.+.+..-..  ..+...+.+. ..+ ..+......   +.....+...+...+...|..+.=
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~--~~~~G~I~~~g~~i-~~~~~~~~~~v~q~~~gl~~~~l~~~la~aL~~~p~  100 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYIN--QTKSYHIITIEDPI-EYVFKHKKSIVNQREVGEDTKSFADALRAALREDPD  100 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHH--HHCCCEEEEEESSC-CSCCCCSSSEEEEEEBTTTBSCHHHHHHHHHHHCCS
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCC--CCCCCEEEEcCCcc-eeecCCcceeeeHHHhCCCHHHHHHHHHHHHhhCCC
Confidence            357899999999999999988765211  0000111000 000 000000000   000000112335566777766777


Q ss_pred             EEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          265 FIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       265 LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      +|++|... +.+....+....   ..|.-|++||.+.++..
T Consensus       101 illlDEp~-D~~~~~~~l~~~---~~g~~vl~t~H~~~~~~  137 (261)
T 2eyu_A          101 VIFVGEMR-DLETVETALRAA---ETGHLVFGTLHTNTAID  137 (261)
T ss_dssp             EEEESCCC-SHHHHHHHHHHH---HTTCEEEEEECCSSHHH
T ss_pred             EEEeCCCC-CHHHHHHHHHHH---ccCCEEEEEeCcchHHH
Confidence            89999997 554443332222   23667888888876543

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.18  E-value=0.045  Score=50.82  Aligned_cols=23  Identities=13%  Similarity=-0.039  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999999874

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=93.13  E-value=0.047  Score=48.21  Aligned_cols=21  Identities=14%  Similarity=0.020  Sum_probs=19.0

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|+.|+||||+|+.+.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            378999999999999999876

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=93.13  E-value=0.098  Score=55.63  Aligned_cols=46  Identities=11%  Similarity=0.085  Sum_probs=36.4

Q ss_pred             CCcccchhhHHHHHHHHhcC-------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEG-------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.+...+...       ......+.++|++|+|||++|+.+.+
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~  510 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK  510 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHH
Confidence            45889999888887776532       12345788999999999999999887

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=93.13  E-value=0.051  Score=55.48  Aligned_cols=46  Identities=15%  Similarity=0.270  Sum_probs=34.6

Q ss_pred             CCcccchhhHHHHHHHHhc----CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIE----GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|.++.+..+.+.+.-    ......++.++|++|+||||||+.+.+
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~  130 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAK  130 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            3478888877777554432    122456899999999999999999987

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=93.11  E-value=0.075  Score=52.50  Aligned_cols=23  Identities=17%  Similarity=0.115  Sum_probs=20.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ...+|.++|.+|+||||++..+.
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA  118 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLA  118 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            47899999999999999987775

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=93.11  E-value=0.088  Score=49.67  Aligned_cols=80  Identities=9%  Similarity=0.093  Sum_probs=45.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccc--cchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHH-HHHHHHH--
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYF--DCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLK-KSILRDF--  258 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F--~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l-~~~l~~~--  258 (425)
                      .++-|.|++|+|||||+.++...  ....+  ..++|+      .....+.++.....- -....+.++. ...+...  
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~~--~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~  106 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVSS--YMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDA  106 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHH--HHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHH
Confidence            37899999999999998877652  21111  123444      122355555443211 1123355555 4333332  


Q ss_pred             h-cCCeEEEEecccC
Q 040913          259 L-TNKKYFIALDDVC  272 (425)
Q Consensus       259 l-~~kr~LlVLDdvw  272 (425)
                      + +++.-|||+|-|.
T Consensus       107 i~~~~~~lvVIDSI~  121 (333)
T 3io5_A          107 IERGEKVVVFIDSLG  121 (333)
T ss_dssp             CCTTCCEEEEEECST
T ss_pred             hhccCceEEEEeccc
Confidence            3 3567899999985

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=93.10  E-value=0.048  Score=48.36  Aligned_cols=22  Identities=9%  Similarity=0.061  Sum_probs=19.9

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..|.|.|++|+||||+|+.+..
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4688999999999999999876

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=93.08  E-value=0.077  Score=51.46  Aligned_cols=35  Identities=11%  Similarity=0.048  Sum_probs=26.0

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++-+.-.-....+++|+|+.|+|||||++.+..
T Consensus       157 ~~l~~~~~~i~~~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          157 DFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             HHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHhcccccCCCCEEEEECCCCCCHHHHHHHHHh
Confidence            34444433333456899999999999999999886

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=93.04  E-value=0.05  Score=48.20  Aligned_cols=23  Identities=22%  Similarity=0.206  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.|+|.+|+|||||+..+..
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~   45 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIA   45 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46889999999999999998874

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=93.03  E-value=0.048  Score=48.65  Aligned_cols=21  Identities=14%  Similarity=0.120  Sum_probs=19.1

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|.|+.|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999876

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=93.02  E-value=0.06  Score=44.44  Aligned_cols=23  Identities=13%  Similarity=0.198  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +-|.++|.+|+|||||...+.+.
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45889999999999999998764

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=92.99  E-value=0.072  Score=55.15  Aligned_cols=42  Identities=14%  Similarity=0.052  Sum_probs=35.5

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.+..++.+...+..+    ..+.|+|++|+||||||+.+..
T Consensus        41 ~~i~G~~~~l~~l~~~i~~g----~~vll~Gp~GtGKTtlar~ia~   82 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQK----RHVLLIGEPGTGKSMLGQAMAE   82 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHTT----CCEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEECchhhHhhccccccCC----CEEEEEeCCCCCHHHHHHHHhc
Confidence            46889888888887777765    3788999999999999999987

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=92.99  E-value=0.06  Score=51.23  Aligned_cols=23  Identities=13%  Similarity=0.307  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|+|+.|+||||||..+..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~   62 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAA   62 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHT
T ss_pred             CceEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999887

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=92.97  E-value=0.051  Score=50.65  Aligned_cols=22  Identities=14%  Similarity=0.335  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5789999999999999999886

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=92.94  E-value=0.046  Score=47.45  Aligned_cols=24  Identities=25%  Similarity=0.338  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+|+|..|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            356889999999999999998774

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=92.92  E-value=0.13  Score=54.80  Aligned_cols=98  Identities=16%  Similarity=0.140  Sum_probs=59.6

Q ss_pred             CCCCCCCcccchhhHHHHHHHHhcC-----------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDLLIEG-----------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~L~~~-----------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~i  230 (425)
                      +.+.-.++.|.++.++.|.+.+.-.           -...+-|.++|++|.|||.||+++.+  +....|-..-  ..++
T Consensus       472 p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~--e~~~~f~~v~--~~~l  547 (806)
T 3cf2_A          472 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQANFISIK--GPEL  547 (806)
T ss_dssp             CCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHH--TTTCEEEECC--HHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHH--HhCCceEEec--cchh
Confidence            4444566788888888887765432           12234567899999999999999999  4444442100  1111


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      +..         ....+...+...+...-+...+.|++|++.
T Consensus       548 ~s~---------~vGese~~vr~lF~~Ar~~~P~IifiDEiD  580 (806)
T 3cf2_A          548 LTM---------WFGESEANVREIFDKARQAAPCVLFFDELD  580 (806)
T ss_dssp             HTT---------TCSSCHHHHHHHHHHHHTTCSEEEECSCGG
T ss_pred             hcc---------ccchHHHHHHHHHHHHHHcCCceeechhhh
Confidence            111         112333444444444445678999999995

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=92.91  E-value=0.059  Score=48.98  Aligned_cols=23  Identities=17%  Similarity=0.276  Sum_probs=20.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ...++.+.|.||+|||||+..+.
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La   35 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFG   35 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHH
Confidence            46788899999999999998886

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=92.89  E-value=0.056  Score=44.65  Aligned_cols=22  Identities=18%  Similarity=0.392  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|.+|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999998764

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=92.86  E-value=0.056  Score=53.09  Aligned_cols=24  Identities=21%  Similarity=0.282  Sum_probs=21.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++|+|..|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            467999999999999999999876

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=92.85  E-value=0.09  Score=49.26  Aligned_cols=23  Identities=22%  Similarity=0.185  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.++|.+|+||||++..+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~  120 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAY  120 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999887763

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=92.85  E-value=0.072  Score=46.95  Aligned_cols=36  Identities=8%  Similarity=0.014  Sum_probs=26.1

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+..++.. -+....+.|+|++|+||||+|..+.+
T Consensus        45 ~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~ala~   80 (212)
T 1tue_A           45 LGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIH   80 (212)
T ss_dssp             HHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHHHHH
Confidence            4555555553 22234689999999999999988877

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=92.85  E-value=0.053  Score=51.00  Aligned_cols=24  Identities=8%  Similarity=0.152  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|+|+.|.|||||++.+..
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhh
Confidence            356899999999999999998875

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=92.81  E-value=0.061  Score=51.80  Aligned_cols=82  Identities=15%  Similarity=0.013  Sum_probs=43.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhc-
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLT-  260 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~-  260 (425)
                      .-.++.|.|.+|+||||||.++........  ..++|+      -......+......- -....+.+++...+....+ 
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~g--~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~~  139 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS  139 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCC--CeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHhc
Confidence            356889999999999999988765211110  012222      011233333221100 0112345556555555443 


Q ss_pred             CCeEEEEecccC
Q 040913          261 NKKYFIALDDVC  272 (425)
Q Consensus       261 ~kr~LlVLDdvw  272 (425)
                      .+--+||+|.+-
T Consensus       140 ~~~~lVVIDsl~  151 (356)
T 1u94_A          140 GAVDVIVVDSVA  151 (356)
T ss_dssp             TCCSEEEEECGG
T ss_pred             cCCCEEEEcCHH
Confidence            455599999984

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=92.80  E-value=0.054  Score=50.04  Aligned_cols=21  Identities=14%  Similarity=0.445  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|+|..|+|||||.+.++.
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            579999999999999999886

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=92.77  E-value=0.087  Score=54.46  Aligned_cols=24  Identities=21%  Similarity=0.151  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|+|+.|.|||||++.+..
T Consensus       380 ~G~~~~ivG~sGsGKSTll~~l~g  403 (598)
T 3qf4_B          380 PGQKVALVGPTGSGKTTIVNLLMR  403 (598)
T ss_dssp             TTCEEEEECCTTSSTTHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            356899999999999999999875

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=92.77  E-value=0.057  Score=48.45  Aligned_cols=23  Identities=17%  Similarity=0.082  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|.|+.|+||||+|+.+.+
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45788999999999999999877

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=92.75  E-value=0.058  Score=51.11  Aligned_cols=22  Identities=14%  Similarity=0.225  Sum_probs=20.1

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|+|+.|+||||||..+..
T Consensus         6 ~~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999998876

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=92.75  E-value=0.086  Score=54.35  Aligned_cols=23  Identities=26%  Similarity=0.249  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||++.+..
T Consensus       369 Ge~~~ivG~sGsGKSTll~~l~g  391 (587)
T 3qf4_A          369 GSLVAVLGETGSGKSTLMNLIPR  391 (587)
T ss_dssp             TCEEEEECSSSSSHHHHHHTTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46899999999999999998875

>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=92.73  E-value=0.058  Score=48.26  Aligned_cols=23  Identities=13%  Similarity=0.007  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.|+|.+|+|||||+..+..
T Consensus        24 G~~~~i~G~~GsGKTtl~~~l~~   46 (243)
T 1n0w_A           24 GSITEMFGEFRTGKTQICHTLAV   46 (243)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH
Confidence            46899999999999999998776

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=92.69  E-value=0.033  Score=52.03  Aligned_cols=23  Identities=13%  Similarity=0.195  Sum_probs=17.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|+|.|..|+||||+|+.+.+
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999998876

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=92.68  E-value=0.059  Score=49.56  Aligned_cols=22  Identities=27%  Similarity=0.282  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|+.|+|||||.+.+..
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhC
Confidence            4799999999999999998864

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=92.67  E-value=0.072  Score=45.42  Aligned_cols=24  Identities=8%  Similarity=0.123  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+++|.+|+|||||...+.+.
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            457899999999999999998874

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=92.64  E-value=0.063  Score=45.04  Aligned_cols=24  Identities=29%  Similarity=0.325  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            345889999999999999998764

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=92.63  E-value=0.061  Score=44.72  Aligned_cols=24  Identities=4%  Similarity=0.126  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            345789999999999999998764

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=92.62  E-value=0.06  Score=47.56  Aligned_cols=22  Identities=18%  Similarity=0.234  Sum_probs=19.6

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +|.|.|++|+||||.|+.+.+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~   23 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKE   23 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5778999999999999998873

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=92.62  E-value=0.064  Score=50.77  Aligned_cols=25  Identities=20%  Similarity=0.223  Sum_probs=22.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+++.|+|+.|.|||||.+.+...
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             cccEEEEEecCCCCHHHHHHHHHhh
Confidence            4789999999999999999998853

>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=92.61  E-value=0.066  Score=50.41  Aligned_cols=23  Identities=22%  Similarity=0.176  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|+|+.|+||||||..+..
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~   25 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAK   25 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHHH
Confidence            46899999999999999999876

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=92.55  E-value=0.064  Score=49.53  Aligned_cols=23  Identities=22%  Similarity=0.208  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.|+|.+|+|||||+..+..
T Consensus        30 G~i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           30 GTVGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999988764

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=92.54  E-value=0.063  Score=48.23  Aligned_cols=24  Identities=17%  Similarity=0.012  Sum_probs=21.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|.|+.|+||||+++.+..
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            466899999999999999998876

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=92.53  E-value=0.073  Score=52.67  Aligned_cols=23  Identities=26%  Similarity=0.260  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.|+|.+|+||||++..+..
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~  121 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLAR  121 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56999999999999999877765

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=92.49  E-value=0.12  Score=49.43  Aligned_cols=34  Identities=15%  Similarity=0.086  Sum_probs=25.7

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhh
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .+++-+.-.-....+++|+|.+|+|||||.+.+.
T Consensus        43 ~~l~~i~~~~~~g~~v~i~G~~GaGKSTLl~~l~   76 (337)
T 2qm8_A           43 DLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALG   76 (337)
T ss_dssp             HHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHH
T ss_pred             HHHHhCCcccCCCeEEEEECCCCCCHHHHHHHHH
Confidence            3444444333457899999999999999999886

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=92.48  E-value=0.11  Score=51.48  Aligned_cols=24  Identities=17%  Similarity=0.174  Sum_probs=20.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.++|.+|+||||++..+..
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            478999999999999998877653

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=92.44  E-value=0.069  Score=44.39  Aligned_cols=21  Identities=29%  Similarity=0.271  Sum_probs=18.7

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|.++|.+|+|||||...+.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            378999999999999998875

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=92.40  E-value=0.069  Score=49.86  Aligned_cols=23  Identities=22%  Similarity=0.225  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~G   86 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMG   86 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46899999999999999999875

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=92.40  E-value=0.069  Score=49.75  Aligned_cols=23  Identities=22%  Similarity=0.325  Sum_probs=20.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.|+|.+|+|||||+..+..
T Consensus        35 G~~~~i~G~~G~GKTTl~~~ia~   57 (296)
T 1cr0_A           35 GEVIMVTSGSGMGKSTFVRQQAL   57 (296)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHH
Confidence            45899999999999999988764

>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=92.40  E-value=0.13  Score=51.22  Aligned_cols=36  Identities=17%  Similarity=0.072  Sum_probs=25.6

Q ss_pred             hhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          174 RAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       174 ~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....+.+.+..++   +.+.|.|.+|+||||++..+..
T Consensus        32 ~av~~~~~~i~~~~---~~~li~G~aGTGKT~ll~~~~~   67 (459)
T 3upu_A           32 NAFNIVMKAIKEKK---HHVTINGPAGTGATTLTKFIIE   67 (459)
T ss_dssp             HHHHHHHHHHHSSS---CEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCC---CEEEEEeCCCCCHHHHHHHHHH
Confidence            33344444555433   3788999999999999988776

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=92.39  E-value=0.069  Score=44.26  Aligned_cols=23  Identities=22%  Similarity=0.325  Sum_probs=20.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-|.++|.+|+|||||...+.+.
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            45789999999999999998764

>1fx0_B ATP synthase beta chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_B*

Probab=92.35  E-value=0.077  Score=52.97  Aligned_cols=92  Identities=12%  Similarity=0.138  Sum_probs=50.9

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCC---------CC
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSR---------VT  241 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~---------~~  241 (425)
                      .++.|..=. .-.-++|.|..|+|||+|++.+.++. .+.+-+.++++        ..++...+.....         ..
T Consensus       155 vID~l~pig-kGqr~gIfgg~GvGKT~L~~~l~~~~-a~~~~~v~V~~~iGER~rEv~e~~~~~~~~~~l~~~~l~~~rt  232 (498)
T 1fx0_B          155 VVNLLAPYR-RGGKIGLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTREGNDLYMEMKESGVINEQNIAESKV  232 (498)
T ss_dssp             THHHHSCCC-TTCCEEEEECSSSSHHHHHHHHHHHT-TTTCSSCEEEEEESCCSHHHHHHHHHHHHTTSSCSSTTCCCCE
T ss_pred             Eeeeecccc-cCCeEEeecCCCCCchHHHHHHHHHH-HhhCCCEEEEEEcccCcHHHHHHHHhhhcccccccccccccce
Confidence            455555422 12357899999999999998887731 12233444444        4555555432210         00


Q ss_pred             ----ccCC------CCHHHHHHHHHHHhc---CCeEEEEecccC
Q 040913          242 ----VIIG------EDYKLKKSILRDFLT---NKKYFIALDDVC  272 (425)
Q Consensus       242 ----~~~~------~~~~~l~~~l~~~l~---~kr~LlVLDdvw  272 (425)
                          ...+      .-.....-.+.++++   ++.+||++||+-
T Consensus       233 vvV~~t~d~p~~~R~~~~~~altiAEyfrd~~G~dVLl~~Dsit  276 (498)
T 1fx0_B          233 ALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIF  276 (498)
T ss_dssp             EEEEECTTSCHHHHTTHHHHHHHTHHHHTTTSCCEEEEEEECSH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhcCCcEEEEeccHH
Confidence                0011      111223344555554   589999999983

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=92.33  E-value=0.049  Score=51.31  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||++.+..
T Consensus        80 Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           80 GQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCEEEEECCCCchHHHHHHHHHc
Confidence            46899999999999999999865

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=92.33  E-value=0.14  Score=48.91  Aligned_cols=35  Identities=11%  Similarity=0.075  Sum_probs=25.5

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.+-+........+|+|+|.+|+|||||+..+..
T Consensus        44 ~~~~~l~~~~~~~~~i~i~G~~g~GKSTl~~~l~~   78 (341)
T 2p67_A           44 QLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGM   78 (341)
T ss_dssp             HHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             HHHHhCCcccCCCEEEEEEcCCCCCHHHHHHHHHH
Confidence            34443333334578999999999999999988753

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=92.28  E-value=0.07  Score=45.64  Aligned_cols=23  Identities=17%  Similarity=0.348  Sum_probs=20.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.++|.+|+|||||+..+.+.
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            45789999999999999998764

>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=92.27  E-value=0.079  Score=45.27  Aligned_cols=22  Identities=18%  Similarity=0.249  Sum_probs=19.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..|+|..|+|||||+..++-
T Consensus        27 g~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999998864

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=92.25  E-value=0.071  Score=45.75  Aligned_cols=25  Identities=12%  Similarity=0.016  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|.|+|.+|+|||||...+.+.
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3557889999999999999998874

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=92.24  E-value=0.081  Score=49.50  Aligned_cols=23  Identities=22%  Similarity=0.078  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+++|+|.+|+||||++..+..
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~  120 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLAL  120 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999988764

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=92.23  E-value=0.1  Score=43.86  Aligned_cols=25  Identities=20%  Similarity=0.222  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3567889999999999999998764

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=92.21  E-value=0.076  Score=44.97  Aligned_cols=23  Identities=13%  Similarity=0.073  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            45789999999999999998764

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=92.19  E-value=0.09  Score=43.81  Aligned_cols=24  Identities=21%  Similarity=0.173  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            345789999999999999988764

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.19  E-value=0.074  Score=44.29  Aligned_cols=23  Identities=17%  Similarity=0.287  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.++|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            34789999999999999998764

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=92.15  E-value=0.076  Score=44.07  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||...+.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999998764

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=92.15  E-value=0.056  Score=53.70  Aligned_cols=35  Identities=23%  Similarity=0.297  Sum_probs=25.2

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.++.|..=. .-.-++|+|..|+|||+|++.+.++
T Consensus       142 r~ID~l~pig-kGQr~~Ifgg~G~GKT~L~~~i~~~  176 (482)
T 2ck3_D          142 KVVDLLAPYA-KGGKIGLFGGAGVGKTVLIMELINN  176 (482)
T ss_dssp             HHHHHHSCEE-TTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEecccccc-cCCeeeeecCCCCChHHHHHHHHHh
Confidence            4566665421 1345789999999999999888773

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=92.12  E-value=0.077  Score=44.24  Aligned_cols=22  Identities=23%  Similarity=0.252  Sum_probs=19.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      --|.|+|.+|+|||||...+.+
T Consensus         3 ~ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            3 FKVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            3478999999999999998864

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.12  E-value=0.077  Score=44.10  Aligned_cols=22  Identities=14%  Similarity=0.243  Sum_probs=19.2

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|.+|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4789999999999999988764

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=92.12  E-value=0.08  Score=49.74  Aligned_cols=24  Identities=17%  Similarity=0.166  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|.|+|+.|+||||||..+..
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~   32 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRK   32 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHH
Confidence            357899999999999999999876

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=92.09  E-value=0.13  Score=51.88  Aligned_cols=23  Identities=17%  Similarity=0.170  Sum_probs=19.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ...+|.|+|.+|+||||++..+.
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA  122 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLA  122 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHH
Confidence            46799999999999999998876

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=92.06  E-value=0.079  Score=43.81  Aligned_cols=22  Identities=27%  Similarity=0.406  Sum_probs=19.2

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||...+.+.
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999888754

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=92.06  E-value=0.079  Score=44.09  Aligned_cols=23  Identities=17%  Similarity=0.260  Sum_probs=19.9

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.|+|.+|+|||||...+.+.
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35789999999999999998764

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.05  E-value=0.069  Score=46.58  Aligned_cols=24  Identities=21%  Similarity=0.018  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+|+|..|+|||||.+.+...
T Consensus        26 ~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           26 GIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            567999999999999999988764

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=92.01  E-value=0.084  Score=47.38  Aligned_cols=25  Identities=16%  Similarity=0.260  Sum_probs=22.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|.|.|+.|+||||+++.+.+.
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            3578999999999999999998873

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=91.97  E-value=0.1  Score=43.90  Aligned_cols=25  Identities=24%  Similarity=0.292  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcC
Confidence            4556889999999999999998764

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=91.95  E-value=0.085  Score=45.01  Aligned_cols=24  Identities=17%  Similarity=0.131  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            7 KCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHhcC
Confidence            445789999999999999998764

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=91.94  E-value=0.082  Score=44.55  Aligned_cols=25  Identities=32%  Similarity=0.396  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3556889999999999999988764

>1h65_A Chloroplast outer envelope protein OEP34; GTPase, translocon; HET: GDP; 2.0A {Pisum sativum} SCOP: c.37.1.8 PDB: 3bb1_A*

Probab=91.93  E-value=0.19  Score=46.00  Aligned_cols=37  Identities=11%  Similarity=0.207  Sum_probs=26.7

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      +++..+.........|.++|.+|+|||||...+.+..
T Consensus        27 ~~~~~~~~~~~~~~~I~vvG~~g~GKSSLin~l~~~~   63 (270)
T 1h65_A           27 ELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGER   63 (270)
T ss_dssp             HHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHhhcCCCCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            3444444444445678899999999999999988743

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=91.93  E-value=0.094  Score=47.20  Aligned_cols=24  Identities=13%  Similarity=0.080  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|.|.|..|+||||+++.+.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHH
Confidence            467999999999999999998873

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=91.89  E-value=0.11  Score=44.25  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=21.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ...|.|+|.+|+|||||...+.+..
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           23 KGEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             TCEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHcCc
Confidence            4568899999999999999988753

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=91.88  E-value=0.55  Score=46.58  Aligned_cols=24  Identities=25%  Similarity=0.350  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.++.|.|.+|+|||||+..+..+
T Consensus       203 G~liiI~G~pG~GKTtl~l~ia~~  226 (454)
T 2r6a_A          203 SDLIIVAARPSVGKTAFALNIAQN  226 (454)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999999887653

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=91.85  E-value=0.086  Score=50.71  Aligned_cols=23  Identities=22%  Similarity=0.215  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            45899999999999999999864

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=91.85  E-value=0.093  Score=44.69  Aligned_cols=22  Identities=9%  Similarity=0.105  Sum_probs=19.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||...+.+.
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4789999999999999998774

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=91.84  E-value=0.11  Score=44.60  Aligned_cols=25  Identities=28%  Similarity=0.444  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|.|+|.+|+|||||...+.+.
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3566889999999999999998774

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=91.83  E-value=0.09  Score=43.74  Aligned_cols=23  Identities=13%  Similarity=0.286  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.|+|.+|+|||||...+.+.
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            45789999999999999988764

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=91.81  E-value=0.082  Score=45.92  Aligned_cols=34  Identities=12%  Similarity=-0.021  Sum_probs=24.1

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +++.+.-... ..-|.++|.+|+|||||...+.+.
T Consensus        15 ~l~~~~~~~~-~~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           15 VLQFLGLYKK-TGKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             HHHHHTCTTC-CEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             HHHHhhccCC-CcEEEEECCCCCCHHHHHHHHhcC
Confidence            4444432222 345789999999999999998763

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=91.77  E-value=0.2  Score=45.78  Aligned_cols=37  Identities=19%  Similarity=0.308  Sum_probs=27.2

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ++.+.+.........|+++|..|+|||||...+....
T Consensus        24 ~~~~~~~~~~~~~~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           24 EFFGKLKQKDMNSMTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             HHHHHHHHTTCCEEEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             HHHHHHhhccCCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            4444444444445678999999999999999988743

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=91.76  E-value=0.13  Score=43.26  Aligned_cols=25  Identities=12%  Similarity=0.255  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|..|+|||||...+.+.
T Consensus         8 ~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            8 ETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3566889999999999999998764

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=91.72  E-value=0.083  Score=45.22  Aligned_cols=23  Identities=13%  Similarity=-0.094  Sum_probs=19.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .--|.|+|.+|+|||||.+.+.+
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~   36 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYS   36 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            34578999999999999987765

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=91.68  E-value=0.091  Score=44.15  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999998764

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=91.65  E-value=0.16  Score=46.57  Aligned_cols=34  Identities=9%  Similarity=0.024  Sum_probs=26.3

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..||....+....|.++|++|.|||++|..+.+
T Consensus        93 l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           93 FLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHh
Confidence            5555555423455689999999999999999887

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=91.63  E-value=0.11  Score=43.89  Aligned_cols=24  Identities=17%  Similarity=0.205  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            6 SRKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            456889999999999999998854

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=91.63  E-value=0.095  Score=43.53  Aligned_cols=23  Identities=13%  Similarity=0.172  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.|+|.+|+|||||...+.+.
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            45789999999999999988753

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=91.62  E-value=0.098  Score=44.01  Aligned_cols=24  Identities=13%  Similarity=0.109  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            345789999999999999988764

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=91.61  E-value=0.089  Score=43.59  Aligned_cols=21  Identities=10%  Similarity=0.025  Sum_probs=18.6

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.+.
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            689999999999999988653

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=91.59  E-value=0.097  Score=45.07  Aligned_cols=23  Identities=17%  Similarity=0.102  Sum_probs=20.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-|.++|.+|+|||||...+.+.
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            35789999999999999988763

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=91.58  E-value=0.11  Score=44.14  Aligned_cols=24  Identities=17%  Similarity=0.351  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCc
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      --|.|+|.+|+|||||...+.+..
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            357899999999999999987643

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=91.58  E-value=0.094  Score=44.93  Aligned_cols=24  Identities=17%  Similarity=0.097  Sum_probs=19.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            445789999999999999877654

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=91.57  E-value=0.098  Score=44.41  Aligned_cols=24  Identities=13%  Similarity=0.221  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999988764

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=91.56  E-value=0.094  Score=46.94  Aligned_cols=23  Identities=26%  Similarity=0.267  Sum_probs=19.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.|.|.+|+|||||+.++..
T Consensus        23 G~~~~i~G~~GsGKTtl~~~~~~   45 (247)
T 2dr3_A           23 RNVVLLSGGPGTGKTIFSQQFLW   45 (247)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            45889999999999999877653

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=91.55  E-value=0.097  Score=43.96  Aligned_cols=24  Identities=13%  Similarity=0.181  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999998764

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=91.53  E-value=0.098  Score=43.60  Aligned_cols=24  Identities=21%  Similarity=0.077  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=91.52  E-value=0.26  Score=55.77  Aligned_cols=23  Identities=22%  Similarity=0.196  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..|+|||..|.|||||++.+..
T Consensus      1105 Ge~vaIVG~SGsGKSTL~~lL~r 1127 (1321)
T 4f4c_A         1105 GQTLALVGPSGCGKSTVVALLER 1127 (1321)
T ss_dssp             TCEEEEECSTTSSTTSHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            45799999999999999999875

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.51  E-value=0.11  Score=45.66  Aligned_cols=25  Identities=12%  Similarity=0.016  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|.++|.+|+|||||...+.+.
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3566889999999999999998774

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=91.51  E-value=0.11  Score=49.78  Aligned_cols=24  Identities=17%  Similarity=0.041  Sum_probs=21.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|.+|+|||||...+..
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~   96 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGK   96 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHH
Confidence            478999999999999999998875

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=91.51  E-value=0.11  Score=49.96  Aligned_cols=24  Identities=17%  Similarity=0.160  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.++.|+|.+|+|||||+.++..
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~  153 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAV  153 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999998875

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=91.50  E-value=0.11  Score=43.94  Aligned_cols=24  Identities=13%  Similarity=0.333  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           18 TYKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456789999999999999998864

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=91.49  E-value=0.088  Score=45.64  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=20.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...-|.|+|.+|+|||||...+.+
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHTCC
T ss_pred             cEEEEEEECCCCCCHHHHHHHHHh
Confidence            356688999999999999999853

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=91.49  E-value=0.086  Score=48.21  Aligned_cols=25  Identities=12%  Similarity=0.078  Sum_probs=22.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|.|.|..|+||||+++.+.+.
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~   47 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQL   47 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHh
Confidence            3678999999999999999998873

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.48  E-value=0.23  Score=42.27  Aligned_cols=24  Identities=21%  Similarity=0.040  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            566889999999999999998854

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=91.47  E-value=0.053  Score=53.58  Aligned_cols=24  Identities=21%  Similarity=0.385  Sum_probs=20.4

Q ss_pred             EEEEecCCCchHHHHHHhhcCccc
Q 040913          193 VAILDSSGFDKTAFAADTYNNNHV  216 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~~~~  216 (425)
                      ++|.|..|+|||+|+.++.+....
T Consensus       154 ~~Ifgg~G~GKt~L~~~Ia~~~~~  177 (465)
T 3vr4_D          154 LPVFSGSGLPHKELAAQIARQATV  177 (465)
T ss_dssp             CCEEECTTSCHHHHHHHHHHHCBC
T ss_pred             EEEeCCCCcChHHHHHHHHHHHHh
Confidence            678999999999999998885443

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.47  E-value=0.097  Score=50.30  Aligned_cols=23  Identities=26%  Similarity=0.202  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999998863

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=91.45  E-value=0.1  Score=43.76  Aligned_cols=23  Identities=13%  Similarity=0.150  Sum_probs=19.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.|+|..|+|||||...+.+.
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45789999999999999998753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=91.43  E-value=0.56  Score=46.40  Aligned_cols=29  Identities=28%  Similarity=0.108  Sum_probs=22.4

Q ss_pred             cCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          185 EGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       185 ~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+=..-.++.|.|.+|+||||||..+..+
T Consensus       195 gGl~~G~l~ii~G~pg~GKT~lal~ia~~  223 (444)
T 2q6t_A          195 GTLGPGSLNIIAARPAMGKTAFALTIAQN  223 (444)
T ss_dssp             CCCCTTCEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCcCCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            33233568889999999999999887653

>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=91.42  E-value=0.19  Score=49.44  Aligned_cols=24  Identities=8%  Similarity=0.122  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|+|+.|+|||||.+.+..
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg  189 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQ  189 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHh
Confidence            357899999999999999998865

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.41  E-value=0.091  Score=44.51  Aligned_cols=25  Identities=20%  Similarity=0.042  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3566889999999999999998754

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=91.40  E-value=0.1  Score=44.79  Aligned_cols=24  Identities=25%  Similarity=0.275  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhC
Confidence            345789999999999999888764

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=91.30  E-value=0.096  Score=50.48  Aligned_cols=23  Identities=22%  Similarity=0.211  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...++|+|..|+|||||++.+..
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~g  192 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAA  192 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHH
Confidence            46889999999999999998865

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=91.27  E-value=0.11  Score=44.05  Aligned_cols=23  Identities=13%  Similarity=0.153  Sum_probs=19.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.++|.+|+|||||...+.++
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35789999999999999888754

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=91.25  E-value=0.11  Score=44.02  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhC
Confidence            456789999999999999998764

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=91.24  E-value=0.096  Score=49.12  Aligned_cols=20  Identities=15%  Similarity=0.413  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |+|+|..|+|||||.+.++.
T Consensus        21 I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           21 LMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEETTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            48999999999999999876

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=91.20  E-value=0.11  Score=44.98  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        14 ~~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           14 LHKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999988764

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=91.19  E-value=0.11  Score=50.09  Aligned_cols=23  Identities=30%  Similarity=0.186  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAG   51 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHHC
Confidence            45899999999999999998864

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=91.15  E-value=0.11  Score=50.42  Aligned_cols=23  Identities=17%  Similarity=0.160  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaG   51 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAG   51 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHHc
Confidence            45899999999999999998864

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=91.14  E-value=0.11  Score=44.21  Aligned_cols=24  Identities=25%  Similarity=0.216  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        11 ~~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           11 LIKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456789999999999999998764

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=91.14  E-value=0.11  Score=43.80  Aligned_cols=23  Identities=13%  Similarity=0.105  Sum_probs=19.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.|+|.+|+|||||...+.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34789999999999999988764

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=91.13  E-value=0.11  Score=44.76  Aligned_cols=23  Identities=4%  Similarity=0.111  Sum_probs=19.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-|.++|.+|+|||||.+.+.+
T Consensus        20 ~~ki~~vG~~~vGKTsLi~~l~~   42 (196)
T 3llu_A           20 KPRILLMGLRRSGKSSIQKVVFH   42 (196)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            34578999999999999987766

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=91.13  E-value=0.11  Score=50.09  Aligned_cols=23  Identities=22%  Similarity=0.216  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAG   51 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            45899999999999999998863

>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=91.13  E-value=0.13  Score=45.10  Aligned_cols=23  Identities=26%  Similarity=0.138  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+.|.|.|+.|+||||||..+..
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~   56 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQ   56 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46688999999999999998865

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=91.13  E-value=0.11  Score=44.57  Aligned_cols=24  Identities=25%  Similarity=0.317  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|..|+|||||...+.+.
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999988764

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=91.09  E-value=0.12  Score=50.50  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|.|+.|+||||||..+..
T Consensus         2 ~~~i~i~GptgsGKttla~~La~   24 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQ   24 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHH
T ss_pred             CcEEEEECcchhhHHHHHHHHHH
Confidence            36899999999999999988765

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=91.08  E-value=0.11  Score=43.73  Aligned_cols=24  Identities=13%  Similarity=0.213  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+...
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            345789999999999999988764

>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=91.07  E-value=0.11  Score=50.26  Aligned_cols=110  Identities=15%  Similarity=0.173  Sum_probs=57.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCC--cc--CCCCHHHHHHHHHHHhcCCeE
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVT--VI--IGEDYKLKKSILRDFLTNKKY  264 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~--~~--~~~~~~~l~~~l~~~l~~kr~  264 (425)
                      .-.+++|+|+.|+|||||++.+..-....  ....+.+..+-. .+.......  ..  ...+...+...+...|....-
T Consensus       135 ~g~~i~ivG~~GsGKTTll~~l~~~~~~~--~~g~I~~~e~~~-e~~~~~~~~~v~Q~~~g~~~~~~~~~l~~~L~~~pd  211 (372)
T 2ewv_A          135 KMGLILVTGPTGSGKSTTIASMIDYINQT--KSYHIITIEDPI-EYVFKHKKSIVNQREVGEDTKSFADALRAALREDPD  211 (372)
T ss_dssp             SSEEEEEECSSSSSHHHHHHHHHHHHHHH--SCCEEEEEESSC-CSCCCCSSSEEEEEEBTTTBSCSHHHHHHHTTSCCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhcCcC--CCcEEEEecccH-hhhhccCceEEEeeecCCCHHHHHHHHHHHhhhCcC
Confidence            35789999999999999998876521100  000000000000 000000000  00  000112334567777777777


Q ss_pred             EEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          265 FIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       265 LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      +|++|.+. +.+.........   ..|..|+.|+...++..
T Consensus       212 ~illdE~~-d~e~~~~~l~~~---~~g~~vi~t~H~~~~~~  248 (372)
T 2ewv_A          212 VIFVGEMR-DLETVETALRAA---ETGHLVFGTLHTNTAID  248 (372)
T ss_dssp             EEEESCCC-SHHHHHHHHHHH---TTTCEEEECCCCCSHHH
T ss_pred             EEEECCCC-CHHHHHHHHHHH---hcCCEEEEEECcchHHH
Confidence            89999997 665544432222   23667888888876544

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=91.06  E-value=0.086  Score=44.49  Aligned_cols=23  Identities=9%  Similarity=0.117  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.++|.+|+|||||...+.+.
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            45789999999999999988764

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=91.04  E-value=0.12  Score=43.90  Aligned_cols=25  Identities=12%  Similarity=0.042  Sum_probs=21.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ..-|.|+|.+|+|||||...+.+..
T Consensus        18 ~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           18 ELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcCC
Confidence            5568899999999999999988754

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=91.02  E-value=0.11  Score=50.20  Aligned_cols=23  Identities=22%  Similarity=0.133  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (372)
T 1g29_1           29 GEFMILLGPSGCGKTTTLRMIAG   51 (372)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCcHHHHHHHHHHc
Confidence            35899999999999999998863

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=91.02  E-value=0.13  Score=46.97  Aligned_cols=21  Identities=24%  Similarity=0.302  Sum_probs=18.0

Q ss_pred             EEEEEEecCCCchHHHHHHhh
Q 040913          191 SVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ++|+|.|-||+||||+|..+.
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA   22 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLT   22 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHH
T ss_pred             cEEEEecCCCCcHHHHHHHHH
Confidence            578889999999999986655

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=90.97  E-value=0.091  Score=54.24  Aligned_cols=22  Identities=14%  Similarity=0.117  Sum_probs=19.7

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|++|+|||+||+.+.+.
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTT
T ss_pred             ceEEECCCchHHHHHHHHHHHh
Confidence            4778999999999999999873

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=90.96  E-value=0.12  Score=43.53  Aligned_cols=24  Identities=21%  Similarity=0.228  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.++|.+|+|||||...+.+.
T Consensus        10 ~~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           10 AFKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456789999999999999998764

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=90.95  E-value=0.12  Score=44.39  Aligned_cols=24  Identities=17%  Similarity=0.275  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|..|+|||||...+.+.
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=90.94  E-value=0.13  Score=44.40  Aligned_cols=24  Identities=8%  Similarity=-0.047  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhC
Confidence            455889999999999999998754

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=90.93  E-value=0.12  Score=50.09  Aligned_cols=23  Identities=22%  Similarity=0.148  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaG   59 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAG   59 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            45899999999999999999864

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=90.92  E-value=0.14  Score=44.22  Aligned_cols=25  Identities=36%  Similarity=0.367  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3556889999999999999988764

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=90.85  E-value=0.24  Score=42.22  Aligned_cols=25  Identities=16%  Similarity=-0.044  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|.+|+|||||...+.++
T Consensus        21 ~~~~i~v~G~~~~GKssli~~l~~~   45 (189)
T 2x77_A           21 RKIRVLMLGLDNAGKTSILYRLHLG   45 (189)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHcC
Confidence            3456889999999999999998654

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=90.85  E-value=0.13  Score=44.50  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=90.83  E-value=0.13  Score=44.63  Aligned_cols=24  Identities=25%  Similarity=0.212  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        24 ~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           24 YRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             cEEEEEECCCCcCHHHHHHHHHhC
Confidence            456889999999999999998864

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=90.82  E-value=0.13  Score=45.07  Aligned_cols=24  Identities=17%  Similarity=0.131  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456789999999999999998764

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=90.80  E-value=0.12  Score=49.52  Aligned_cols=24  Identities=21%  Similarity=0.268  Sum_probs=21.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||.+.+.+.
T Consensus        71 Gq~~gIiG~nGaGKTTLl~~I~g~   94 (347)
T 2obl_A           71 GQRIGIFAGSGVGKSTLLGMICNG   94 (347)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            458999999999999999999874

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=90.78  E-value=0.16  Score=43.61  Aligned_cols=26  Identities=12%  Similarity=-0.018  Sum_probs=22.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ...-|.|+|.+|+|||||...+.+..
T Consensus        16 ~~~ki~v~G~~~~GKSsl~~~l~~~~   41 (199)
T 4bas_A           16 TKLQVVMCGLDNSGKTTIINQVKPAQ   41 (199)
T ss_dssp             CEEEEEEECCTTSCHHHHHHHHSCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            46778999999999999999988753

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=90.77  E-value=0.13  Score=44.41  Aligned_cols=24  Identities=21%  Similarity=0.288  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            445789999999999999988764

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=90.74  E-value=0.18  Score=44.77  Aligned_cols=25  Identities=8%  Similarity=0.108  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|.|+|.+|+|||||...+.+.
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3567889999999999999998774

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=90.73  E-value=0.1  Score=45.98  Aligned_cols=22  Identities=14%  Similarity=0.107  Sum_probs=20.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|.|+.|+||||+++.+..
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999998876

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=90.72  E-value=0.18  Score=43.95  Aligned_cols=24  Identities=13%  Similarity=0.130  Sum_probs=20.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.++
T Consensus        30 ~~ki~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           30 AIKCVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            445789999999999999888764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=90.71  E-value=0.13  Score=44.13  Aligned_cols=24  Identities=13%  Similarity=0.134  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            345789999999999999998875

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=90.70  E-value=0.11  Score=50.16  Aligned_cols=23  Identities=17%  Similarity=0.252  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~  197 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQ  197 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            35799999999999999999876

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=90.69  E-value=0.14  Score=47.97  Aligned_cols=25  Identities=12%  Similarity=0.179  Sum_probs=21.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|+|+|.+|+|||||...+...
T Consensus         7 r~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            7 YCGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHCC
Confidence            3568999999999999999998764

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=90.66  E-value=0.15  Score=44.58  Aligned_cols=24  Identities=13%  Similarity=0.036  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|.|+|.+|+|||||...+.+.
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            446789999999999999998764

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=90.65  E-value=0.16  Score=47.73  Aligned_cols=26  Identities=15%  Similarity=0.295  Sum_probs=23.0

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .....|+|+|.+|+|||||...+...
T Consensus         8 ~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            8 MKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            45789999999999999999998764

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=90.63  E-value=0.15  Score=47.15  Aligned_cols=22  Identities=18%  Similarity=0.291  Sum_probs=18.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .++|+|.|-||+||||+|..+.
T Consensus         2 MkvIavs~KGGvGKTT~a~nLA   23 (289)
T 2afh_E            2 MRQCAIYGKGGIGKSTTTQNLV   23 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHH
T ss_pred             ceEEEEeCCCcCcHHHHHHHHH
Confidence            4688899999999999987665

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=90.60  E-value=0.13  Score=44.35  Aligned_cols=24  Identities=13%  Similarity=0.131  Sum_probs=20.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            455789999999999999988764

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=90.58  E-value=0.14  Score=44.43  Aligned_cols=24  Identities=21%  Similarity=0.281  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456789999999999999988764

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=90.57  E-value=0.13  Score=43.86  Aligned_cols=24  Identities=17%  Similarity=0.260  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999998764

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=90.56  E-value=0.21  Score=42.63  Aligned_cols=25  Identities=16%  Similarity=0.212  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..--|.|+|..|+|||||...+.+.
T Consensus        15 ~~~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           15 YLFKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3456889999999999999998864

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=90.56  E-value=0.14  Score=43.90  Aligned_cols=24  Identities=13%  Similarity=0.018  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcC
Confidence            345789999999999999998764

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=90.55  E-value=0.14  Score=44.06  Aligned_cols=24  Identities=8%  Similarity=0.105  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.++|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcC
Confidence            445789999999999999998874

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=90.54  E-value=0.097  Score=50.17  Aligned_cols=23  Identities=26%  Similarity=0.193  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaG   48 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAG   48 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCccHHHHHHHHHc
Confidence            45899999999999999999874

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=90.53  E-value=0.12  Score=49.14  Aligned_cols=104  Identities=14%  Similarity=0.080  Sum_probs=54.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCC-CCCC-ccCCCCHHHHHHHHHHHhcCCeEEEEe
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPP-SRVT-VIIGEDYKLKKSILRDFLTNKKYFIAL  268 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~-~~~~-~~~~~~~~~l~~~l~~~l~~kr~LlVL  268 (425)
                      .+++|+|..|+|||||++.+..-.....   ..+.+ .+. ..+... .... .............+...|..+.-+|+|
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~~---g~i~i-~~~-~e~~~~~~~~~i~~~~ggg~~~r~~la~aL~~~p~ilil  246 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKEE---RIISI-EDT-EEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIIL  246 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTTS---CEEEE-ESS-CCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCCC---cEEEE-CCe-eccccccchhEEEEEeCCChhHHHHHHHHhhhCCCEEEE
Confidence            4789999999999999999886321111   01110 000 000000 0000 000001223445666777778889999


Q ss_pred             cccCCChhhHHHHHhhCCCCCCCcEEEEecCChhH
Q 040913          269 DDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSL  303 (425)
Q Consensus       269 Ddvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~v  303 (425)
                      |.+. +.+.++.+... ..+  +..+|+||...+.
T Consensus       247 dE~~-~~e~~~~l~~~-~~g--~~tvi~t~H~~~~  277 (330)
T 2pt7_A          247 GELR-SSEAYDFYNVL-CSG--HKGTLTTLHAGSS  277 (330)
T ss_dssp             CCCC-STHHHHHHHHH-HTT--CCCEEEEEECSSH
T ss_pred             cCCC-hHHHHHHHHHH-hcC--CCEEEEEEcccHH
Confidence            9998 76666655443 221  2236666665553

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=90.52  E-value=0.13  Score=44.14  Aligned_cols=24  Identities=13%  Similarity=0.188  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            8 DYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCcHHHHHHHHHcC
Confidence            456789999999999999998763

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=90.52  E-value=0.13  Score=44.31  Aligned_cols=23  Identities=17%  Similarity=0.206  Sum_probs=19.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-|.|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            34588999999999999988764

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=90.51  E-value=0.13  Score=44.04  Aligned_cols=24  Identities=21%  Similarity=0.277  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            445789999999999999988764

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=90.48  E-value=0.13  Score=44.82  Aligned_cols=24  Identities=17%  Similarity=0.302  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456889999999999999987753

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=90.47  E-value=0.14  Score=43.89  Aligned_cols=25  Identities=20%  Similarity=0.037  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      .--|.|+|..|+|||||...+.+..
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           21 EVHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             CEEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcCC
Confidence            3457899999999999999988754

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=90.46  E-value=0.14  Score=43.94  Aligned_cols=24  Identities=17%  Similarity=0.250  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            345789999999999999988764

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=90.46  E-value=0.13  Score=44.15  Aligned_cols=24  Identities=25%  Similarity=0.289  Sum_probs=20.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|..|+|||||...+.+.
T Consensus        26 ~~ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           26 KLQVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHCC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            345789999999999999998764

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=90.40  E-value=0.14  Score=43.36  Aligned_cols=24  Identities=21%  Similarity=0.040  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|..|+|||||...+.+.
T Consensus        21 ~~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           21 EHKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            446789999999999999998764

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=90.40  E-value=0.19  Score=50.72  Aligned_cols=44  Identities=5%  Similarity=-0.069  Sum_probs=29.2

Q ss_pred             cccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          169 ISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+.+.+..+.+.+.......+..+|.+.|+.|+||||+|+.+..
T Consensus       374 ~f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~  417 (511)
T 1g8f_A          374 WFSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLS  417 (511)
T ss_dssp             TTSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHH
T ss_pred             cccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHH
Confidence            33444443444443322223457899999999999999999887

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=90.38  E-value=0.14  Score=49.77  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhC
Confidence            45899999999999999999874

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=90.37  E-value=0.15  Score=44.67  Aligned_cols=29  Identities=17%  Similarity=0.103  Sum_probs=23.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCccccccc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      ..+|+|.|+.|+||||+++.+..  +..-.|
T Consensus         6 ~~iI~i~g~~GsGk~ti~~~la~--~lg~~~   34 (201)
T 3fdi_A            6 QIIIAIGREFGSGGHLVAKKLAE--HYNIPL   34 (201)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHH--HTTCCE
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHH--HhCcCE
Confidence            35899999999999999999988  444333

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=90.37  E-value=0.14  Score=43.68  Aligned_cols=24  Identities=13%  Similarity=0.191  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|..|+|||||...+.+.
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            456889999999999999998754

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=90.35  E-value=0.15  Score=44.31  Aligned_cols=24  Identities=17%  Similarity=0.286  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            8 LFKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=90.34  E-value=0.15  Score=43.63  Aligned_cols=24  Identities=17%  Similarity=0.256  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        15 ~~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           15 TLKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            346789999999999999998764

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=90.29  E-value=0.14  Score=44.20  Aligned_cols=24  Identities=13%  Similarity=0.221  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            456889999999999999998764

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=90.22  E-value=0.15  Score=44.72  Aligned_cols=24  Identities=17%  Similarity=0.174  Sum_probs=20.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC-
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            456789999999999999998764

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=90.18  E-value=0.14  Score=50.39  Aligned_cols=20  Identities=15%  Similarity=0.451  Sum_probs=18.9

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|+|..|+|||||.+.++.
T Consensus        45 vaLvG~nGaGKSTLln~L~G   64 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFN   64 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            99999999999999999876

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=90.14  E-value=0.16  Score=44.29  Aligned_cols=24  Identities=8%  Similarity=0.086  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           25 RKKLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHhcC
Confidence            346889999999999999988764

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=90.12  E-value=0.17  Score=49.80  Aligned_cols=23  Identities=22%  Similarity=0.078  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.++|.+|+||||++..+..
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~  120 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLAL  120 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999887764

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=90.09  E-value=0.057  Score=58.56  Aligned_cols=21  Identities=14%  Similarity=0.037  Sum_probs=19.6

Q ss_pred             cEEEEEEecCCCchHHHHHHh
Q 040913          190 LSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      -.+++|+|+.|.||||+.+.+
T Consensus       662 g~i~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHH
Confidence            578999999999999999988

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=90.08  E-value=0.089  Score=50.55  Aligned_cols=23  Identities=30%  Similarity=0.224  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~llGpnGsGKSTLLr~iaG   53 (353)
T 1oxx_K           31 GERFGILGPSGAGKTTFMRIIAG   53 (353)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999998863

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=90.08  E-value=0.22  Score=43.66  Aligned_cols=24  Identities=8%  Similarity=-0.103  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|+|+|++|+||+|.|..+.+
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~   33 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQS   33 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHH
Confidence            467999999999999999988765

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=90.03  E-value=0.72  Score=52.16  Aligned_cols=24  Identities=25%  Similarity=0.235  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -..++|||..|+|||||++.+..-
T Consensus       444 G~~vaivG~sGsGKSTll~ll~~~  467 (1321)
T 4f4c_A          444 GQTVALVGSSGCGKSTIISLLLRY  467 (1321)
T ss_dssp             TCEEEEEECSSSCHHHHHHHHTTS
T ss_pred             CcEEEEEecCCCcHHHHHHHhccc
Confidence            468999999999999999998763

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=90.03  E-value=0.19  Score=46.11  Aligned_cols=24  Identities=21%  Similarity=0.212  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+++|.+|+|||||...+...
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            456899999999999999998764

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=89.96  E-value=0.19  Score=45.00  Aligned_cols=26  Identities=12%  Similarity=0.196  Sum_probs=22.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ...-|+++|.+|+|||||...+....
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCCC
Confidence            35678999999999999999988743

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=89.92  E-value=0.15  Score=45.75  Aligned_cols=22  Identities=18%  Similarity=0.098  Sum_probs=19.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-++|.|++|+||||+|+.+.+
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~   30 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKE   30 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHH
Confidence            4579999999999999998876

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=89.90  E-value=0.17  Score=43.42  Aligned_cols=24  Identities=13%  Similarity=0.202  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        18 ~~ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           18 MLKCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            346889999999999999998864

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=89.89  E-value=0.18  Score=51.18  Aligned_cols=23  Identities=13%  Similarity=0.128  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.++|++|+||||+|+.+..
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~   57 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTR   57 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999865

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=89.88  E-value=0.17  Score=44.12  Aligned_cols=24  Identities=13%  Similarity=0.072  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus         9 ~~ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A            9 FIKCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            345789999999999999988764

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=89.88  E-value=0.17  Score=43.91  Aligned_cols=24  Identities=13%  Similarity=0.152  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        29 ~~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           29 LFKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhhC
Confidence            556889999999999999988764

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=89.79  E-value=0.18  Score=43.74  Aligned_cols=24  Identities=13%  Similarity=0.098  Sum_probs=20.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus        25 ~~ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           25 RKKLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            345789999999999999988764

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=89.78  E-value=0.29  Score=48.92  Aligned_cols=35  Identities=23%  Similarity=0.094  Sum_probs=23.5

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHH-HHhhcC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFA-ADTYNN  213 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa-~~v~~~  213 (425)
                      +.++.|..=. .-.-++|+|..|+|||+|| ..+.|.
T Consensus       164 raID~l~Pig-rGQR~~I~g~~g~GKT~Lal~~I~~~  199 (515)
T 2r9v_A          164 KAIDSMIPIG-RGQRELIIGDRQTGKTAIAIDTIINQ  199 (515)
T ss_dssp             HHHHHHSCEE-TTCBEEEEEETTSSHHHHHHHHHHTT
T ss_pred             cccccccccc-cCCEEEEEcCCCCCccHHHHHHHHHh
Confidence            3455554321 1234789999999999995 577774

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=89.69  E-value=0.17  Score=44.64  Aligned_cols=23  Identities=17%  Similarity=0.206  Sum_probs=19.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..-|.|+|.+|+|||||...+..
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            45588999999999999998764

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=89.69  E-value=0.14  Score=51.10  Aligned_cols=24  Identities=21%  Similarity=0.140  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|+|..|+|||||++.+..-
T Consensus       138 Ge~v~IvGpnGsGKSTLlr~L~Gl  161 (460)
T 2npi_A          138 GPRVVIVGGSQTGKTSLSRTLCSY  161 (460)
T ss_dssp             CCCEEEEESTTSSHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCc
Confidence            457999999999999999988763

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=89.69  E-value=0.093  Score=51.86  Aligned_cols=25  Identities=24%  Similarity=0.337  Sum_probs=20.8

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccc
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHV  216 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~  216 (425)
                      -++|.|..|+|||+|+.++.+....
T Consensus       149 r~~Ifgg~G~GKt~L~~~Ia~~~~a  173 (464)
T 3gqb_B          149 KLPIFSGSGLPANEIAAQIARQATV  173 (464)
T ss_dssp             BCCEEEETTSCHHHHHHHHHHHCBC
T ss_pred             EEEEecCCCCCchHHHHHHHHHHHh
Confidence            4678999999999999998885443

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=89.67  E-value=0.17  Score=48.53  Aligned_cols=23  Identities=13%  Similarity=0.180  Sum_probs=20.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+++|+|++|+|||||.+.+...
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~  238 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGL  238 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CEEEEECCCCccHHHHHHHHhcc
Confidence            47899999999999999999873

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=89.66  E-value=0.17  Score=43.93  Aligned_cols=24  Identities=13%  Similarity=0.313  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+...
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999988754

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=89.62  E-value=0.11  Score=44.03  Aligned_cols=24  Identities=21%  Similarity=0.235  Sum_probs=10.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-|.|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            8 LFKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEEECCCCC------------
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999887753

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=89.61  E-value=0.23  Score=49.71  Aligned_cols=77  Identities=12%  Similarity=0.091  Sum_probs=44.2

Q ss_pred             EEEEEEecCCCchHHHH-HHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC----------ccCC--C---
Q 040913          191 SVVAILDSSGFDKTAFA-ADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT----------VIIG--E---  246 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa-~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~----------~~~~--~---  246 (425)
                      .-++|+|..|+|||+|| ..+.|..  ...+- ++++        ..++.+.+.......          ....  .   
T Consensus       164 QR~~Ifg~~g~GKT~Lal~~I~~~~--~~dv~-~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~  240 (507)
T 1fx0_A          164 QRELIIGDRQTGKTAVATDTILNQQ--GQNVI-CVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAP  240 (507)
T ss_dssp             CBCBEEESSSSSHHHHHHHHHHTCC--TTTCE-EEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHH
T ss_pred             CEEEEecCCCCCccHHHHHHHHHhh--cCCcE-EEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHHH
Confidence            34689999999999995 5777743  22221 2233        666666665432110          0000  1   


Q ss_pred             -CHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          247 -DYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       247 -~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                       ..-.+.+.++.  +|+..||++||+-
T Consensus       241 ~~a~tiAEyfrd--~G~dVLli~Dslt  265 (507)
T 1fx0_A          241 YTGAALAEYFMY--RERHTLIIYDDLS  265 (507)
T ss_dssp             HHHHHHHHHHHH--TTCEEEEEEECHH
T ss_pred             HHHHHHHHHHHH--cCCcEEEEEecHH
Confidence             11233344444  5899999999984

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=89.56  E-value=0.22  Score=41.30  Aligned_cols=23  Identities=13%  Similarity=0.182  Sum_probs=19.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++..|+|+.|.||||+..+++-
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~   45 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILV   45 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999888753

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=89.55  E-value=0.14  Score=52.26  Aligned_cols=23  Identities=22%  Similarity=0.049  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+|.|+|+.|+|||||++.+..
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~  391 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAA  391 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHH
Confidence            57899999999999999999887

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=89.54  E-value=0.18  Score=47.20  Aligned_cols=31  Identities=19%  Similarity=0.203  Sum_probs=25.0

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhh
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .+++.+.+.     -.+++++|+.|+|||||.+.+.
T Consensus       156 i~~L~~~l~-----G~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          156 IDELVDYLE-----GFICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             HHHHHHHTT-----TCEEEEECSTTSSHHHHHHHHH
T ss_pred             HHHHHhhcc-----CcEEEEECCCCCCHHHHHHHHH
Confidence            556666554     2478999999999999999987

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=89.40  E-value=0.2  Score=43.86  Aligned_cols=24  Identities=33%  Similarity=0.358  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|..|+|||||...+.+.
T Consensus        25 ~~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           25 LIKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHCS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=89.39  E-value=0.35  Score=48.31  Aligned_cols=35  Identities=20%  Similarity=0.063  Sum_probs=23.3

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHH-HHhhcC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFA-ADTYNN  213 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa-~~v~~~  213 (425)
                      +.++.|..=.. -.-++|+|..|+|||+|| ..+.|.
T Consensus       151 raID~l~Pigr-GQR~~Ifg~~g~GKT~Lal~~I~~~  186 (502)
T 2qe7_A          151 KAIDSMIPIGR-GQRELIIGDRQTGKTTIAIDTIINQ  186 (502)
T ss_dssp             HHHHHSSCCBT-TCBCEEEECSSSCHHHHHHHHHHGG
T ss_pred             eeccccccccc-CCEEEEECCCCCCchHHHHHHHHHh
Confidence            34555543211 234689999999999995 577774

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=89.32  E-value=0.18  Score=49.63  Aligned_cols=21  Identities=14%  Similarity=0.401  Sum_probs=19.1

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |+|+|..|+|||||.+.+...
T Consensus        34 I~lvG~sGaGKSTLln~L~g~   54 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLT   54 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            499999999999999998864

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=89.31  E-value=0.19  Score=44.55  Aligned_cols=22  Identities=14%  Similarity=0.199  Sum_probs=18.6

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|-+|+|||+|...+.++
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            3678999999999999987653

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=89.28  E-value=0.19  Score=44.12  Aligned_cols=24  Identities=13%  Similarity=0.079  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        27 ~~ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           27 RCKLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            345779999999999999998764

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=89.24  E-value=0.19  Score=51.21  Aligned_cols=23  Identities=30%  Similarity=0.420  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.++.
T Consensus       294 Gei~~i~G~nGsGKSTLl~~l~G  316 (538)
T 3ozx_A          294 GEIIGILGPNGIGKTTFARILVG  316 (538)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999875

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=89.13  E-value=0.19  Score=49.71  Aligned_cols=34  Identities=12%  Similarity=0.069  Sum_probs=25.1

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +++-+.. =..-.+++|+|..|+|||||.+.+.+.
T Consensus       147 vld~vl~-i~~Gq~~~IvG~sGsGKSTLl~~Iag~  180 (438)
T 2dpy_A          147 AINALLT-VGRGQRMGLFAGSGVGKSVLLGMMARY  180 (438)
T ss_dssp             HHHHHSC-CBTTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEeeeEE-ecCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            4444432 123468999999999999999999874

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=89.09  E-value=0.2  Score=43.15  Aligned_cols=21  Identities=14%  Similarity=-0.088  Sum_probs=17.3

Q ss_pred             EEEEEEecCCCchHHHHHHhh
Q 040913          191 SVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .++.|+|+.|+||||++..+.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~   24 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFV   24 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            477899999999999985444

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=88.99  E-value=0.22  Score=49.79  Aligned_cols=23  Identities=9%  Similarity=0.105  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+|.++|++|+||||+++.+..
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~   61 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTR   61 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHH
Confidence            56788999999999999998865

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=88.98  E-value=0.2  Score=51.02  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.++.
T Consensus       312 Ge~~~i~G~NGsGKSTLlk~l~G  334 (538)
T 1yqt_A          312 GEVIGIVGPNGIGKTTFVKMLAG  334 (538)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            35899999999999999999876

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=88.96  E-value=0.26  Score=44.69  Aligned_cols=25  Identities=12%  Similarity=0.170  Sum_probs=21.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ....|+|+|.+|+|||||...+...
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~~   45 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILRK   45 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhCC
Confidence            3567899999999999999998764

>1mky_A Probable GTP-binding protein ENGA; GTPase, DER, KH-domain, tandem G-domains, ligand binding protein; HET: GDP; 1.90A {Thermotoga maritima} SCOP: c.37.1.8 c.37.1.8 d.52.5.1

Probab=88.93  E-value=0.41  Score=47.26  Aligned_cols=45  Identities=18%  Similarity=0.147  Sum_probs=32.7

Q ss_pred             ccchhhHHHHHHHHhcC---------CCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          170 SEFERAREEWFDLLIEG---------PIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~---------~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      .|.++-.+.|.+.+...         .....-|+|+|.+|+|||||...+....
T Consensus       151 ~gv~~L~~~i~~~l~~~~~~~~~~~~~~~~~kvaivG~~gvGKSTLln~l~g~~  204 (439)
T 1mky_A          151 INLDTMLETIIKKLEEKGLDLESKPEITDAIKVAIVGRPNVGKSTLFNAILNKE  204 (439)
T ss_dssp             BSHHHHHHHHHHHHHHTTCCSSSCCCCCSCEEEEEECSTTSSHHHHHHHHHTST
T ss_pred             CCHHHHHHHHHHhcccccccchhccccccCceEEEECCCCCCHHHHHHHHhCCc
Confidence            35566677777666521         1234678999999999999999987753

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=88.84  E-value=0.22  Score=48.64  Aligned_cols=23  Identities=9%  Similarity=0.027  Sum_probs=19.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .-.++.|+|.+|+|||||+..+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la  199 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLA  199 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHH
Confidence            35689999999999999999664

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=88.84  E-value=0.17  Score=44.51  Aligned_cols=26  Identities=15%  Similarity=0.024  Sum_probs=22.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ....|.|+|..|+|||||...+.+..
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~~   53 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQK   53 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTCS
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            35678899999999999999998754

>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=88.76  E-value=0.24  Score=43.80  Aligned_cols=23  Identities=13%  Similarity=-0.018  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|-|+.|+||||+++.+.+
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~   28 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAE   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHH
Confidence            46789999999999999999876

>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8 d.52.3.1

Probab=88.75  E-value=0.26  Score=46.07  Aligned_cols=24  Identities=17%  Similarity=0.225  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+|+|.+|+|||||...+...
T Consensus         7 ~g~V~ivG~~nvGKSTLln~l~g~   30 (301)
T 1wf3_A            7 SGFVAIVGKPNVGKSTLLNNLLGV   30 (301)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            567999999999999999998764

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=88.74  E-value=0.45  Score=43.92  Aligned_cols=38  Identities=11%  Similarity=0.161  Sum_probs=27.5

Q ss_pred             HHHHHHHhcC----CCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          177 EEWFDLLIEG----PIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       177 ~~l~~~L~~~----~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      +++.+.|...    .....-|+|+|.+|+|||||...+....
T Consensus         9 ~~l~~~l~~~~~~~~~~~~~i~vvG~~~~GKSSLln~l~g~~   50 (299)
T 2aka_B            9 NRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVGRD   50 (299)
T ss_dssp             HHHHHHHTTSCCCTTCCCCEEEEEEBTTSCHHHHHHHHHTSC
T ss_pred             HHHHHHHHhcCCCCCCCCCeEEEEeCCCCCHHHHHHHHHCCC
Confidence            4444545432    2346679999999999999999988753

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=88.72  E-value=0.22  Score=44.58  Aligned_cols=21  Identities=19%  Similarity=0.091  Sum_probs=17.2

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.+.|.||+||||+|..+..
T Consensus         8 ~I~~~~kgGvGKTt~a~~la~   28 (228)
T 2r8r_A            8 KVFLGAAPGVGKTYAMLQAAH   28 (228)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHH
Confidence            467789999999999766654

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=88.69  E-value=0.21  Score=50.79  Aligned_cols=23  Identities=22%  Similarity=0.133  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        47 Ge~~~LvG~NGaGKSTLlk~l~G   69 (538)
T 1yqt_A           47 GMVVGIVGPNGTGKSTAVKILAG   69 (538)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            45899999999999999999875

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=88.69  E-value=0.23  Score=50.53  Aligned_cols=23  Identities=17%  Similarity=0.245  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        25 Gei~gLiGpNGaGKSTLlkiL~G   47 (538)
T 3ozx_A           25 NTILGVLGKNGVGKTTVLKILAG   47 (538)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            57899999999999999999876

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=88.68  E-value=0.22  Score=49.82  Aligned_cols=22  Identities=18%  Similarity=0.161  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|+.|+|||||.+.+..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~G   51 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVT   51 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHhc
Confidence            6899999999999999998875

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=88.66  E-value=0.23  Score=46.49  Aligned_cols=33  Identities=18%  Similarity=0.196  Sum_probs=26.3

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+++.+.+..     .+++|+|+.|+|||||.+.+...
T Consensus       160 v~~lf~~l~g-----eiv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          160 IEELKEYLKG-----KISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             HHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             HHHHHHHhcC-----CeEEEECCCCCcHHHHHHHhccc
Confidence            5666666542     47899999999999999999873

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=88.57  E-value=0.29  Score=43.73  Aligned_cols=24  Identities=17%  Similarity=0.075  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....|.|.|..|+||||+++.+.+
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~   43 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAE   43 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999999999877

>3t5d_A Septin-7; GTP-binding protein, cytoskeleton, signaling protein; HET: GDP; 3.30A {Homo sapiens} PDB: 3tw4_A*

Probab=88.55  E-value=0.22  Score=45.71  Aligned_cols=23  Identities=13%  Similarity=0.326  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      --|.|+|.+|+|||||...++..
T Consensus         9 ~~I~vvG~~g~GKSTLin~L~~~   31 (274)
T 3t5d_A            9 FTLMVVGESGLGKSTLINSLFLT   31 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHSSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            35789999999999999987764

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=88.48  E-value=0.18  Score=50.97  Aligned_cols=53  Identities=15%  Similarity=0.181  Sum_probs=34.9

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLM  235 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~  235 (425)
                      ++++.|..=. .-.-++|.|..|+|||+|++.+.+...    -+.++++        ..+++..+.
T Consensus       216 rvID~l~Pig-kGqr~~I~g~~g~GKT~L~~~ia~~~~----~~~~V~~~iGER~~Ev~e~~~~~~  276 (588)
T 3mfy_A          216 RVIDTFFPQA-KGGTAAIPGPAGSGKTVTQHQLAKWSD----AQVVIYIGCGERGNEMTDVLEEFP  276 (588)
T ss_dssp             HHHHHHSCEE-TTCEEEECSCCSHHHHHHHHHHHHHSS----CSEEEEEECCSSSSHHHHHHHHTT
T ss_pred             chhhccCCcc-cCCeEEeecCCCCCHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHHH
Confidence            4566665421 134578999999999999999877322    2334444        677777764

>1jwy_B Dynamin A GTPase domain; dynamin, GTPase, GDP, myosin, fusion-protein, hydrolase; HET: BGC ADP GDP; 2.30A {Dictyostelium discoideum} SCOP: c.37.1.8 PDB: 1jx2_B*

Probab=88.47  E-value=0.22  Score=46.55  Aligned_cols=26  Identities=12%  Similarity=0.258  Sum_probs=22.5

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .....|+|+|..|+|||||...+...
T Consensus        22 ~~~~~I~vvG~~~~GKSTlln~l~g~   47 (315)
T 1jwy_B           22 LDLPQIVVVGSQSSGKSSVLENIVGR   47 (315)
T ss_dssp             TCCCEEEEEECSSSSHHHHHHHHHTS
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHCC
Confidence            35778999999999999999998764

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=88.35  E-value=0.23  Score=51.30  Aligned_cols=114  Identities=12%  Similarity=0.138  Sum_probs=60.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCcc-----c----------cc---cccchHHH---------------HHHHHHHhCC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNNH-----V----------KF---YFDCLAWI---------------LDDIIRSLMP  236 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~~-----~----------~~---~F~~~~wv---------------~~~il~~l~~  236 (425)
                      -.+++|+|+.|+|||||.+.+..-..     +          +.   .|+..+.-               ..+++..+..
T Consensus       382 Gei~~i~G~NGsGKSTLlk~l~Gl~~p~~G~I~~~~~i~~v~Q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l~~~~l  461 (607)
T 3bk7_A          382 GEVIGIVGPNGIGKTTFVKMLAGVEEPTEGKVEWDLTVAYKPQYIKAEYEGTVYELLSKIDSSKLNSNFYKTELLKPLGI  461 (607)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCCSBSCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHHCHHHHHHTHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEEeeEEEEEecCccCCCCCcHHHHHHhhhccCCCHHHHHHHHHHHcCC
Confidence            35899999999999999999875311     1          00   11211111               2234444443


Q ss_pred             CCCCC-ccCCCCHHHH-HHHHHHHhcCCeEEEEecccCCCh---hhHHHHHhhCCC--CCCCcEEEEecCChhHH
Q 040913          237 PSRVT-VIIGEDYKLK-KSILRDFLTNKKYFIALDDVCHNI---EIWDDLEEVLPD--NQNGSRVLITVINPSLL  304 (425)
Q Consensus       237 ~~~~~-~~~~~~~~~l-~~~l~~~l~~kr~LlVLDdvw~~~---~~~~~l~~~l~~--~~~gskIivTTR~~~va  304 (425)
                      ..... .....+..+. .-.|...|....-+++||.-- +.   ..-..+...+..  ...|..||++|.+...+
T Consensus       462 ~~~~~~~~~~LSGGe~QRv~iAraL~~~p~lLlLDEPt-~~LD~~~~~~l~~~l~~l~~~~g~tvi~vsHd~~~~  535 (607)
T 3bk7_A          462 IDLYDRNVEDLSGGELQRVAIAATLLRDADIYLLDEPS-AYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDVLMI  535 (607)
T ss_dssp             TTTTTSBGGGCCHHHHHHHHHHHHHTSCCSEEEEECTT-TTCCHHHHHHHHHHHHHHHHHTTCEEEEECSCHHHH
T ss_pred             chHhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEeCCc-cCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHH
Confidence            21111 2223343333 345666677778899999864 32   221222222221  12356688888876654

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=88.34  E-value=0.24  Score=42.84  Aligned_cols=22  Identities=23%  Similarity=0.299  Sum_probs=17.9

Q ss_pred             EEEEEE-ecCCCchHHHHHHhhc
Q 040913          191 SVVAIL-DSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~Iv-G~gGvGKTtLa~~v~~  212 (425)
                      ++|+|+ +-||+||||+|..+..
T Consensus         2 ~vi~v~s~kgG~GKTt~a~~la~   24 (206)
T 4dzz_A            2 KVISFLNPKGGSGKTTAVINIAT   24 (206)
T ss_dssp             EEEEECCSSTTSSHHHHHHHHHH
T ss_pred             eEEEEEeCCCCccHHHHHHHHHH
Confidence            678888 6789999999877654

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=88.25  E-value=0.25  Score=45.02  Aligned_cols=23  Identities=13%  Similarity=0.159  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.|+++|.+|+|||||...+...
T Consensus         2 ~kI~lvG~~n~GKSTL~n~L~g~   24 (256)
T 3iby_A            2 THALLIGNPNCGKTTLFNALTNA   24 (256)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            46899999999999999998764

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=88.20  E-value=0.25  Score=43.62  Aligned_cols=24  Identities=21%  Similarity=0.340  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|.+|+|||||...+.+.
T Consensus        13 ~~ki~v~G~~~vGKSsli~~l~~~   36 (223)
T 3cpj_B           13 LFKIVLIGDSGVGKSNLLSRFTKN   36 (223)
T ss_dssp             EEEEEEESCTTSSHHHHHHHHHHC
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcC
Confidence            456889999999999999988764

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=88.15  E-value=0.35  Score=54.48  Aligned_cols=111  Identities=15%  Similarity=0.106  Sum_probs=0.0

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHH---------------------------------------------
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI---------------------------------------------  226 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv---------------------------------------------  226 (425)
                      +++|+|..|.|||||++.+..   .-..-...+.+                                             
T Consensus       418 ~~~ivG~sGsGKSTl~~ll~g---~~~~~~G~i~i~g~~i~~~~~~~~r~~i~~v~Q~~~l~~~ti~eNi~~g~~~~~~~  494 (1284)
T 3g5u_A          418 TVALVGNSGCGKSTTVQLMQR---LYDPLDGMVSIDGQDIRTINVRYLREIIGVVSQEPVLFATTIAENIRYGREDVTMD  494 (1284)
T ss_dssp             EEEEECCSSSSHHHHHHHTTT---SSCCSEEEEEETTEEGGGSCHHHHHHHEEEECSSCCCCSSCHHHHHHHHCSSCCHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC---CCCCCCeEEEECCEEHHhCCHHHHHhheEEEcCCCccCCccHHHHHhcCCCCCCHH


Q ss_pred             ----------HHHHHHHhCCCCCCC----ccCCCCHHHHHHHHHHHhcCCeEEEEecccCC--ChhhHHHHHhhCCCCCC
Q 040913          227 ----------LDDIIRSLMPPSRVT----VIIGEDYKLKKSILRDFLTNKKYFIALDDVCH--NIEIWDDLEEVLPDNQN  290 (425)
Q Consensus       227 ----------~~~il~~l~~~~~~~----~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l~~~l~~~~~  290 (425)
                                ..+.+..+.......    ...-+.-+.-.-.|.+.|-.+.-+++||+.-.  +.+.-..+...+.....
T Consensus       495 ~~~~~~~~~~~~~~i~~l~~g~~t~~~~~g~~LSgGq~QriaiARal~~~p~iliLDEpts~LD~~~~~~i~~~l~~~~~  574 (1284)
T 3g5u_A          495 EIEKAVKEANAYDFIMKLPHQFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAVVQAALDKARE  574 (1284)
T ss_dssp             HHHHHHHHTTCHHHHHHSTTGGGCCCSSSSCSSCHHHHHHHHHHHHHHHCCSEEEEESTTCSSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCcHHHHHhccccccccccCCCCccCHHHHHHHHHHHHHhcCCCEEEEECCCCCCCHHHHHHHHHHHHHHcC


Q ss_pred             CcEEEEecCChhHHH
Q 040913          291 GSRVLITVINPSLLT  305 (425)
Q Consensus       291 gskIivTTR~~~va~  305 (425)
                      |..+|+.|...+...
T Consensus       575 ~~t~i~itH~l~~i~  589 (1284)
T 3g5u_A          575 GRTTIVIAHRLSTVR  589 (1284)
T ss_dssp             TSEEEEECSCHHHHT
T ss_pred             CCEEEEEecCHHHHH

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=88.11  E-value=0.25  Score=50.80  Aligned_cols=23  Identities=26%  Similarity=0.229  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus       369 G~~~~ivG~sGsGKSTLl~~l~g  391 (582)
T 3b60_A          369 GKTVALVGRSGSGKSTIASLITR  391 (582)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhh
Confidence            46899999999999999999875

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=88.10  E-value=0.24  Score=51.14  Aligned_cols=114  Identities=11%  Similarity=0.018  Sum_probs=60.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCccc------------------cccccchHH--H-------------HHHHHHHhCCC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHV------------------KFYFDCLAW--I-------------LDDIIRSLMPP  237 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~------------------~~~F~~~~w--v-------------~~~il~~l~~~  237 (425)
                      .+++|+|+.|+|||||++.+..-.+-                  ...|+..++  +             ..+++..+...
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl~~p~~G~~~~~~~i~~~~q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l~~l~l~  458 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKIRGQFLNPQFQTDVVKPLRID  458 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTSSCCSBCCCCCSCCEEEECSSCCCCCCSBHHHHHHHHCSSTTTSHHHHHHTHHHHTST
T ss_pred             eEEEEECCCCCcHHHHHHHHhcCCCCCCCcCccCCcEEEecccccccCCccHHHHHHHHhhcccccHHHHHHHHHHcCCh
Confidence            57999999999999999998752110                  111221111  0             23344444322


Q ss_pred             CCCC-ccCCCCHHHH-HHHHHHHhcCCeEEEEecccCCCh---hhHHHHHhhCCC--CCCCcEEEEecCChhHHH
Q 040913          238 SRVT-VIIGEDYKLK-KSILRDFLTNKKYFIALDDVCHNI---EIWDDLEEVLPD--NQNGSRVLITVINPSLLT  305 (425)
Q Consensus       238 ~~~~-~~~~~~~~~l-~~~l~~~l~~kr~LlVLDdvw~~~---~~~~~l~~~l~~--~~~gskIivTTR~~~va~  305 (425)
                      .... .....+..+. .-.|...|..+.-+|+||.-- +.   ..-..+...+..  ...|..||++|.+...+.
T Consensus       459 ~~~~~~~~~LSGGqkQRv~iAraL~~~p~lLlLDEPT-~gLD~~~~~~i~~ll~~l~~~~g~tviivtHdl~~~~  532 (608)
T 3j16_B          459 DIIDQEVQHLSGGELQRVAIVLALGIPADIYLIDEPS-AYLDSEQRIICSKVIRRFILHNKKTAFIVEHDFIMAT  532 (608)
T ss_dssp             TTSSSBSSSCCHHHHHHHHHHHHTTSCCSEEEECCTT-TTCCHHHHHHHHHHHHHHHHHHTCEEEEECSCHHHHH
T ss_pred             hhhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEECCC-CCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            1111 2233444443 345667788888899999864 22   111122222211  122667888888766553

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=88.10  E-value=0.25  Score=47.64  Aligned_cols=25  Identities=12%  Similarity=0.139  Sum_probs=21.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.++|+|+|.+|+|||||...+.+.
T Consensus       178 ~~~~V~lvG~~naGKSTLln~L~~~  202 (364)
T 2qtf_A          178 NIPSIGIVGYTNSGKTSLFNSLTGL  202 (364)
T ss_dssp             -CCEEEEECBTTSSHHHHHHHHHCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHCC
Confidence            4677999999999999999998874

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=88.07  E-value=0.38  Score=44.25  Aligned_cols=24  Identities=13%  Similarity=0.195  Sum_probs=21.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+++|.+|+|||||...+...
T Consensus         3 ~~kI~lvG~~nvGKSTL~n~L~g~   26 (272)
T 3b1v_A            3 MTEIALIGNPNSGKTSLFNLITGH   26 (272)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHCC
Confidence            456899999999999999998864

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=87.99  E-value=0.22  Score=44.66  Aligned_cols=23  Identities=13%  Similarity=0.003  Sum_probs=17.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..|.|-|+.|+||||+++.+.+
T Consensus        25 g~~I~~eG~~GsGKsT~~~~l~~   47 (227)
T 3v9p_A           25 GKFITFEGIDGAGKTTHLQWFCD   47 (227)
T ss_dssp             CCEEEEECCC---CHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999887

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=87.92  E-value=0.28  Score=44.19  Aligned_cols=23  Identities=13%  Similarity=0.073  Sum_probs=20.8

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...|.|.|+.|+||||+++.+.+
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~   49 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVE   49 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999876

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=87.81  E-value=0.34  Score=43.27  Aligned_cols=23  Identities=17%  Similarity=0.186  Sum_probs=18.2

Q ss_pred             CcEEEEEEe-cCCCchHHHHHHhh
Q 040913          189 GLSVVAILD-SSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG-~gGvGKTtLa~~v~  211 (425)
                      ..++|+|++ -||+||||+|..+.
T Consensus         3 ~~~vI~v~s~kGGvGKTt~a~~LA   26 (245)
T 3ea0_A            3 AKRVFGFVSAKGGDGGSCIAANFA   26 (245)
T ss_dssp             CCEEEEEEESSTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcchHHHHHHHH
Confidence            367899985 58899999987654

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=87.76  E-value=0.13  Score=48.35  Aligned_cols=22  Identities=14%  Similarity=0.182  Sum_probs=20.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++|+|++|+|||||.+.+..
T Consensus       174 ~~~~lvG~sG~GKSTLln~L~g  195 (307)
T 1t9h_A          174 KTTVFAGQSGVGKSSLLNAISP  195 (307)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHhcc
Confidence            4889999999999999999887

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=87.73  E-value=0.27  Score=50.82  Aligned_cols=23  Identities=13%  Similarity=0.159  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus       103 Gei~~LvGpNGaGKSTLLkiL~G  125 (608)
T 3j16_B          103 GQVLGLVGTNGIGKSTALKILAG  125 (608)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            45899999999999999999875

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=87.73  E-value=0.26  Score=50.84  Aligned_cols=23  Identities=26%  Similarity=0.147  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus       117 Ge~~~LiG~NGsGKSTLlkiL~G  139 (607)
T 3bk7_A          117 GMVVGIVGPNGTGKTTAVKILAG  139 (607)
T ss_dssp             TSEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhC
Confidence            45899999999999999999875

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi}

Probab=87.71  E-value=0.17  Score=44.32  Aligned_cols=24  Identities=13%  Similarity=0.344  Sum_probs=20.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .--|.|+|..|+|||||...+.+.
T Consensus        11 ~~ki~vvG~~~~GKSsli~~l~~~   34 (218)
T 4djt_A           11 TYKICLIGDGGVGKTTYINRVLDG   34 (218)
T ss_dssp             EEEEEEECCTTSSHHHHHCBCTTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            345789999999999999988753

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=87.58  E-value=0.28  Score=43.76  Aligned_cols=22  Identities=32%  Similarity=0.356  Sum_probs=18.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -.++-|.|.+|+|||+||.++.
T Consensus        30 G~l~~i~G~pG~GKT~l~l~~~   51 (251)
T 2zts_A           30 GTTVLLTGGTGTGKTTFAAQFI   51 (251)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHH
Confidence            4588899999999999998754

>2qag_A Septin-2, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=87.55  E-value=0.24  Score=47.63  Aligned_cols=22  Identities=14%  Similarity=0.383  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|+|+|..|+|||||...++..
T Consensus        39 ~I~vvG~~g~GKSTLln~L~~~   60 (361)
T 2qag_A           39 TLMVVGESGLGKSTLINSLFLT   60 (361)
T ss_dssp             CEEECCCTTSCHHHHHHHHTTC
T ss_pred             EEEEEcCCCCCHHHHHHHHhCC
Confidence            3689999999999999998764

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=87.50  E-value=0.31  Score=49.91  Aligned_cols=24  Identities=13%  Similarity=-0.115  Sum_probs=21.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.|.|+.|+||||+|+.+.+
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~  418 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQV  418 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHH
Confidence            457899999999999999999877

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=87.45  E-value=0.19  Score=44.14  Aligned_cols=22  Identities=18%  Similarity=0.279  Sum_probs=18.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .--|.|+|.+|+|||||...+.
T Consensus        15 ~~ki~v~G~~~~GKSsli~~~~   36 (221)
T 3gj0_A           15 QFKLVLVGDGGTGKTTFVKRHL   36 (221)
T ss_dssp             EEEEEEEECTTSSHHHHHTTBH
T ss_pred             ceEEEEECCCCCCHHHHHHHHH
Confidence            3457899999999999999844

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=87.34  E-value=0.76  Score=46.62  Aligned_cols=53  Identities=13%  Similarity=0.188  Sum_probs=35.7

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLM  235 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~  235 (425)
                      ++++.|..=. .-.-++|.|..|+|||+|++++.+...    -+.++++        ..+++..+.
T Consensus       221 rvID~l~Pig-rGqr~~Ifgg~g~GKT~L~~~ia~~~~----~~v~V~~~iGER~~Ev~e~~~~~~  281 (600)
T 3vr4_A          221 RVIDTFFPVT-KGGAAAVPGPFGAGKTVVQHQIAKWSD----VDLVVYVGCGERGNEMTDVVNEFP  281 (600)
T ss_dssp             HHHHHHSCCB-TTCEEEEECCTTSCHHHHHHHHHHHSS----CSEEEEEEEEECHHHHHHHHHHTT
T ss_pred             hhhhccCCcc-CCCEEeeecCCCccHHHHHHHHHhccC----CCEEEEEEecccHHHHHHHHHHHH
Confidence            4566665432 134578999999999999999987422    2344444        667777764

>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A

Probab=87.31  E-value=0.34  Score=44.15  Aligned_cols=24  Identities=17%  Similarity=0.173  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...|+++|.+|+|||||...+...
T Consensus         5 ~~kI~lvG~~nvGKTsL~n~l~g~   28 (258)
T 3a1s_A            5 MVKVALAGCPNVGKTSLFNALTGT   28 (258)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHTT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHCC
Confidence            456899999999999999998764

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=87.27  E-value=0.3  Score=42.04  Aligned_cols=21  Identities=10%  Similarity=0.134  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.|+|.+|+||||+|.++...
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            679999999999999988763

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=87.21  E-value=0.32  Score=50.22  Aligned_cols=24  Identities=21%  Similarity=0.058  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.+.|+.|+||||+|+.+.+
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~   74 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEE   74 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            467899999999999999999876

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	425
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	2e-05

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 43.7 bits (102), Expect = 2e-05
 Identities = 22/162 (13%), Positives = 45/162 (27%), Gaps = 27/162 (16%)

Query: 165 PRLDISEFERAREEWFDLLIE-GPIGLSVVAILDSSGFDKTAFAADTYNNNH--VKFYFD 221
            ++     E   +     L E   +    + +   +G  K+  A+   + +   +   +D
Sbjct: 18  KQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYD 77

Query: 222 CLAW-----------ILDDIIRSLMPPSRV------TVIIGEDYKLKKSILRDFLTNKKY 264
            + W                   LM  S        +V       LK+ I    +     
Sbjct: 78  SIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNT 137

Query: 265 FIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS 306
               DDV          E +    +   R L+T  +  +  +
Sbjct: 138 LFVFDDV-------VQEETIRWAQELRLRCLVTTRDVEISNA 172

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	425
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.2
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.16
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.11
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.91
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.9
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.9
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.87
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.85
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.83
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.83
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.81
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.76
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.68
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.61
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.6
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.56
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	97.29
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.26
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.16
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.15
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.08
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.06
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.89
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.84
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.82
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.79
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.77
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.71
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.69
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.64
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.58
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.55
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.49
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.46
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.41
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.4
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.39
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.36
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	96.32
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.27
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.25
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.25
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.24
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.24
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.21
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.21
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.15
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.08
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.08
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	96.06
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.04
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.97
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.96
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.94
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	95.92
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.91
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	95.89
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.82
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.82
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.81
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.76
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.73
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.67
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.64
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.58
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	95.57
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	95.55
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.39
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	95.37
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.25
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	95.25
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.19
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.15
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	95.13
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	95.08
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.88
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.86
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.82
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	94.8
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	94.77
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.76
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.76
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.74
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	94.69
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.63
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.58
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	94.51
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.47
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.46
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.39
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	94.38
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.23
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	94.23
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.21
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.2
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.19
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.12
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.12
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.04
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.02
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	93.93
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	93.92
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.92
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.89
d2awna2	232	Maltose transport protein MalK, N-terminal domain	93.85
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	93.75
d1j8yf2	211	GTPase domain of the signal sequence recognition p	93.74
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	93.7
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.67
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	93.67
d1ls1a2	207	GTPase domain of the signal sequence recognition p	93.64
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	93.58
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	93.47
d1vmaa2	213	GTPase domain of the signal recognition particle r	93.41
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	93.38
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.35
d1okkd2	207	GTPase domain of the signal recognition particle r	93.35
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	93.34
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	93.34
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.31
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	93.3
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	93.3
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.29
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.17
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	93.13
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	93.02
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.02
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	92.96
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	92.96
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	92.88
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.86
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.8
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	92.8
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	92.79
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	92.79
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	92.77
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	92.75
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	92.68
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	92.67
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.67
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	92.62
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	92.61
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	92.48
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	92.46
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	92.46
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.42
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	92.42
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.39
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	92.36
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.34
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	92.33
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.3
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	92.26
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.24
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	92.24
d1nrjb_	209	Signal recognition particle receptor beta-subunit	92.23
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	92.2
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.19
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.17
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.12
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	92.11
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	92.09
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	92.08
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	91.97
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	91.97
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	91.92
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	91.91
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	91.88
d2fh5b1	207	Signal recognition particle receptor beta-subunit	91.8
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	91.77
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	91.76
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	91.7
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.62
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	91.6
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.55
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	91.53
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.51
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.42
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	91.39
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	91.35
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	91.29
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	91.15
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	91.15
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	91.12
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	91.1
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	91.08
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	91.07
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	91.06
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	91.05
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.0
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	90.93
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	90.88
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	90.87
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	90.87
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.86
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	90.85
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	90.69
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	90.59
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	90.54
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	90.33
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	90.31
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	90.27
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	90.19
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	90.14
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.74
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	89.64
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	89.52
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	89.28
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	88.37
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	88.34
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	88.24
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	87.96
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	87.95
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.89
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	87.65
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	87.12
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	87.02
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	86.82
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	86.09
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	85.75
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	85.73
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	85.72
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	85.58
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	85.4
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	84.46
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.94
d1tuea_	205	Replication protein E1 helicase domain {Human papi	83.13
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	82.83
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	82.7
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	82.1
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	81.71
d1jala1	278	YchF GTP-binding protein N-terminal domain {Haemop	81.69
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	81.59
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	81.44
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	81.18
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	80.85
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	80.6
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	80.33

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=100.00  E-value=2.8e-34  Score=270.14  Aligned_cols=202  Identities=15%  Similarity=0.149  Sum_probs=157.1

Q ss_pred             CCCCCCcccchhhHHHHHHHHhc-CCCCcEEEEEEecCCCchHHHHHHhhcCcc--ccccccchHHH-------------
Q 040913          163 GQPRLDISEFERAREEWFDLLIE-GPIGLSVVAILDSSGFDKTAFAADTYNNNH--VKFYFDCLAWI-------------  226 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~-~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~--~~~~F~~~~wv-------------  226 (425)
                      .+..+.++||+.++++|+++|.. .+...++|+|+||||+||||||+++|++..  ++.+|++++||             
T Consensus        16 ~p~~~~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~   95 (277)
T d2a5yb3          16 VPKQMTCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDL   95 (277)
T ss_dssp             CBCCCCSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHH
T ss_pred             CCCCCceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHH
Confidence            34566789999999999999976 345688999999999999999999998643  67789999999             


Q ss_pred             -HHHHHHHhCCCCCCC---ccCCCCHHHHHHHHHHHhcCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          227 -LDDIIRSLMPPSRVT---VIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       227 -~~~il~~l~~~~~~~---~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                       +..++..+.......   .....+.......+.+.+.+||+|+|||||| +.+.|..+..      .|||||||||+..
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~-~~~~~~~~~~------~~srilvTTR~~~  168 (277)
T d2a5yb3          96 FTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVV-QEETIRWAQE------LRLRCLVTTRDVE  168 (277)
T ss_dssp             HHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEEC-CHHHHHHHHH------TTCEEEEEESBGG
T ss_pred             HHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhh-HHhhhhhhcc------cCceEEEEeehHH
Confidence             233333333322111   1222334455567888899999999999999 9988876643      3899999999999


Q ss_pred             HHHH------------------hcCcC---------------CCCc--ccc-----chhhhccccCCChHHHHHHHHHhc
Q 040913          303 LLTS------------------FELLN---------------GEKI--RCD-----YVLVEGPLIRIKHSAWQFFVLHYG  342 (425)
Q Consensus       303 va~~------------------~~Lf~---------------~~~I--kC~-----i~~~g~~L~~~~~~~w~~~~~~~~  342 (425)
                      ++..                  |+||.               +++|  +|+     ++++|+.|+.++...|.+..+.+.
T Consensus       169 v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~GlPLAl~~ig~~l~~k~~~~~~~~~~~L~  248 (277)
T d2a5yb3         169 ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSGNPATLMMFFKSCEPKTFEKMAQLNNKLE  248 (277)
T ss_dssp             GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTTCHHHHHHHHTTCCSSSHHHHHHHHHHHH
T ss_pred             HHHhcCCCCceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCCCHHHHHHHHHHhccCCHHHHHHHHHHHh
Confidence            9875                  77773               3555  787     999999999887779998888775


Q ss_pred             hhccCCCCchHHHHHHhchhhcccCCChhhHHHHhhh
Q 040913          343 SAALGNYMDEKMVLAVLSRTCSVFELPLHLKVCCIYL  379 (425)
Q Consensus       343 ~~~~~~~~~~~~~~~~l~~~~sy~~Lp~~lk~cfly~  379 (425)
                      ....     . .+.+++.  +||++||+++|+||-++
T Consensus       249 ~~~~-----~-~v~~il~--~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         249 SRGL-----V-GVECITP--YSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HHCS-----S-TTCCCSS--SSSSSHHHHHHHHHHTS
T ss_pred             cCcH-----H-HHHHHHH--HHHhcccHHHHHHHHhC
Confidence            4321     2 6888999  99999999999999874

>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=98.20  E-value=6.9e-06  Score=73.59  Aligned_cols=104  Identities=19%  Similarity=0.117  Sum_probs=65.8

Q ss_pred             CCCcccchhhHHHHHHHHhc----CCCCcEEEEEEecCCCchHHHHHHhhcCccccccccc-----hH----HH-HHHHH
Q 040913          166 RLDISEFERAREEWFDLLIE----GPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDC-----LA----WI-LDDII  231 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~----~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~-----~~----wv-~~~il  231 (425)
                      +..++||+.++++|.++|..    .....+.+.|+|++|+||||+|+.+.+.-.-...|..     ..    .. +..+.
T Consensus        15 p~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~   94 (276)
T d1fnna2          15 PKRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIA   94 (276)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhhhhhhhhhH
Confidence            44689999999999998864    3345678889999999999999999873211111111     00    00 45555


Q ss_pred             HHhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccC
Q 040913          232 RSLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVC  272 (425)
Q Consensus       232 ~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw  272 (425)
                      ..+.....   ........+...+.+.+.  .....+++|++.
T Consensus        95 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d  134 (276)
T d1fnna2          95 RSLNIPFP---RRGLSRDEFLALLVEHLRERDLYMFLVLDDAF  134 (276)
T ss_dssp             HHTTCCCC---SSCCCHHHHHHHHHHHHHHTTCCEEEEEETGG
T ss_pred             Hhhhhhhh---hhccchhHHHHHHHHHHhhcccccccchhHHH
Confidence            55544432   223345566666666553  356677778776

>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=98.16  E-value=1.3e-06  Score=78.78  Aligned_cols=44  Identities=18%  Similarity=0.142  Sum_probs=36.5

Q ss_pred             CCCCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          163 GQPRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       163 ~~~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....+|+||+++.++|.+.      ..+++.|+|++|+|||+|++++.+
T Consensus         8 ~~~~~~f~GR~~el~~l~~~------~~~~i~i~G~~G~GKTsLl~~~~~   51 (283)
T d2fnaa2           8 KDNRKDFFDREKEIEKLKGL------RAPITLVLGLRRTGKSSIIKIGIN   51 (283)
T ss_dssp             CCSGGGSCCCHHHHHHHHHT------CSSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCChhhCCChHHHHHHHHhc------cCCEEEEEcCCCCcHHHHHHHHHH
Confidence            34567899999999998763      245788999999999999999876

>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=98.11  E-value=2.9e-06  Score=75.72  Aligned_cols=46  Identities=13%  Similarity=-0.013  Sum_probs=36.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.++..+.|.+++..... ..-+-++|++|+||||+|+.+.+
T Consensus        10 ~~diig~~~~~~~L~~~~~~~~~-~~~lll~Gp~G~GKTt~~~~la~   55 (252)
T d1sxje2          10 LNALSHNEELTNFLKSLSDQPRD-LPHLLLYGPNGTGKKTRCMALLE   55 (252)
T ss_dssp             GGGCCSCHHHHHHHHTTTTCTTC-CCCEEEECSTTSSHHHHHHTHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCCC-CCeEEEECCCCCCHHHHHHHHHH
Confidence            34699998888888887765532 33356999999999999999877

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.91  E-value=9.5e-06  Score=71.16  Aligned_cols=119  Identities=13%  Similarity=0.118  Sum_probs=68.9

Q ss_pred             CCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCcccccc-ccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          167 LDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFY-FDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~-F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      .+++|.++.++.|.+|+..+.  .+.+-++|++|+||||+|+.+.+.  +... +.   +.    ...+.      ....
T Consensus        14 ~divg~~~~~~~L~~~i~~~~--~~~lLl~Gp~G~GKttl~~~la~~--l~~~~~~---~~----~~e~~------~~~~   76 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEGK--LPHLLFYGPPGTGKTSTIVALARE--IYGKNYS---NM----VLELN------ASDD   76 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTTC--CCCEEEECSSSSSHHHHHHHHHHH--HHTTSHH---HH----EEEEC------TTSC
T ss_pred             HHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChhHHHHHHHHH--hhcCCCc---ce----eEEec------cccc
Confidence            569999999999999998765  333668999999999999998872  2110 00   00    00000      0011


Q ss_pred             CCHHHHHHHHHHHh------cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          246 EDYKLKKSILRDFL------TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       246 ~~~~~l~~~l~~~l------~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      ..............      .+++-.+|+|++.. +...-..+...+......++++++|....
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~  140 (227)
T d1sxjc2          77 RGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNALRRVIERYTKNTRFCVLANYAH  140 (227)
T ss_dssp             CSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHHHHHHHHHTTTTEEEEEEESCGG
T ss_pred             CCeeeeecchhhccccccccCCCeEEEEEeccccchhhHHHHHHHHhhhcccceeeccccCcHH
Confidence            11222211111111      23455889999962 23444555656655556788888776643

>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=97.90  E-value=1.3e-05  Score=71.19  Aligned_cols=133  Identities=14%  Similarity=0.066  Sum_probs=74.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc----ccc-cc-ccchHHHHHHHHHHhCCCCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN----HVK-FY-FDCLAWILDDIIRSLMPPSR  239 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~----~~~-~~-F~~~~wv~~~il~~l~~~~~  239 (425)
                      -.+++|.+..++.+.+++..+. -.+.+-++|++|+||||+|+.+.+.-    ... .. +.+..  ...+...-....-
T Consensus        11 ~~dlig~~~~~~~L~~~i~~~~-~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~--~~~i~~~~~~~~~   87 (239)
T d1njfa_          11 FADVVGQEHVLTALANGLSLGR-IHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDN--CREIEQGRFVDLI   87 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHTTC-CCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHH--HHHHHHTCCTTEE
T ss_pred             HHHccChHHHHHHHHHHHHcCC-CCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchH--HHHHHcCCCCeEE
Confidence            3578999999999999998764 23456799999999999999876521    110 01 11100  1111111000000


Q ss_pred             CC-ccCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          240 VT-VIIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       240 ~~-~~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .. .......+.+.. +.+.+     .++..++|+|++.. +.+.-+.+...+......+++|+||.+..
T Consensus        88 ~~~~~~~~~i~~ir~-~~~~~~~~~~~~~~kviiIde~d~l~~~~q~~Llk~lE~~~~~~~~il~tn~~~  156 (239)
T d1njfa_          88 EIDAASRTKVEDTRD-LLDNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQ  156 (239)
T ss_dssp             EEETTCSSSHHHHHH-HHHSCCCSCSSSSSEEEEEETGGGSCHHHHHHHHHHHHSCCTTEEEEEEESCGG
T ss_pred             EecchhcCCHHHHHH-HHHHHHhccccCCCEEEEEECcccCCHHHHHHHHHHHhcCCCCeEEEEEcCCcc
Confidence            00 011122333333 33332     24667999999973 33445566666655556778888876643

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.90  E-value=5.9e-06  Score=72.87  Aligned_cols=45  Identities=13%  Similarity=0.048  Sum_probs=37.9

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.+..++.|.+++....  .+.+-++|++|+||||+|+.+.+
T Consensus        11 ~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtl~~~i~~   55 (237)
T d1sxjd2          11 LDEVTAQDHAVTVLKKTLKSAN--LPHMLFYGPPGTGKTSTILALTK   55 (237)
T ss_dssp             TTTCCSCCTTHHHHHHHTTCTT--CCCEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCChHHHHHHHHH
Confidence            3568999999999999997665  34477999999999999999887

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.87  E-value=1.3e-05  Score=70.46  Aligned_cols=45  Identities=18%  Similarity=0.114  Sum_probs=39.2

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.++.++.|.+|+..+.  .+-+-++|++|+||||+|+.+.+
T Consensus        23 ~~diig~~~~~~~l~~~i~~~~--~~~lll~Gp~G~GKTtla~~iak   67 (231)
T d1iqpa2          23 LDDIVGQEHIVKRLKHYVKTGS--MPHLLFAGPPGVGKTTAALALAR   67 (231)
T ss_dssp             TTTCCSCHHHHHHHHHHHHHTC--CCEEEEESCTTSSHHHHHHHHHH
T ss_pred             HHHccCcHHHHHHHHHHHHcCC--CCeEEEECCCCCcHHHHHHHHHH
Confidence            4679999999999999998775  44577999999999999999877

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.85  E-value=1.4e-05  Score=71.98  Aligned_cols=125  Identities=17%  Similarity=0.188  Sum_probs=74.0

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc---ccccc-ccchHHH--HHHHHHHhCCCCCCC
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN---HVKFY-FDCLAWI--LDDIIRSLMPPSRVT  241 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~---~~~~~-F~~~~wv--~~~il~~l~~~~~~~  241 (425)
                      .++||+++.++++..|.....  .-+.+||++|+|||+++..+...-   .+... ....+|.  +..++..        
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~k--~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag--------   88 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRRK--NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAG--------   88 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSS--CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CC--------
T ss_pred             cccChHHHHHHHHHHHhcCcc--CCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhcc--------
Confidence            489999999999999987652  234589999999999887776521   11111 1222332  1111110        


Q ss_pred             ccCCCCHHHHHHHHHHHh-cCCeEEEEecccCCCh----------hhHHHH-HhhCCCCCCCcEEEEecCChhHHH
Q 040913          242 VIIGEDYKLKKSILRDFL-TNKKYFIALDDVCHNI----------EIWDDL-EEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       242 ~~~~~~~~~l~~~l~~~l-~~kr~LlVLDdvw~~~----------~~~~~l-~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      .....+.++....+.+.+ +.+..++++|++. .-          .+...+ +++|.  ...-++|.||..+....
T Consensus        89 ~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih-~l~~~g~~~g~~~d~a~~Lkp~L~--rg~i~vIgatT~eey~~  161 (268)
T d1r6bx2          89 TKYRGDFEKRFKALLKQLEQDTNSILFIDEIH-TIIGAGAASGGQVDAANLIKPLLS--SGKIRVIGSTTYQEFSN  161 (268)
T ss_dssp             CCCSSCHHHHHHHHHHHHSSSSCEEEEETTTT-TTTTSCCSSSCHHHHHHHHSSCSS--SCCCEEEEEECHHHHHC
T ss_pred             CccchhHHHHHHHHHHHhhccCCceEEecchH-HHhcCCCCCCccccHHHHhhHHHh--CCCCeEEEeCCHHHHHH
Confidence            111245566666666665 4567999999974 21          122333 33332  22468888888877653

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.83  E-value=9.7e-06  Score=71.07  Aligned_cols=120  Identities=13%  Similarity=0.092  Sum_probs=68.7

Q ss_pred             CCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCC
Q 040913          166 RLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIG  245 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~  245 (425)
                      -.+++|.++.++.|.+|+..+.  .+-+-++|++|+||||+|+.+.+  .+...+.  .|       .+.. ..  ..+.
T Consensus        14 ~~d~ig~~~~~~~L~~~~~~~~--~~~~ll~Gp~G~GKTt~a~~la~--~l~~~~~--~~-------~~~~-~n--~~~~   77 (224)
T d1sxjb2          14 LSDIVGNKETIDRLQQIAKDGN--MPHMIISGMPGIGKTTSVHCLAH--ELLGRSY--AD-------GVLE-LN--ASDD   77 (224)
T ss_dssp             GGGCCSCTHHHHHHHHHHHSCC--CCCEEEECSTTSSHHHHHHHHHH--HHHGGGH--HH-------HEEE-EC--TTSC
T ss_pred             HHHhcCCHHHHHHHHHHHHcCC--CCeEEEECCCCCCchhhHHHHHH--HHhcccc--cc-------cccc-cc--cccc
Confidence            3568999999999999998765  33466899999999999998876  2221110  00       0000 00  0111


Q ss_pred             CCHHHHHHHHHHHhc-------CCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCCh
Q 040913          246 EDYKLKKSILRDFLT-------NKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINP  301 (425)
Q Consensus       246 ~~~~~l~~~l~~~l~-------~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~  301 (425)
                      .....+...+.....       ++.-++|+|++.. +......+...+......+++++||.+.
T Consensus        78 ~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~~~~~ll~~~e~~~~~~~~i~~~~~~  141 (224)
T d1sxjb2          78 RGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQQALRRTMELYSNSTRFAFACNQS  141 (224)
T ss_dssp             CSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHHHTTHHHHHHTTTTEEEEEEESCG
T ss_pred             CCceehhhHHHHHHHhhccCCCcceEEEEEecccccchhHHHHHhhhccccccceeeeeccCch
Confidence            223333333333321       3566889999963 2233344444444445566776666553

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=97.83  E-value=9.8e-06  Score=69.12  Aligned_cols=124  Identities=8%  Similarity=0.047  Sum_probs=70.0

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc---cccc-cccchHHH--HHHHHHHhCCCCCCC
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN---HVKF-YFDCLAWI--LDDIIRSLMPPSRVT  241 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~---~~~~-~F~~~~wv--~~~il~~l~~~~~~~  241 (425)
                      .++||+++++++++.|.....+  -+.+||.+|+|||+++..+...-   ++-. ..+..+|.  +..++.....     
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~k~--n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~-----   95 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRTKN--NPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKY-----   95 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSSSC--EEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCS-----
T ss_pred             CCcCcHHHHHHHHHHHhccCCC--CeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCc-----
Confidence            4889999999999999876532  35689999999999987766511   1111 12233333  3333321110     


Q ss_pred             ccCCCCHHHHHHHHHHHh-c-CCeEEEEecccCCCh----------hhHHHHHhhCCCCCCCcEEEEecCChhHH
Q 040913          242 VIIGEDYKLKKSILRDFL-T-NKKYFIALDDVCHNI----------EIWDDLEEVLPDNQNGSRVLITVINPSLL  304 (425)
Q Consensus       242 ~~~~~~~~~l~~~l~~~l-~-~kr~LlVLDdvw~~~----------~~~~~l~~~l~~~~~gskIivTTR~~~va  304 (425)
                         ..+.++....+.+.+ + ..+.++++|++- .-          +.-+-+++.|..  ..-++|.||..+...
T Consensus        96 ---rG~~E~rl~~il~e~~~~~~~iILfIDeih-~l~~~g~~~g~~d~~~~Lkp~L~r--g~l~~IgatT~eey~  164 (195)
T d1jbka_          96 ---RGEFEERLKGVLNDLAKQEGNVILFIDELH-TMVGAGKADGAMDAGNMLKPALAR--GELHCVGATTLDEYR  164 (195)
T ss_dssp             ---HHHHHHHHHHHHHHHHHSTTTEEEEEETGG-GGTT------CCCCHHHHHHHHHT--TSCCEEEEECHHHHH
T ss_pred             ---cHHHHHHHHHHHHHHhcCCCcEEEEcchHH-HHhcCCCCCCcccHHHHHHHHHhC--CCceEEecCCHHHHH
Confidence               012333333333333 3 347999999995 21          122344444432  235677777655543

>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=97.81  E-value=1.6e-05  Score=71.50  Aligned_cols=103  Identities=20%  Similarity=0.128  Sum_probs=63.6

Q ss_pred             CCCCcccchhhHHHHHHHHhc----CC---CCcEEEEEEecCCCchHHHHHHhhcCcccccc-------cc---------
Q 040913          165 PRLDISEFERAREEWFDLLIE----GP---IGLSVVAILDSSGFDKTAFAADTYNNNHVKFY-------FD---------  221 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~----~~---~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~-------F~---------  221 (425)
                      .+..++||+.+.++|.+.+..    +.   ....++.++|++|+||||+++.+.+.  ....       +.         
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~   91 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVNAFNA   91 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEEGGGC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHH--HHhhcccccCCceeeeeccccc
Confidence            456789999999999887642    22   12334566899999999999999873  2111       10         


Q ss_pred             -chHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--CCeEEEEecccC
Q 040913          222 -CLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--NKKYFIALDDVC  272 (425)
Q Consensus       222 -~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~kr~LlVLDdvw  272 (425)
                       ....+...+...+.....   ........+...+.....  +...++++|.+.
T Consensus        92 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          92 PNLYTILSLIVRQTGYPIQ---VRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             CSHHHHHHHHHHHHTCCCC---CTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             cchhhHHHHHhhhcccccc---cccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence             111224555555554432   123455566666666553  466777888764

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.76  E-value=0.00014  Score=62.69  Aligned_cols=127  Identities=11%  Similarity=0.041  Sum_probs=71.2

Q ss_pred             chhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC----cc-c-cccccchHHHHHHHHHHhCCCCCC----C
Q 040913          172 FERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN----NH-V-KFYFDCLAWILDDIIRSLMPPSRV----T  241 (425)
Q Consensus       172 r~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~----~~-~-~~~F~~~~wv~~~il~~l~~~~~~----~  241 (425)
                      .+...+++.+.+..+. -.+.+-++|+.|+||||+|+.+.+.    .. . .....+.-  ...+..........    .
T Consensus         7 ~~~~~~~l~~~~~~~~-l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~--~~~i~~~~~~~~~~~~~~~   83 (207)
T d1a5ta2           7 LRPDFEKLVASYQAGR-GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRG--CQLMQAGTHPDYYTLAPEK   83 (207)
T ss_dssp             GHHHHHHHHHHHHTTC-CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHH--HHHHHHTCCTTEEEECCCT
T ss_pred             cHHHHHHHHHHHHcCC-cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccch--hhhhhhccccccchhhhhh
Confidence            4456777888777654 2445788999999999999976651    10 0 00111100  11111111110000    0


Q ss_pred             ccCCCCHHHHHHHHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          242 VIIGEDYKLKKSILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       242 ~~~~~~~~~l~~~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                      .......+++. .+.+.+     .+++-++|+||+.. +.+....+...+-.....+.+|.||++.+
T Consensus        84 ~~~~i~~~~ir-~l~~~~~~~~~~~~~kviIide~d~l~~~a~n~Llk~lEep~~~~~fIl~t~~~~  149 (207)
T d1a5ta2          84 GKNTLGVDAVR-EVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPE  149 (207)
T ss_dssp             TCSSBCHHHHH-HHHHHTTSCCTTSSCEEEEESCGGGBCHHHHHHHHHHHTSCCTTEEEEEEESCGG
T ss_pred             cccccccchhh-HHhhhhhhccccCccceEEechhhhhhhhhhHHHHHHHHhhcccceeeeeecChh
Confidence            11122334433 333433     35677999999963 45677788877776667888888887754

>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=97.68  E-value=9.7e-05  Score=65.60  Aligned_cols=46  Identities=20%  Similarity=0.055  Sum_probs=34.2

Q ss_pred             CCcccchhhHHHHHHHHh-------cC-CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLI-------EG-PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~-------~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++|..+.++.+++.+.       .+ ....+-|.++|++|+|||++|+.+.+
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~   62 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE   62 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhh
Confidence            348887777776665543       22 23456688999999999999999998

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=97.61  E-value=2.2e-05  Score=74.46  Aligned_cols=124  Identities=8%  Similarity=0.079  Sum_probs=65.8

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhh----cCcccc-ccccchHHH--HHHHHHHhCCCCCC
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY----NNNHVK-FYFDCLAWI--LDDIIRSLMPPSRV  240 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~----~~~~~~-~~F~~~~wv--~~~il~~l~~~~~~  240 (425)
                      .++||+.+++++++.|.....+.  +.+||.+|||||+++..+.    +. .+- ...+.++|.  +..++.....    
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k~n--~llvG~~GvGKtaiv~~la~~i~~~-~vp~~l~~~~i~~ld~~~l~ag~~~----   95 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTKNN--PVLIGEPGVGKTAIVEGLAQRIVKG-DVPEGLKGKRIVSLQMGSLLAGAKY----   95 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSCCC--CEEEECTTSCHHHHHHHHHHHHHHT-CSCTTSTTCEEEEECC-------------
T ss_pred             CCcCcHHHHHHHHHHHhcCCCCC--CeEECCCCCCHHHHHHHHHHHHHhC-CCCHHHcCceEEEeeHhhhhcccCc----
Confidence            48899999999999998765332  3568999999999775444    32 221 122344443  2222221111    


Q ss_pred             CccCCCCHHHHHHHHHHHh-cC-CeEEEEecccCCCh----------hhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          241 TVIIGEDYKLKKSILRDFL-TN-KKYFIALDDVCHNI----------EIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       241 ~~~~~~~~~~l~~~l~~~l-~~-kr~LlVLDdvw~~~----------~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                          ....++....+...+ +. ..++|++|++- .-          +.-+-|+++|..+  .-++|-||..+....
T Consensus        96 ----~g~~e~r~~~i~~~~~~~~~~~ilfide~h-~l~~~g~~~g~~d~a~~Lkp~L~rg--~~~~I~~tT~~ey~~  165 (387)
T d1qvra2          96 ----RGEFEERLKAVIQEVVQSQGEVILFIDELH-TVVGAGKAEGAVDAGNMLKPALARG--ELRLIGATTLDEYRE  165 (387)
T ss_dssp             ------CHHHHHHHHHHHHHTTCSSEEEEECCC--------------------HHHHHTT--CCCEEEEECHHHHHH
T ss_pred             ----chhHHHHHHHHHHHhccCCCceEEEeccHH-HHhcCCCCCCcccHHHHHHHHHhCC--CcceeeecCHHHHHH
Confidence                124444444444444 33 47999999995 21          1223344455322  346777776666543

>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=97.60  E-value=2.1e-05  Score=68.49  Aligned_cols=120  Identities=14%  Similarity=0.000  Sum_probs=61.5

Q ss_pred             CCCcccchhhH--HHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH-----HHHHHHHhCCCC
Q 040913          166 RLDISEFERAR--EEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI-----LDDIIRSLMPPS  238 (425)
Q Consensus       166 ~~~~vGr~~~~--~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv-----~~~il~~l~~~~  238 (425)
                      +.-++|-.+..  ..+.++..........+-|+|+.|+|||.|++++++.  ........+++     ...+...+... 
T Consensus        10 dnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~-   86 (213)
T d1l8qa2          10 ENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSSADDFAQAMVEHLKKG-   86 (213)
T ss_dssp             SSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEEHHHHHHHHHHHHHHT-
T ss_pred             hhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHH--hccCccceEEechHHHHHHHHHHHHcc-
Confidence            44456754432  3334444444333444779999999999999999984  32221111221     11111111110 


Q ss_pred             CCCccCCCCHHHHHHHHHHHhcCCeEEEEecccCC--ChhhHHHH-HhhCCC-CCCCcEEEEecCCh
Q 040913          239 RVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVCH--NIEIWDDL-EEVLPD-NQNGSRVLITVINP  301 (425)
Q Consensus       239 ~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~--~~~~~~~l-~~~l~~-~~~gskIivTTR~~  301 (425)
                              ...+    +.+.++ .--+|++||+..  ....|+.. ...+.. ...|.+||+||+..
T Consensus        87 --------~~~~----~~~~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~  140 (213)
T d1l8qa2          87 --------TINE----FRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRH  140 (213)
T ss_dssp             --------CHHH----HHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             --------chhh----HHHHHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCc
Confidence                    1111    112222 346899999962  22455442 222221 24577899998774

>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=97.56  E-value=0.00022  Score=63.71  Aligned_cols=93  Identities=14%  Similarity=0.118  Sum_probs=57.2

Q ss_pred             CCcccchhhHHHHHHHHh----cC-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhC
Q 040913          167 LDISEFERAREEWFDLLI----EG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLM  235 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~----~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~  235 (425)
                      .++.|.+..+++|.+.+.    ..       -...+-|.++|++|+|||+||+.+.+  ....+|-..-      ...+.
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~--~~~~~~~~i~------~~~l~   75 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAFFFLIN------GPEIM   75 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHH--HTTCEEEEEC------HHHHT
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHH--HhCCeEEEEE------chhhc
Confidence            468899999988877643    21       12355678999999999999999998  4444431100      00111


Q ss_pred             CCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          236 PPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       236 ~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      ...     .......+...+...-..++++|++||+.
T Consensus        76 ~~~-----~g~~~~~l~~~f~~A~~~~p~il~iDeid  107 (258)
T d1e32a2          76 SKL-----AGESESNLRKAFEEAEKNAPAIIFIDELD  107 (258)
T ss_dssp             TSC-----TTHHHHHHHHHHHHHHHTCSEEEEESSGG
T ss_pred             ccc-----cccHHHHHHHHHHHHHhcCCeEEEehhhh
Confidence            111     11123334444444445788999999996

>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=97.29  E-value=0.00036  Score=62.13  Aligned_cols=94  Identities=18%  Similarity=0.191  Sum_probs=57.4

Q ss_pred             CCCCcccchhhHHHHHHH---HhcC-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccc-cchHHHHHHHHHH
Q 040913          165 PRLDISEFERAREEWFDL---LIEG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-DCLAWILDDIIRS  233 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~---L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~il~~  233 (425)
                      .-.+++|.++.+++|.+.   +...       ....+-+.++|++|+|||+||+.+.+  ....+| .....       .
T Consensus        10 t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~--~~~~~~~~i~~~-------~   80 (256)
T d1lv7a_          10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG--EAKVPFFTISGS-------D   80 (256)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHH--HHTCCEEEECSC-------S
T ss_pred             CHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHH--HcCCCEEEEEhH-------H
Confidence            346799999888887553   3322       12356678999999999999999987  333332 11000       0


Q ss_pred             hCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          234 LMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       234 l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      +..     .....+...+...+...-+..+++|++||+.
T Consensus        81 l~~-----~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD  114 (256)
T d1lv7a_          81 FVE-----MFVGVGASRVRDMFEQAKKAAPCIIFIDEID  114 (256)
T ss_dssp             STT-----SCCCCCHHHHHHHHHHHHTTCSEEEEETTHH
T ss_pred             hhh-----cchhHHHHHHHHHHHHHHHcCCEEEEEEChh
Confidence            000     1112344555555555556778999999994

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=97.26  E-value=6.1e-05  Score=66.28  Aligned_cols=47  Identities=17%  Similarity=0.052  Sum_probs=37.8

Q ss_pred             CCCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|.+..+++|..++...   ....+-+-++|++|+||||+|+.+.+
T Consensus         8 ~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~   57 (238)
T d1in4a2           8 LDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIAS   57 (238)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHh
Confidence            356899999999998888632   22344567999999999999999988

>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=97.16  E-value=0.00013  Score=64.11  Aligned_cols=47  Identities=17%  Similarity=0.116  Sum_probs=37.4

Q ss_pred             CCCcccchhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          166 RLDISEFERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+++||-+..+++|..++...   ...++-+-++|++|+||||+|+.+.+
T Consensus         8 ~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~   57 (239)
T d1ixsb2           8 LDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAH   57 (239)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            356899999999988887642   22345566899999999999999988

>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=97.15  E-value=0.00061  Score=60.26  Aligned_cols=97  Identities=15%  Similarity=0.170  Sum_probs=55.7

Q ss_pred             CCCCCCCcccchhhHHHHHHH---HhcC-------CCCcEEEEEEecCCCchHHHHHHhhcCccccccc-cchHHHHHHH
Q 040913          162 EGQPRLDISEFERAREEWFDL---LIEG-------PIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-DCLAWILDDI  230 (425)
Q Consensus       162 ~~~~~~~~vGr~~~~~~l~~~---L~~~-------~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~i  230 (425)
                      |.+.-.+++|.++.+++|.+.   +..+       ....+-|-++|++|+|||+||+.+.+  +...+| ...   ..++
T Consensus         4 p~~~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~--~~~~~~~~i~---~~~l   78 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG--EARVPFITAS---GSDF   78 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHH--HTTCCEEEEE---HHHH
T ss_pred             CCCcHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHH--HcCCCEEEEE---hHHh
Confidence            334445789998887776543   3321       12345678999999999999999998  443333 110   1111


Q ss_pred             HHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          231 IRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       231 l~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                      +..    .     ...+...+...+...-...+++|++||+.
T Consensus        79 ~~~----~-----~g~~~~~l~~~f~~a~~~~p~Ii~iDeid  111 (247)
T d1ixza_          79 VEM----F-----VGVGAARVRDLFETAKRHAPCIVFIDEID  111 (247)
T ss_dssp             HHS----C-----TTHHHHHHHHHHHHHTTSSSEEEEEETHH
T ss_pred             hhc----c-----ccHHHHHHHHHHHHHHHcCCEEEEEEChh
Confidence            111    0     01122233333333334678899999984

>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=97.08  E-value=0.00022  Score=63.03  Aligned_cols=48  Identities=13%  Similarity=0.068  Sum_probs=39.4

Q ss_pred             CCCcccchhhHHHHHHHHhc---------------CCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          166 RLDISEFERAREEWFDLLIE---------------GPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       166 ~~~~vGr~~~~~~l~~~L~~---------------~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -.+++|.+..+++|.++|..               +....+.+.++|++|+||||+|+.+.+.
T Consensus        13 ~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~   75 (253)
T d1sxja2          13 LQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE   75 (253)
T ss_dssp             GGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            46799999999999999853               1123567889999999999999999983

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.06  E-value=0.00049  Score=61.59  Aligned_cols=95  Identities=18%  Similarity=0.198  Sum_probs=57.7

Q ss_pred             CCCCCcccchhhHHHHHHHHh----c-------CCCCcEEEEEEecCCCchHHHHHHhhcCccccccc-cchHHHHHHHH
Q 040913          164 QPRLDISEFERAREEWFDLLI----E-------GPIGLSVVAILDSSGFDKTAFAADTYNNNHVKFYF-DCLAWILDDII  231 (425)
Q Consensus       164 ~~~~~~vGr~~~~~~l~~~L~----~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F-~~~~wv~~~il  231 (425)
                      ..-.+++|.++.+++|.+.+.    .       +-...+-|-++|++|+|||+||+.+.+  ....+| ....   .++.
T Consensus         4 ~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~--~~~~~~~~~~~---~~l~   78 (265)
T d1r7ra3           4 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQANFISIKG---PELL   78 (265)
T ss_dssp             CSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHH--HTTCEEEEECH---HHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHH--HhCCcEEEEEH---HHhh
Confidence            344568898888777766543    1       112355677999999999999999998  444443 2211   1111


Q ss_pred             HHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEecccC
Q 040913          232 RSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIALDDVC  272 (425)
Q Consensus       232 ~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw  272 (425)
                          ..     ........+...+...-...+++|++||+.
T Consensus        79 ----~~-----~~~~~~~~l~~~f~~A~~~~p~il~ideid  110 (265)
T d1r7ra3          79 ----TM-----WFGESEANVREIFDKARQAAPCVLFFDELD  110 (265)
T ss_dssp             ----TS-----CTTTHHHHHHHHHHHHHHTCSEEEEESSGG
T ss_pred             ----hc-----cccchHHHHHHHHHHHHhcCCcceeHHhhh
Confidence                11     111223334444444445688999999995

>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=96.89  E-value=0.00019  Score=58.92  Aligned_cols=23  Identities=22%  Similarity=0.239  Sum_probs=21.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+||.|+|..|+|||||++++.+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~   24 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46999999999999999999976

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.84  E-value=0.00021  Score=59.33  Aligned_cols=23  Identities=22%  Similarity=0.211  Sum_probs=21.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+.|.|.|+.|+||||||+.+.+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            67899999999999999999987

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.82  E-value=0.0011  Score=55.15  Aligned_cols=62  Identities=16%  Similarity=0.135  Sum_probs=39.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeEEEEe
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKYFIAL  268 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~LlVL  268 (425)
                      .+.+|.++|++|+||||+|+......... ++.     .+               ...+...+...+...|+.++ .+|+
T Consensus        13 ~p~liil~G~pGsGKST~a~~l~~~~~~~-~i~-----~D---------------~~~~~~~~~~~~~~~l~~g~-~vIi   70 (172)
T d1yj5a2          13 NPEVVVAVGFPGAGKSTFIQEHLVSAGYV-HVN-----RD---------------TLGSWQRCVSSCQAALRQGK-RVVI   70 (172)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHTGGGTCE-EEE-----HH---------------HHCSHHHHHHHHHHHHHTTC-CEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhcCCE-EEc-----hH---------------HHHHHHHHHHHHHHHHHCCC-Ccee
Confidence            47799999999999999999886521110 010     00               01233455666666776544 5778


Q ss_pred             cccC
Q 040913          269 DDVC  272 (425)
Q Consensus       269 Ddvw  272 (425)
                      |+.-
T Consensus        71 D~t~   74 (172)
T d1yj5a2          71 DNTN   74 (172)
T ss_dssp             ESCC
T ss_pred             eCcC
Confidence            9874

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.79  E-value=0.0021  Score=54.62  Aligned_cols=110  Identities=9%  Similarity=0.008  Sum_probs=66.2

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCccc--cccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHH
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNNHV--KFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKS  253 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~~~--~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~  253 (425)
                      .+-+.+++..+.  .+.+-++|.+|+||||+|..+.+....  ..|-|.. +        +..     +......+++.+
T Consensus         3 ~~~l~~~i~~~~--~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~-~--------i~~-----~~~~I~Id~IR~   66 (198)
T d2gnoa2           3 LETLKRIIEKSE--GISILINGEDLSYPREVSLELPEYVEKFPPKASDVL-E--------IDP-----EGENIGIDDIRT   66 (198)
T ss_dssp             HHHHHHHHHTCS--SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEE-E--------ECC-----SSSCBCHHHHHH
T ss_pred             HHHHHHHHhcCC--CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEE-E--------EeC-----CcCCCCHHHHHH
Confidence            344555555543  778899999999999999987762111  1121210 0        000     011224455544


Q ss_pred             HHHHHh-----cCCeEEEEecccCC-ChhhHHHHHhhCCCCCCCcEEEEecCChh
Q 040913          254 ILRDFL-----TNKKYFIALDDVCH-NIEIWDDLEEVLPDNQNGSRVLITVINPS  302 (425)
Q Consensus       254 ~l~~~l-----~~kr~LlVLDdvw~-~~~~~~~l~~~l~~~~~gskIivTTR~~~  302 (425)
                       +.+.+     .+++-++|+|++.. +.+.++.+...+-.-..++..|++|.+.+
T Consensus        67 -i~~~~~~~~~~~~~KviIId~ad~l~~~aqNaLLK~LEEPp~~t~fiLit~~~~  120 (198)
T d2gnoa2          67 -IKDFLNYSPELYTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWH  120 (198)
T ss_dssp             -HHHHHTSCCSSSSSEEEEETTGGGBCHHHHHHTHHHHHSCCTTEEEEEEESCGG
T ss_pred             -HHHHHhhCcccCCCEEEEEeCccccchhhhhHHHHHHhCCCCCceeeeccCChh
Confidence             44444     24656899999964 55778888777766566788777776644

>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=96.77  E-value=0.00021  Score=58.10  Aligned_cols=22  Identities=9%  Similarity=0.166  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|.++|++|+||||+|+.+..
T Consensus         3 k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4578889999999999999988

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.71  E-value=0.00038  Score=56.12  Aligned_cols=22  Identities=14%  Similarity=0.335  Sum_probs=19.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|.|++|+||||||+.+..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5788999999999999998765

>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=96.69  E-value=0.00088  Score=56.18  Aligned_cols=37  Identities=19%  Similarity=0.073  Sum_probs=27.5

Q ss_pred             HHHHHHHHhcC-CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEG-PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~-~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++.|...+..- ..+.-+|+|.|.+|+||||||+.+.+
T Consensus         7 ~~~~~~~~~~~~~~~~~iIgI~G~~GSGKSTla~~L~~   44 (198)
T d1rz3a_           7 IDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQ   44 (198)
T ss_dssp             HHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34444444333 34577999999999999999999876

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.64  E-value=0.00044  Score=56.65  Aligned_cols=22  Identities=14%  Similarity=0.157  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|.|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6799999999999999998876

>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=96.58  E-value=0.001  Score=58.84  Aligned_cols=40  Identities=18%  Similarity=0.258  Sum_probs=29.6

Q ss_pred             hhhHHHHHHHHhcC---CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          173 ERAREEWFDLLIEG---PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       173 ~~~~~~l~~~L~~~---~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++...+.++.+..+   ...++.|.++|++|+||||||+.+.+
T Consensus        12 ~~~~~~~~~~~~~~~~~~~~P~~ilL~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          12 ENRLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             HHHHHHHHHHHHTTCCCCSSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccCCCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34444555556543   24577788999999999999999988

>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=96.55  E-value=0.00051  Score=56.65  Aligned_cols=24  Identities=13%  Similarity=-0.115  Sum_probs=21.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +-.+|.++|++|+||||+|+.+..
T Consensus         5 ~g~~I~l~G~~GsGKTTia~~La~   28 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIARALQV   28 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357899999999999999999886

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.49  E-value=0.0026  Score=55.24  Aligned_cols=53  Identities=15%  Similarity=0.234  Sum_probs=34.0

Q ss_pred             HHHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          251 KKSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       251 l~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      -.-.|...|..+.-+|++|.--.  +.    +.|+.+....  ...|..||++|.+.+++.
T Consensus       152 QRvaIAraL~~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~--~~~g~tii~vTHd~~~a~  210 (230)
T d1l2ta_         152 QRVAIARALANNPPIILADQPTGALDSKTGEKIMQLLKKLN--EEDGKTVVVVTHDINVAR  210 (230)
T ss_dssp             HHHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHH--HTTCCEEEEECSCHHHHT
T ss_pred             HHHHHHhhhhcCCCEEEecCCccccCHHHHHHHHHHHHHHH--HhhCCEEEEECCCHHHHH
Confidence            34556667778888999998742  11    3444444331  234788888898888764

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=96.46  E-value=0.00077  Score=56.88  Aligned_cols=26  Identities=23%  Similarity=0.234  Sum_probs=23.1

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.+.+|.|+|++|+||||+|+.+.+.
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35789999999999999999999873

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=96.41  E-value=0.00064  Score=55.71  Aligned_cols=22  Identities=14%  Similarity=0.288  Sum_probs=19.5

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..|.|.|++|+||||+|+.+..
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4577999999999999999987

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=96.40  E-value=0.0014  Score=57.60  Aligned_cols=23  Identities=22%  Similarity=0.235  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|+|..|+|||||++.+..
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            45799999999999999999875

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.39  E-value=0.00053  Score=56.73  Aligned_cols=22  Identities=18%  Similarity=0.228  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|.|+|++|+|||||++.+..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~   23 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASE   23 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHH
Confidence            4588999999999999999886

>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=96.36  E-value=0.00073  Score=55.54  Aligned_cols=22  Identities=14%  Similarity=0.060  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +||+|+|..|+|||||+.++..
T Consensus         2 kii~I~G~~gSGKTTli~~l~~   23 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVA   23 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            6899999999999999998876

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.32  E-value=0.0015  Score=57.74  Aligned_cols=23  Identities=26%  Similarity=0.229  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            45899999999999999999864

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=96.27  E-value=0.00099  Score=56.61  Aligned_cols=23  Identities=9%  Similarity=0.105  Sum_probs=20.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.+|.++|.+|+||||||+++..
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999886

>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=96.25  E-value=0.00088  Score=55.49  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=20.3

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|.|+.|+||||+++.+..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999998876

>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=96.25  E-value=0.0013  Score=53.95  Aligned_cols=23  Identities=17%  Similarity=0.202  Sum_probs=21.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -++|.|.|++|+||||+|+.+.+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            57899999999999999999977

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.24  E-value=0.0013  Score=55.62  Aligned_cols=26  Identities=19%  Similarity=0.226  Sum_probs=23.4

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..+||.|.|++|+||||+|+.+.+.
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            35889999999999999999999883

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.24  E-value=0.0035  Score=55.24  Aligned_cols=23  Identities=30%  Similarity=0.270  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||++.+..
T Consensus        40 Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          40 GEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46899999999999999999874

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.21  E-value=0.0009  Score=54.98  Aligned_cols=26  Identities=8%  Similarity=0.109  Sum_probs=20.6

Q ss_pred             EEEEecCCCchHHHHHHhhcCccccccc
Q 040913          193 VAILDSSGFDKTAFAADTYNNNHVKFYF  220 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~~~~~~~F  220 (425)
                      |.++||+|+||||+++.+.+  +..-.|
T Consensus         4 IvliG~~G~GKSTig~~La~--~l~~~f   29 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAK--ALGVGL   29 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHH--HHTCCE
T ss_pred             EEEECCCCCCHHHHHHHHHH--HhCCCe
Confidence            34569999999999999988  555444

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=96.21  E-value=0.0011  Score=54.47  Aligned_cols=23  Identities=9%  Similarity=0.053  Sum_probs=21.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|.|.+|+||||+|+.+.+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999988

>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=96.15  E-value=0.0014  Score=53.62  Aligned_cols=24  Identities=21%  Similarity=0.325  Sum_probs=22.0

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+++.|.|++|+||||+|+.+..
T Consensus         5 ~~~iivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           5 DHHIYVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999999876

>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=96.08  E-value=0.0015  Score=53.46  Aligned_cols=24  Identities=21%  Similarity=0.090  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ....|.|.|++|+||||+|+.+.+
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            345688999999999999999987

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=96.08  E-value=0.0032  Score=54.99  Aligned_cols=54  Identities=11%  Similarity=0.154  Sum_probs=33.3

Q ss_pred             HHHHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          250 LKKSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       250 ~l~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      ...-.|...|..+.-+|++|.--.  +.    ..|+.+....  ...|..||++|.+-..+.
T Consensus       145 kQRv~IAraL~~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~--~~~g~tvi~vTHd~~~~~  204 (240)
T d1g2912         145 RQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQ--RQLGVTTIYVTHDQVEAM  204 (240)
T ss_dssp             HHHHHHHHHHHTCCSEEEEECTTTTSCHHHHHHHHHHHHHHH--HHHTCEEEEEESCHHHHH
T ss_pred             HHHHHHHHHHhcCCCEEEecCCCcccCHHHHHHHHHHHHHHH--hccCCEEEEEcCCHHHHH
Confidence            334567777788888999998641  11    2333333321  122778888998877654

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=96.06  E-value=0.0011  Score=54.28  Aligned_cols=20  Identities=15%  Similarity=0.217  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++||+|+||||+++.+..
T Consensus         3 I~liG~~GsGKsTi~k~La~   22 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAK   22 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67789999999999999988

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.04  E-value=0.0019  Score=57.13  Aligned_cols=23  Identities=22%  Similarity=0.083  Sum_probs=20.3

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|+|..|+|||||++.+..
T Consensus        44 Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          44 GETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHh
Confidence            45899999999999999998864

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.97  E-value=0.00096  Score=55.90  Aligned_cols=24  Identities=21%  Similarity=0.058  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+|.++|++|+||||+|+.+..
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~   41 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEE   41 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356888999999999999999976

>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=95.96  E-value=0.0015  Score=53.90  Aligned_cols=20  Identities=20%  Similarity=0.338  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.|+|++|+|||||++.+..
T Consensus         3 i~I~G~~G~GKSTLl~~i~~   22 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVE   22 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHh
Confidence            78999999999999999886

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=95.94  E-value=0.0059  Score=53.22  Aligned_cols=77  Identities=8%  Similarity=0.106  Sum_probs=42.3

Q ss_pred             HHHHHHHhCCCCCCC-ccCCCCHH-HHHHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEEec
Q 040913          227 LDDIIRSLMPPSRVT-VIIGEDYK-LKKSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLITV  298 (425)
Q Consensus       227 ~~~il~~l~~~~~~~-~~~~~~~~-~l~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIivTT  298 (425)
                      ..+++..++-..... .....+.. .-.-.|...|..+.-+|++|.--.  +.    ..|+.+...-  ...|..||++|
T Consensus       121 v~~~L~~vgL~~~~~~~~~~LSGG~~QRvaiAraL~~~P~lLllDEPt~~LD~~~~~~i~~~l~~l~--~~~g~tvi~vT  198 (240)
T d3dhwc1         121 VTELLSLVGLGDKHDSYPSNLSGGQKQRVAIARALASNPKVLLCDEATSALDPATTRSILELLKDIN--RRLGLTILLIT  198 (240)
T ss_dssp             HHHHHHHHSTTTTTSSCBSCCCHHHHHHHHHHHHHHTCCSEEEEESGGGSSCHHHHHHHHHHHHHHH--HHHCCEEEEEB
T ss_pred             HHHHHHHcCCchhhhCChhhCCHHHHHHHHHhhhhccCCCeEEeccccccCCHHHhhHHHHHHHHHH--hccCCEEEEEc
Confidence            445555555432221 12233333 333456677778888999998631  11    2333333321  12377899999


Q ss_pred             CChhHHH
Q 040913          299 INPSLLT  305 (425)
Q Consensus       299 R~~~va~  305 (425)
                      .+...+.
T Consensus       199 Hdl~~~~  205 (240)
T d3dhwc1         199 HEMDVVK  205 (240)
T ss_dssp             SCHHHHH
T ss_pred             CCHHHHH
Confidence            9987765

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=95.92  E-value=0.0016  Score=59.37  Aligned_cols=45  Identities=16%  Similarity=0.092  Sum_probs=34.4

Q ss_pred             CcccchhhHHHHHHHHhc----C--------CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIE----G--------PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~----~--------~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.++.++.+...+..    .        ....+-+.++|++|+|||.||+.+.+
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~   71 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   71 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhh
Confidence            478999998888766521    0        11346677899999999999999987

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.91  E-value=0.0039  Score=54.31  Aligned_cols=52  Identities=2%  Similarity=0.058  Sum_probs=32.2

Q ss_pred             HHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          252 KSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       252 ~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      .-.|...|..+.-+|+||.--.  +.    ..|+.+...-.  ..|..||++|.+...+.
T Consensus       144 RvaiAraL~~~P~iLllDEPts~LD~~~~~~i~~ll~~l~~--~~g~tii~vTHd~~~a~  201 (239)
T d1v43a3         144 RVAVARAIVVEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQ--KLKVTTIYVTHDQVEAM  201 (239)
T ss_dssp             HHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHH--HHTCEEEEEESCHHHHH
T ss_pred             HHHHHhhhccCCCceeecCCcccCCHHHHHHHHHHHHHHHH--hcCCeEEEEeCCHHHHH
Confidence            3456667778888999998741  11    33443433211  22777888888877664

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.89  E-value=0.0031  Score=54.96  Aligned_cols=112  Identities=13%  Similarity=0.113  Sum_probs=61.1

Q ss_pred             EEEEEecCCCchHHHHHHhhcCcc----------------------cccc------cc-chHHH----------------
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNH----------------------VKFY------FD-CLAWI----------------  226 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~----------------------~~~~------F~-~~~wv----------------  226 (425)
                      +++|+|+.|.|||||.+.+..-.+                      +.--      |+ ..++=                
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl~~p~~G~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~ltV~enl~~~l~~~~~~~~~~  105 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGIVKPDRGEVRLNGADITPLPPERRGIGFVPQDYALFPHLSVYRNIAYGLRNVERVERDR  105 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEEEEETTEECTTSCTTTSCCBCCCSSCCCCTTSCHHHHHHTTCTTSCHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCCCceEEEECCEECCcCCHHHcCceeeccchhhcccchhhHhhhhhhcccCHHHHHH
Confidence            778999999999999999873111                      0000      11 11110                


Q ss_pred             -HHHHHHHhCCCCCCC-ccCCCCH-HHHHHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEEe
Q 040913          227 -LDDIIRSLMPPSRVT-VIIGEDY-KLKKSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLIT  297 (425)
Q Consensus       227 -~~~il~~l~~~~~~~-~~~~~~~-~~l~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIivT  297 (425)
                       ..+++..+.-..... .....+. +...-.+...|-.+.-+|+||.--.  +.    ..|+.+...-  ...|..||++
T Consensus       106 ~v~~~l~~~gl~~~~~~~~~~LSGG~kQRvaiAral~~~P~illlDEPts~LD~~~~~~i~~~i~~l~--~~~g~tvi~v  183 (240)
T d2onka1         106 RVREMAEKLGIAHLLDRKPARLSGGERQRVALARALVIQPRLLLLDEPLSAVDLKTKGVLMEELRFVQ--REFDVPILHV  183 (240)
T ss_dssp             HHHHHHHTTTCTTTTTCCGGGSCHHHHHHHHHHHHHTTCCSSBEEESTTSSCCHHHHHHHHHHHHHHH--HHHTCCEEEE
T ss_pred             HHHHHHHhcCcHhhhhCChhhCCHHHHHHHHHHHHHhccCCceEecCccccCCHHHHHHHHHHHHHHH--HhcCCeEEEE
Confidence             445555554332211 1222333 3334456677778888999998741  11    3444443321  1226668888


Q ss_pred             cCChhHHH
Q 040913          298 VINPSLLT  305 (425)
Q Consensus       298 TR~~~va~  305 (425)
                      |.+...+.
T Consensus       184 tHd~~~~~  191 (240)
T d2onka1         184 THDLIEAA  191 (240)
T ss_dssp             ESCHHHHH
T ss_pred             eCCHHHHH
Confidence            88765543

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.82  E-value=0.0022  Score=53.87  Aligned_cols=23  Identities=26%  Similarity=0.211  Sum_probs=21.1

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.+|.|.|++|+||||.|+.+.+
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~   23 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVE   23 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.82  E-value=0.0036  Score=53.51  Aligned_cols=24  Identities=17%  Similarity=0.148  Sum_probs=19.2

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhh
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ..+.||.++|+.|+||||.+-++.
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA   30 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLA   30 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            357899999999999999554444

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=95.81  E-value=0.0013  Score=54.16  Aligned_cols=21  Identities=10%  Similarity=0.183  Sum_probs=18.7

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.++|++|+||||+|+.+.+
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            456889999999999999987

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=95.76  E-value=0.0062  Score=53.11  Aligned_cols=52  Identities=19%  Similarity=0.285  Sum_probs=32.9

Q ss_pred             HHHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          251 KKSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       251 l~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      ..-.+...|..+.-+++||.--.  +.    ..|+-+... .  ..|..||+||.+-+.+.
T Consensus       140 qrv~iA~al~~~p~illLDEPt~gLD~~~~~~i~~~i~~~-~--~~g~tii~~tH~l~~~~  197 (238)
T d1vpla_         140 RKLLIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQA-S--QEGLTILVSSHNMLEVE  197 (238)
T ss_dssp             HHHHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHH-H--HTTCEEEEEECCHHHHT
T ss_pred             HHHHHHHHHhcCCCEEEecCCCCCCCHHHHHHHHHHHHHH-H--hcCCEEEEEeCCHHHHH
Confidence            34466677778888899998751  11    234433332 1  23778999998877653

>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=95.73  E-value=0.0025  Score=52.77  Aligned_cols=22  Identities=14%  Similarity=0.188  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|.|+.|+||||+++.+..
T Consensus         2 kiivi~G~~GsGKTT~~~~La~   23 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6889999999999999999876

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.67  E-value=0.0028  Score=54.12  Aligned_cols=23  Identities=9%  Similarity=0.138  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +-||+|.|..|+||||+|+.+.+
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~   24 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQ   24 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999998755

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=95.64  E-value=0.0024  Score=54.62  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=21.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+||+|-|++|+||||+|+.+.+
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999988

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=95.58  E-value=0.0071  Score=55.08  Aligned_cols=45  Identities=11%  Similarity=0.057  Sum_probs=36.3

Q ss_pred             CcccchhhHHHHHHHHhc-------CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIE-------GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.+..++.+...+..       .+....++..+|+.|+|||.||+.+..
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~   74 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSK   74 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHh
Confidence            488999999998776642       233466888999999999999999876

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon 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: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=95.57  E-value=0.0046  Score=53.93  Aligned_cols=23  Identities=30%  Similarity=0.224  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~sGsGKSTll~~i~g   53 (242)
T d1oxxk2          31 GERFGILGPSGAGKTTFMRIIAG   53 (242)
T ss_dssp             TCEEEEECSCHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            45899999999999999998863

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=95.55  E-value=0.0097  Score=51.38  Aligned_cols=114  Identities=17%  Similarity=0.072  Sum_probs=62.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcCc------------cccc----------------ccc-chHHH--------------
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNNN------------HVKF----------------YFD-CLAWI--------------  226 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~~------------~~~~----------------~F~-~~~wv--------------  226 (425)
                      -.+++|+|+.|.|||||.+.+..-.            .+..                .|+ ..++=              
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl~~p~sG~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~~tV~enl~~~~~~~~~~~~  105 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGFHVPDSGRILLDGKDVTDLSPEKHDIAFVYQNYSLFPHMNVKKNLEFGMRMKKIKDP  105 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSSCCSEEEEEETTEECTTSCHHHHTCEEECTTCCCCTTSCHHHHHHHHHHHHCCCCH
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCcCCCCCEEEEccEeccccchhHhcceeeccccccCccccHHHHHHHHHhhccccHH
Confidence            4589999999999999999986321            1100                011 01111              


Q ss_pred             --HHHHHHHhCCCCCCC-ccCCCCH-HHHHHHHHHHhcCCeEEEEecccCC--Ch----hhHHHHHhhCCCCCCCcEEEE
Q 040913          227 --LDDIIRSLMPPSRVT-VIIGEDY-KLKKSILRDFLTNKKYFIALDDVCH--NI----EIWDDLEEVLPDNQNGSRVLI  296 (425)
Q Consensus       227 --~~~il~~l~~~~~~~-~~~~~~~-~~l~~~l~~~l~~kr~LlVLDdvw~--~~----~~~~~l~~~l~~~~~gskIiv  296 (425)
                        ..+++..+.-..... .....+. +...-.|...|-.+.-+|+||.--.  +.    +.|+.+....  ...|..||+
T Consensus       106 ~~~~~~l~~~~l~~~~~~~~~~LSGG~~QRvaiAraL~~~P~iLllDEPts~LD~~~~~~i~~~l~~l~--~~~g~tii~  183 (229)
T d3d31a2         106 KRVLDTARDLKIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSVLH--KKNKLTVLH  183 (229)
T ss_dssp             HHHHHHHHHTTCTTTTTSCGGGSCHHHHHHHHHHHHTTSCCSEEEEESSSTTSCHHHHHHHHHHHHHHH--HHTTCEEEE
T ss_pred             HHHHHHHHHhcchhhHhCChhhCCHHHhcchhhhhhhhccCCceeecCCCcCCCHHHHHHHHHHHHHHH--hcCCcEEEE
Confidence              455555554432211 1222333 3334566777778888999998741  11    2333333221  123677888


Q ss_pred             ecCChhHHH
Q 040913          297 TVINPSLLT  305 (425)
Q Consensus       297 TTR~~~va~  305 (425)
                      +|.+...+.
T Consensus       184 vtHd~~~~~  192 (229)
T d3d31a2         184 ITHDQTEAR  192 (229)
T ss_dssp             EESCHHHHH
T ss_pred             EcCCHHHHH
Confidence            888876554

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=95.39  E-value=0.0046  Score=51.70  Aligned_cols=24  Identities=21%  Similarity=0.155  Sum_probs=20.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+-+|+|.|+.|+||||+|..+-+
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            367999999999999999998743

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

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: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=95.37  E-value=0.0073  Score=55.17  Aligned_cols=37  Identities=14%  Similarity=0.073  Sum_probs=29.4

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+++.+.....+..+|+|.|++|+|||||...+..
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~   73 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGS   73 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHH
Confidence            4556666665556789999999999999999887764

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=95.25  E-value=0.0037  Score=52.28  Aligned_cols=24  Identities=13%  Similarity=-0.093  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..|.|.|++|+||||+|+.+.+.
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            345779999999999999998773

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=95.25  E-value=0.0085  Score=54.80  Aligned_cols=37  Identities=11%  Similarity=0.068  Sum_probs=29.0

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..++++.+.....+..+|+|.|.+|+|||||...+..
T Consensus        40 ~~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~   76 (327)
T d2p67a1          40 STQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGM   76 (327)
T ss_dssp             HHHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHH
Confidence            3456666655555689999999999999999987754

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=95.19  E-value=0.0052  Score=51.27  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=19.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.++| |+|++|+||||+|+.+..
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHH
Confidence            45666 789999999999999887

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=95.15  E-value=0.0045  Score=52.91  Aligned_cols=22  Identities=18%  Similarity=0.049  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+|+|-|++|+||||+|+.+..
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~   25 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAK   25 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3688999999999999999988

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.13  E-value=0.0044  Score=51.13  Aligned_cols=20  Identities=15%  Similarity=0.190  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.|.|++|+||||+|+.+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~   22 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVA   22 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999876

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=95.08  E-value=0.0051  Score=51.61  Aligned_cols=23  Identities=9%  Similarity=0.172  Sum_probs=21.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|.|.|++|+||||+|+.+.+
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999999987

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=94.88  E-value=0.0057  Score=50.69  Aligned_cols=21  Identities=14%  Similarity=0.216  Sum_probs=19.1

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678999999999999999883

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.86  E-value=0.0058  Score=50.55  Aligned_cols=21  Identities=24%  Similarity=0.249  Sum_probs=18.9

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|.|++|+||||+|+.+.+.
T Consensus         3 I~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            678899999999999999873

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=94.82  E-value=0.006  Score=51.14  Aligned_cols=22  Identities=18%  Similarity=0.209  Sum_probs=19.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      --|.|.|++|+||||+|+.+..
T Consensus         7 mrIiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHHHHH
Confidence            3455789999999999999987

>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=94.80  E-value=0.0047  Score=51.85  Aligned_cols=20  Identities=20%  Similarity=0.368  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.|+|++|+|||||++.+..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            67999999999999999876

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.77  E-value=0.0054  Score=51.23  Aligned_cols=21  Identities=19%  Similarity=0.322  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|.|+|++|+|||||++.+.+
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~   23 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            477999999999999999876

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.76  E-value=0.0065  Score=50.40  Aligned_cols=22  Identities=18%  Similarity=0.158  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.|+|++|+|||||++.+..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~   24 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRE   24 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            4788999999999999999876

>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=94.76  E-value=0.0088  Score=49.99  Aligned_cols=26  Identities=19%  Similarity=0.061  Sum_probs=22.6

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+.+|+|-|.-|+||||+++.+.+.
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHH
Confidence            34678999999999999999998763

>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=94.74  E-value=0.0093  Score=51.53  Aligned_cols=82  Identities=15%  Similarity=0.026  Sum_probs=46.3

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCC-----------CccCCCCHH
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRV-----------TVIIGEDYK  249 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~-----------~~~~~~~~~  249 (425)
                      .-.++.|.|.+|+|||+|+.++..+  ...+....+|+        +......+......           .........
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  102 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLE  102 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGGGSCHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccCCHHHHHHHHHHcCCChHHHhhcCceEEEEeecchhhHH
Confidence            4678899999999999999888764  22222222233        11222222111000           011234566


Q ss_pred             HHHHHHHHHhcC-CeEEEEecccC
Q 040913          250 LKKSILRDFLTN-KKYFIALDDVC  272 (425)
Q Consensus       250 ~l~~~l~~~l~~-kr~LlVLDdvw  272 (425)
                      .....+...+.. +.-++|+|.+.
T Consensus       103 ~~~~~i~~~i~~~~~~~vviDs~~  126 (242)
T d1tf7a2         103 DHLQIIKSEINDFKPARIAIDSLS  126 (242)
T ss_dssp             HHHHHHHHHHHTTCCSEEEEECHH
T ss_pred             HHHHHHHHHHHhcCCceeeeecch
Confidence            666777766654 55688889863

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=94.69  E-value=0.0087  Score=50.99  Aligned_cols=24  Identities=13%  Similarity=0.019  Sum_probs=21.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..||-+.|++|+||||||+.+..
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            477999999999999999999875

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.63  E-value=0.0063  Score=50.55  Aligned_cols=22  Identities=9%  Similarity=0.261  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|.|+|+.|+|||||++.+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~   25 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLIT   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            5688999999999999998875

>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=94.58  E-value=0.008  Score=51.84  Aligned_cols=21  Identities=19%  Similarity=0.354  Sum_probs=19.0

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ||.|+|+.|+|||||...+..
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHH
Confidence            789999999999999988853

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=94.51  E-value=0.013  Score=54.34  Aligned_cols=35  Identities=11%  Similarity=0.048  Sum_probs=27.4

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .....+..+.+..+.+.++|++|+|||++|..+.+
T Consensus       142 ~~l~~~~~~~~~~~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         142 DFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             HHHHHHHHCCTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCcCeEEEECCCCCCHHHHHHHHHH
Confidence            33344445555667899999999999999999988

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.47  E-value=0.011  Score=51.87  Aligned_cols=45  Identities=16%  Similarity=0.017  Sum_probs=35.3

Q ss_pred             CcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          168 DISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       168 ~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++||....++++.+.+..-...-.-|.|.|..|+|||++|+.++.
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~   45 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHK   45 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHH
Confidence            478888888888888876422223367899999999999999976

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.46  E-value=0.0086  Score=49.33  Aligned_cols=20  Identities=15%  Similarity=0.054  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.|.|++|+||||+|+.+.+
T Consensus         3 I~i~G~pGSGKsT~~~~La~   22 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIME   22 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999987

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.39  E-value=0.0088  Score=49.44  Aligned_cols=22  Identities=18%  Similarity=0.326  Sum_probs=18.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+++ |.|++|+||||+|+.+.+
T Consensus         3 mrIv-l~G~pGSGKtT~a~~La~   24 (180)
T d1akya1           3 IRMV-LIGPPGAGKGTQAPNLQE   24 (180)
T ss_dssp             CEEE-EECCTTSSHHHHHHHHHH
T ss_pred             eEEE-EECCCCCCHHHHHHHHHH
Confidence            4444 779999999999999987

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=94.38  E-value=0.01  Score=52.32  Aligned_cols=21  Identities=24%  Similarity=0.302  Sum_probs=18.2

Q ss_pred             EEEEEEecCCCchHHHHHHhh
Q 040913          191 SVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      +.|+|+|=||+||||+|-.+.
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA   22 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLT   22 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHH
T ss_pred             CEEEEECCCcCCHHHHHHHHH
Confidence            689999999999999986643

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=94.23  E-value=0.025  Score=51.06  Aligned_cols=72  Identities=11%  Similarity=-0.034  Sum_probs=42.7

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC-------ccc----cccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHH
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN-------NHV----KFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILR  256 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~-------~~~----~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~  256 (425)
                      ..+-+|+|.|..|+||||+|+.+...       +++    .+.|-.    ....+..-........+...|.+.+.+.+.
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~~----~~~~l~~~~~~~~~g~Pes~D~~~L~~~L~  153 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFLH----PNQVLKERGLMKKKGFPESYDMHRLVKFVS  153 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGBC----CHHHHHHHTCTTCTTSGGGBCHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeEC----CchHHHHhcCCccCCchHhhhHHHHHHHHH
Confidence            45889999999999999999887651       111    112211    112222222111111345678888888888


Q ss_pred             HHhcCCe
Q 040913          257 DFLTNKK  263 (425)
Q Consensus       257 ~~l~~kr  263 (425)
                      ....++.
T Consensus       154 ~lk~g~~  160 (308)
T d1sq5a_         154 DLKSGVP  160 (308)
T ss_dssp             HHTTTCS
T ss_pred             HHHcCCC
Confidence            8776653

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.23  E-value=0.016  Score=51.27  Aligned_cols=83  Identities=17%  Similarity=0.097  Sum_probs=53.0

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLT  260 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~  260 (425)
                      +.-+++-|.|.+|+||||||.+++....-..  ...+|+      -.+-+.+++.....- -....+.++..+.+...++
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g--~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~  135 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVANAQAAG--GVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHHHHHTT--CEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHHHhcCC--CEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            4568899999999999999977765322222  234555      234456665543311 1233456777776666665


Q ss_pred             -CCeEEEEecccC
Q 040913          261 -NKKYFIALDDVC  272 (425)
Q Consensus       261 -~kr~LlVLDdvw  272 (425)
                       ++.-|||+|.+-
T Consensus       136 ~~~~~liIiDSi~  148 (269)
T d1mo6a1         136 SGALDIVVIDSVA  148 (269)
T ss_dssp             TTCEEEEEEECST
T ss_pred             cCCCCEEEEeccc
Confidence             457799999985

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=94.21  E-value=0.019  Score=46.84  Aligned_cols=34  Identities=12%  Similarity=-0.048  Sum_probs=24.4

Q ss_pred             HHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          179 WFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       179 l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +++.+.-.....+ |.++|.+|+|||||...+...
T Consensus         3 ~~~~~~~~~k~~k-I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_           3 VLQFLGLYKKTGK-LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             HHHHHTCTTCCEE-EEEEEETTSSHHHHHHHHSCC
T ss_pred             hHHhccccCCCCE-EEEECCCCCCHHHHHHHHhCC
Confidence            3444544443444 669999999999999887664

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=94.20  E-value=0.01  Score=54.28  Aligned_cols=45  Identities=16%  Similarity=0.154  Sum_probs=31.9

Q ss_pred             CCCCcccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhh
Q 040913          165 PRLDISEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       165 ~~~~~vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      +-++++|.+..+..|.-.+...  +.+-+-+.|.+|+||||||+.+.
T Consensus         5 ~f~~I~Gq~~~kral~laa~~~--~~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           5 PFSAIVGQEDMKLALLLTAVDP--GIGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             CGGGSCSCHHHHHHHHHHHHCG--GGCCEEEECCGGGCTTHHHHHHH
T ss_pred             ChhhccCcHHHHHHHHHHHhcc--CCCeEEEECCCCccHHHHHHHHH
Confidence            4567899998777654333311  12346789999999999999774

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=94.19  E-value=0.0096  Score=50.39  Aligned_cols=23  Identities=22%  Similarity=0.232  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|+|||||.+.+..
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            45899999999999999999875

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=94.12  E-value=0.02  Score=46.71  Aligned_cols=29  Identities=14%  Similarity=0.106  Sum_probs=21.8

Q ss_pred             cCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          185 EGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       185 ~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+..--|.++|.+|+|||||...+.+.
T Consensus        11 ~~~~~~~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          11 SAPDQEVRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             SCCSSCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CCCCCEEEEEEECCCCCCHHHHHHHHhcC
Confidence            33333344679999999999999998764

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=94.12  E-value=0.015  Score=48.56  Aligned_cols=26  Identities=27%  Similarity=0.369  Sum_probs=22.4

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.+.|+|+|.+|+|||||...+.+.
T Consensus        21 ~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            34667999999999999999999863

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.04  E-value=0.024  Score=50.54  Aligned_cols=27  Identities=19%  Similarity=0.175  Sum_probs=22.7

Q ss_pred             CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          186 GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       186 ~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +...+-+|+|-|..|+|||||+..+..
T Consensus        23 ~~~~P~iIGi~G~qGSGKSTl~~~l~~   49 (286)
T d1odfa_          23 GNKCPLFIFFSGPQGSGKSFTSIQIYN   49 (286)
T ss_dssp             TCCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCCCEEEEeECCCCCCHHHHHHHHHH
Confidence            345578999999999999999987754

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=94.02  E-value=0.013  Score=47.08  Aligned_cols=21  Identities=24%  Similarity=0.186  Sum_probs=19.0

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||.+.+.++
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            679999999999999988775

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.93  E-value=0.014  Score=51.47  Aligned_cols=23  Identities=30%  Similarity=0.307  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||++.+..
T Consensus        28 GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          28 GDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHc
Confidence            45899999999999999999864

>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=93.92  E-value=0.027  Score=51.05  Aligned_cols=44  Identities=16%  Similarity=0.123  Sum_probs=34.4

Q ss_pred             cccchhhHHHHHHHHhc-------CCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          169 ISEFERAREEWFDLLIE-------GPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       169 ~vGr~~~~~~l~~~L~~-------~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ++|.+..++.|.+.+..       ++....++..+|+.|+|||.||+.+.+
T Consensus        25 v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~   75 (315)
T d1qvra3          25 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAA   75 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHH
T ss_pred             EeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHH
Confidence            78999888888776542       123456889999999999999988765

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=93.92  E-value=0.012  Score=46.98  Aligned_cols=21  Identities=10%  Similarity=0.025  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||...+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            569999999999999988754

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=93.89  E-value=0.015  Score=50.65  Aligned_cols=23  Identities=22%  Similarity=0.135  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -..++|+|+.|+|||||++.+..
T Consensus        28 Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          28 NSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            56899999999999999999863

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.85  E-value=0.015  Score=50.32  Aligned_cols=22  Identities=18%  Similarity=0.161  Sum_probs=20.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -.+++|+|+.|+|||||.+.+.
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~   47 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIA   47 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHHHh
Confidence            4589999999999999999986

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=93.75  E-value=0.021  Score=50.46  Aligned_cols=82  Identities=15%  Similarity=0.053  Sum_probs=52.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLTN  261 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~~  261 (425)
                      .-+++-|.|.+|+||||||.++.....-..  ..++|+      -.+++..++.....- -....+.++..+.+...++.
T Consensus        56 ~g~itei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~~  133 (268)
T d1xp8a1          56 RGRITEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVRS  133 (268)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHTT
T ss_pred             CceEEEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHhc
Confidence            456899999999999999988766322111  123455      235667776554321 12344667777777666654


Q ss_pred             -CeEEEEecccC
Q 040913          262 -KKYFIALDDVC  272 (425)
Q Consensus       262 -kr~LlVLDdvw  272 (425)
                       +.-|||+|-+-
T Consensus       134 ~~~~liIiDSi~  145 (268)
T d1xp8a1         134 GAIDVVVVDSVA  145 (268)
T ss_dssp             TCCSEEEEECTT
T ss_pred             CCCcEEEEeccc
Confidence             46699999884

>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=93.74  E-value=0.018  Score=49.07  Aligned_cols=23  Identities=17%  Similarity=0.114  Sum_probs=14.9

Q ss_pred             CCcEEEEEEecCCCchHHHHHHh
Q 040913          188 IGLSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      ..+.||.+||+.|+||||.+-.+
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKL   32 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKL   32 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHH
Confidence            46899999999999999954433

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=93.70  E-value=0.022  Score=46.87  Aligned_cols=35  Identities=26%  Similarity=0.208  Sum_probs=24.7

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.+.|.......++ .++|.+|+|||||...+.+.
T Consensus         6 ~~~~~l~~~~k~~KI-~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_           6 SMFDKLWGSNKELRI-LILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             HHHGGGTTCSSCEEE-EEEEETTSSHHHHHHHTCCS
T ss_pred             HHHHHHhCCCceEEE-EEECCCCCCHHHHHHHHhcC
Confidence            344444444445664 59999999999999998654

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.67  E-value=0.03  Score=49.34  Aligned_cols=33  Identities=18%  Similarity=0.280  Sum_probs=24.9

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHh
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      ...+.+.+...  ..+||.+.|=||+||||+|-.+
T Consensus         8 ~~~~~~~~~~~--~~~iii~sGKGGVGKTT~a~nL   40 (279)
T d1ihua2           8 LSALVDDIARN--EHGLIMLMGKGGVGKTTMAAAI   40 (279)
T ss_dssp             HHHHHHHHHTT--SCEEEEEECSTTSSHHHHHHHH
T ss_pred             HHHHHHHhhcC--CCEEEEEECCCCCCHHHHHHHH
Confidence            45566666644  4889999999999999976554

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.67  E-value=0.017  Score=51.60  Aligned_cols=24  Identities=25%  Similarity=0.191  Sum_probs=21.2

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.+++|+|+.|+|||||++.+..
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~G   84 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILG   84 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhC
Confidence            356899999999999999999875

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=93.64  E-value=0.02  Score=48.52  Aligned_cols=23  Identities=22%  Similarity=0.122  Sum_probs=18.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      +.+||.++|+.|+||||.+.++.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA   31 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLA   31 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHH
Confidence            46899999999999999554443

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.58  E-value=0.016  Score=51.26  Aligned_cols=35  Identities=26%  Similarity=0.392  Sum_probs=25.7

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.++.|..=..+ .-++|.|..|+|||+|+..+.++
T Consensus        57 raID~l~pigkG-Qr~~If~~~g~GKt~l~~~i~~~   91 (276)
T d2jdid3          57 KVVDLLAPYAKG-GKIGLFGGAGVGKTVLIMELINN   91 (276)
T ss_dssp             HHHHHHSCEETT-CEEEEEECTTSSHHHHHHHHHHH
T ss_pred             eeeeeeccccCC-CEEEeeCCCCCCHHHHHHHHHHH
Confidence            566766643222 23899999999999999888764

>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=93.47  E-value=0.016  Score=49.85  Aligned_cols=24  Identities=13%  Similarity=0.095  Sum_probs=21.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.|+|-|+-|+||||+++.+.+.
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999998873

>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=93.41  E-value=0.02  Score=48.73  Aligned_cols=24  Identities=17%  Similarity=0.104  Sum_probs=19.1

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhh
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      ..+.||.++|+.|+||||.+-++.
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLA   32 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLA   32 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            457899999999999999544443

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.38  E-value=0.022  Score=49.12  Aligned_cols=24  Identities=17%  Similarity=0.165  Sum_probs=21.9

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +++.|+|=|+-|+||||+++.+.+
T Consensus         1 ~pk~IviEG~~GsGKST~~~~L~~   24 (241)
T d2ocpa1           1 GPRRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            368899999999999999999986

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.35  E-value=0.019  Score=46.22  Aligned_cols=21  Identities=14%  Similarity=0.245  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988764

>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=93.35  E-value=0.02  Score=48.51  Aligned_cols=24  Identities=25%  Similarity=0.180  Sum_probs=19.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.+||.++|+.|+||||.+-++..
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~   28 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGR   28 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999996544443

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=93.34  E-value=0.026  Score=50.05  Aligned_cols=92  Identities=14%  Similarity=0.190  Sum_probs=50.2

Q ss_pred             EEEEEecCCCchHHHHHHhhcCccccccccchHHH--------HHHHHHHhCCCCCCC----------ccC--CCCHHHH
Q 040913          192 VVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI--------LDDIIRSLMPPSRVT----------VII--GEDYKLK  251 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv--------~~~il~~l~~~~~~~----------~~~--~~~~~~l  251 (425)
                      -++|+|..|+|||+|+.....+. ..+. +.++++        ..++...+.......          ...  ..-....
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~~-~~~~-~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~  146 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILNQ-QGQN-VICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYT  146 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHTC-CTTT-CEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHH
T ss_pred             eEeeccCCCCChHHHHHHHHhhh-cccC-ceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHH
Confidence            37889999999999998754421 1222 233333        555555554432111          000  0111233


Q ss_pred             HHHHHHHh--cCCeEEEEecccCCChhhHHHHHhhC
Q 040913          252 KSILRDFL--TNKKYFIALDDVCHNIEIWDDLEEVL  285 (425)
Q Consensus       252 ~~~l~~~l--~~kr~LlVLDdvw~~~~~~~~l~~~l  285 (425)
                      .-.+.+++  ++|+.|+++||+---...+.++...+
T Consensus       147 a~tiAEyfrd~G~~Vlll~Dsltr~A~A~rEis~~~  182 (276)
T d1fx0a3         147 GAALAEYFMYRERHTLIIYDDLSKQAQAYRQMSLLL  182 (276)
T ss_dssp             HHHHHHHHHHTTCEEEEEEECHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCceeEEeeccHHHHHHHHHHHHHc
Confidence            34445555  47999999999941235666665443

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=93.34  E-value=0.021  Score=50.87  Aligned_cols=21  Identities=19%  Similarity=0.322  Sum_probs=17.7

Q ss_pred             cEEEEEEecCCCchHHHHHHh
Q 040913          190 LSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      .+.|+|.|=||+||||+|..+
T Consensus         2 Mr~IaisgKGGVGKTT~a~NL   22 (289)
T d2afhe1           2 MRQCAIYGKGGIGKSTTTQNL   22 (289)
T ss_dssp             CEEEEEEECTTSSHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHH
Confidence            467889999999999987655

>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=93.31  E-value=0.019  Score=48.60  Aligned_cols=22  Identities=14%  Similarity=0.231  Sum_probs=19.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|.|+|++|+|||||.+.+..
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~   24 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLK   24 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            5788999999999999998876

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=93.30  E-value=0.023  Score=50.10  Aligned_cols=82  Identities=15%  Similarity=0.013  Sum_probs=49.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCccccccccchHHH------HHHHHHHhCCCCCCC-ccCCCCHHHHHHHHHHHhc-
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNNHVKFYFDCLAWI------LDDIIRSLMPPSRVT-VIIGEDYKLKKSILRDFLT-  260 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~~~~~~F~~~~wv------~~~il~~l~~~~~~~-~~~~~~~~~l~~~l~~~l~-  260 (425)
                      .-+++-|+|.+|+|||||+.++.....-..  ...+|+      -.+.+..++.....- -....+.++..+.+....+ 
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~~q~~g--~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~~  130 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAAAQREG--KTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARS  130 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHH
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCC--CEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHhc
Confidence            456899999999999999988776322111  123344      234455555543211 1123456666666666665 


Q ss_pred             CCeEEEEecccC
Q 040913          261 NKKYFIALDDVC  272 (425)
Q Consensus       261 ~kr~LlVLDdvw  272 (425)
                      ++.-|||+|-+-
T Consensus       131 ~~~~liViDSi~  142 (263)
T d1u94a1         131 GAVDVIVVDSVA  142 (263)
T ss_dssp             TCCSEEEEECGG
T ss_pred             CCCCEEEEECcc
Confidence            445699999884

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.30  E-value=0.023  Score=45.83  Aligned_cols=21  Identities=5%  Similarity=0.218  Sum_probs=18.1

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999887754

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=93.29  E-value=0.022  Score=45.95  Aligned_cols=21  Identities=14%  Similarity=0.124  Sum_probs=18.5

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||...+.+.
T Consensus         5 i~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHcCC
Confidence            569999999999999998663

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {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: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.17  E-value=0.021  Score=46.57  Aligned_cols=21  Identities=14%  Similarity=0.294  Sum_probs=18.5

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999987764

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=93.13  E-value=0.022  Score=48.17  Aligned_cols=20  Identities=25%  Similarity=0.265  Sum_probs=18.1

Q ss_pred             EEEEEecCCCchHHHHHHhh
Q 040913          192 VVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~  211 (425)
                      +|+|+|+.|+||||.|+.+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998653

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {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: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.02  E-value=0.024  Score=45.60  Aligned_cols=21  Identities=14%  Similarity=0.235  Sum_probs=18.5

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999988754

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {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: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.02  E-value=0.024  Score=45.88  Aligned_cols=21  Identities=14%  Similarity=0.234  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||+..+.++
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999887654

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=92.96  E-value=0.014  Score=51.99  Aligned_cols=24  Identities=13%  Similarity=0.171  Sum_probs=17.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..||+|.|.+|+||||+++.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHH
Confidence            356999999999999999987654

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=92.96  E-value=0.025  Score=49.19  Aligned_cols=23  Identities=17%  Similarity=0.238  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999999874

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, 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: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.88  E-value=0.029  Score=45.67  Aligned_cols=24  Identities=13%  Similarity=0.242  Sum_probs=21.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           5 CGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             ccEEEEECCCCCCHHHHHHHHhCC
Confidence            577999999999999999999863

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {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: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.86  E-value=0.031  Score=45.28  Aligned_cols=21  Identities=19%  Similarity=0.376  Sum_probs=18.2

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568999999999999887764

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=92.80  E-value=0.027  Score=47.52  Aligned_cols=21  Identities=24%  Similarity=0.169  Sum_probs=18.9

Q ss_pred             EEEEEEecCCCchHHHHHHhh
Q 040913          191 SVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      -+|+|.|..|+||||+|+.+-
T Consensus         3 ~iIgITG~igSGKStv~~~l~   23 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH
Confidence            589999999999999998764

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=92.80  E-value=0.029  Score=45.55  Aligned_cols=21  Identities=14%  Similarity=0.200  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|+|+|.+|+|||||...+..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999875

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {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: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.79  E-value=0.027  Score=46.38  Aligned_cols=21  Identities=33%  Similarity=0.401  Sum_probs=18.6

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||+..+.++
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999988764

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.79  E-value=0.027  Score=49.41  Aligned_cols=23  Identities=17%  Similarity=0.170  Sum_probs=20.6

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||++.+..
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~G   52 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITG   52 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHHC
Confidence            45899999999999999999874

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {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: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.77  E-value=0.034  Score=45.41  Aligned_cols=24  Identities=17%  Similarity=0.225  Sum_probs=21.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .+.|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           5 SGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999999998864

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {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: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.75  E-value=0.028  Score=45.67  Aligned_cols=22  Identities=14%  Similarity=0.311  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|.+|+|||||.+.+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999987764

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.68  E-value=0.032  Score=45.09  Aligned_cols=21  Identities=19%  Similarity=0.344  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999988764

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.67  E-value=0.028  Score=45.59  Aligned_cols=21  Identities=24%  Similarity=0.363  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            779999999999999987653

>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=92.67  E-value=0.035  Score=51.37  Aligned_cols=46  Identities=17%  Similarity=0.142  Sum_probs=33.6

Q ss_pred             CCcccchhhHHHHHHHHh----------------------------cCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLI----------------------------EGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~----------------------------~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+||.++.++.+...+.                            +.+...+.+..+|+.|+|||.||+.+..
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHh
Confidence            347898888777765442                            1123456688899999999999998754

>d2gjsa1 c.37.1.8 (A:91-258) Rad {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: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.62  E-value=0.03  Score=45.41  Aligned_cols=21  Identities=29%  Similarity=0.264  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999987663

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.61  E-value=0.034  Score=47.62  Aligned_cols=25  Identities=20%  Similarity=0.223  Sum_probs=22.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..+|..|.|+-|.|||||.+++.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            4788999999999999999998764

>d1r2qa_ c.37.1.8 (A:) Rab5a {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: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.48  E-value=0.031  Score=45.35  Aligned_cols=21  Identities=14%  Similarity=0.259  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987754

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.46  E-value=0.032  Score=45.00  Aligned_cols=21  Identities=14%  Similarity=0.362  Sum_probs=18.6

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988764

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {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: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.46  E-value=0.031  Score=45.20  Aligned_cols=21  Identities=24%  Similarity=0.302  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||+..+.++
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999987653

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {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: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.42  E-value=0.032  Score=45.41  Aligned_cols=22  Identities=14%  Similarity=0.324  Sum_probs=18.7

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||...+.++
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4669999999999999887754

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.42  E-value=0.036  Score=45.03  Aligned_cols=21  Identities=38%  Similarity=0.480  Sum_probs=18.5

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            779999999999999987653

>d1kaoa_ c.37.1.8 (A:) Rap2a {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: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.39  E-value=0.037  Score=44.65  Aligned_cols=21  Identities=29%  Similarity=0.452  Sum_probs=18.5

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999888764

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {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: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.36  E-value=0.039  Score=44.50  Aligned_cols=23  Identities=17%  Similarity=0.244  Sum_probs=19.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      .-|.|+|..|+|||||...+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            34778999999999999987653

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {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: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.34  E-value=0.034  Score=45.23  Aligned_cols=21  Identities=10%  Similarity=0.260  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.++
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999987653

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {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: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.33  E-value=0.039  Score=44.47  Aligned_cols=21  Identities=19%  Similarity=0.438  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999988764

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=92.30  E-value=0.036  Score=44.89  Aligned_cols=33  Identities=18%  Similarity=0.099  Sum_probs=23.8

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++..++...+  .+ |.|+|.+|+|||||...+..+
T Consensus         6 ~~~~~~~~k~--~k-I~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1           6 RIWRLFNHQE--HK-VIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             HHHHHHTTSC--EE-EEEEESTTSSHHHHHHHHHTT
T ss_pred             HHHHHhCCCe--EE-EEEECCCCCCHHHHHHHHhcC
Confidence            4454444333  44 669999999999999987764

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {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: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.26  E-value=0.039  Score=44.65  Aligned_cols=21  Identities=24%  Similarity=0.415  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||+|.....++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568899999999999988764

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.24  E-value=0.035  Score=43.96  Aligned_cols=22  Identities=18%  Similarity=0.101  Sum_probs=19.1

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|.+|+|||||...+.+.
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999987764

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {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: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=92.24  E-value=0.024  Score=46.47  Aligned_cols=20  Identities=15%  Similarity=0.199  Sum_probs=18.6

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |+|+|.+|+|||||...+.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            89999999999999999875

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.23  E-value=0.034  Score=46.47  Aligned_cols=23  Identities=13%  Similarity=0.098  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhcC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.|.|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999998764

>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=92.20  E-value=0.033  Score=47.17  Aligned_cols=22  Identities=5%  Similarity=0.074  Sum_probs=19.7

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..|+|-|+-|+||||+++.+.+
T Consensus         4 ~lI~ieG~dGsGKsT~~~~L~~   25 (209)
T d1nn5a_           4 ALIVLEGVDRAGKSTQSRKLVE   25 (209)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5688899999999999998877

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {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: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.19  E-value=0.042  Score=44.54  Aligned_cols=21  Identities=14%  Similarity=0.366  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999887664

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.17  E-value=0.04  Score=45.76  Aligned_cols=21  Identities=14%  Similarity=0.335  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.|+|.+|+|||||...+.++
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            679999999999999988764

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=92.12  E-value=0.037  Score=45.24  Aligned_cols=22  Identities=9%  Similarity=0.105  Sum_probs=19.6

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999998863

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {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: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.11  E-value=0.035  Score=45.22  Aligned_cols=22  Identities=23%  Similarity=0.350  Sum_probs=19.0

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|..|+|||||+..+.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3779999999999999987664

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.09  E-value=0.036  Score=46.39  Aligned_cols=21  Identities=19%  Similarity=0.254  Sum_probs=18.8

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .|+|-|.-|+||||+++.+.+
T Consensus         2 lI~ieG~dGsGKST~~~~L~~   22 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG   22 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999998775

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=92.08  E-value=0.036  Score=49.13  Aligned_cols=23  Identities=17%  Similarity=0.125  Sum_probs=18.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhh
Q 040913          189 GLSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .+++|.+.|=||+||||+|..+.
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA   29 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATA   29 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHH
T ss_pred             CCeEEEEECCCcChHHHHHHHHH
Confidence            36788899999999999765543

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=91.97  E-value=0.031  Score=45.96  Aligned_cols=21  Identities=10%  Similarity=0.116  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|+|+|.+|+|||||...+.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            389999999999999999865

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=91.97  E-value=0.042  Score=46.76  Aligned_cols=23  Identities=17%  Similarity=0.252  Sum_probs=19.0

Q ss_pred             cEEEEEE-ecCCCchHHHHHHhhc
Q 040913          190 LSVVAIL-DSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~Iv-G~gGvGKTtLa~~v~~  212 (425)
                      .+||+|. |-||+||||+|..+..
T Consensus         1 ~kvIav~s~KGGvGKTtia~nlA~   24 (232)
T d1hyqa_           1 VRTITVASGKGGTGKTTITANLGV   24 (232)
T ss_dssp             CEEEEEEESSSCSCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCChHHHHHHHHHH
Confidence            3789998 7899999999987553

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=91.92  E-value=0.03  Score=48.29  Aligned_cols=23  Identities=13%  Similarity=0.235  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.+++|+|+.|.|||||.+.+..
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999998764

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=91.91  E-value=0.094  Score=45.74  Aligned_cols=41  Identities=10%  Similarity=0.153  Sum_probs=31.0

Q ss_pred             hhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          173 ERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       173 ~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...+.++...+.......--|.++|..|+|||||...++..
T Consensus        15 ~~~l~e~~~~l~~~~~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          15 QTKLLELLGNLKQEDVNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHHHTTCCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHHhhcCCCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            34455666666665545556789999999999999999874

>d1c1ya_ c.37.1.8 (A:) Rap1A {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: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.88  E-value=0.046  Score=44.08  Aligned_cols=21  Identities=24%  Similarity=0.430  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||+|...+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            578999999999999987654

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.80  E-value=0.04  Score=46.14  Aligned_cols=22  Identities=14%  Similarity=0.066  Sum_probs=19.5

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||||...+.+.
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5889999999999999988764

>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=91.77  E-value=0.038  Score=45.98  Aligned_cols=24  Identities=13%  Similarity=-0.009  Sum_probs=20.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.++.|.|.+|+||||||.++..
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~   45 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAV   45 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHH
Confidence            356889999999999999988765

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.76  E-value=0.042  Score=44.44  Aligned_cols=21  Identities=14%  Similarity=0.281  Sum_probs=18.1

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|..|+|||+|...+.++
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999987664

>d1kmqa_ c.37.1.8 (A:) RhoA {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: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.70  E-value=0.044  Score=44.66  Aligned_cols=22  Identities=14%  Similarity=0.179  Sum_probs=18.5

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||+|...+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3568899999999999887664

>d1i2ma_ c.37.1.8 (A:) Ran {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: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.62  E-value=0.036  Score=44.99  Aligned_cols=21  Identities=19%  Similarity=0.403  Sum_probs=17.2

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999987664

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=91.60  E-value=0.043  Score=44.57  Aligned_cols=25  Identities=12%  Similarity=0.084  Sum_probs=20.5

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      ..+ |.++|.+|+|||||...+.++.
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcCC
Confidence            466 5589999999999999987653

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=91.55  E-value=0.046  Score=43.94  Aligned_cols=21  Identities=14%  Similarity=0.116  Sum_probs=18.0

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+...
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            568899999999999987654

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {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: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.53  E-value=0.056  Score=43.67  Aligned_cols=22  Identities=23%  Similarity=0.309  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999987654

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=91.51  E-value=0.066  Score=46.95  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=18.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++.|.|.+|+||||++.++..
T Consensus        36 ~l~vi~G~~G~GKT~~~~~la~   57 (277)
T d1cr2a_          36 EVIMVTSGSGMGKSTFVRQQAL   57 (277)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHH
Confidence            4777899999999999877654

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {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: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=91.42  E-value=0.046  Score=44.42  Aligned_cols=25  Identities=20%  Similarity=0.003  Sum_probs=21.4

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ...-|+|+|.+++|||||..++...
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4667999999999999999988653

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {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: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.39  E-value=0.057  Score=44.41  Aligned_cols=22  Identities=14%  Similarity=0.209  Sum_probs=18.9

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||+|...+.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3778999999999999887764

>d1mh1a_ c.37.1.8 (A:) Rac {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: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.35  E-value=0.049  Score=44.70  Aligned_cols=22  Identities=14%  Similarity=0.187  Sum_probs=18.7

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.|+|.+|+|||+|...+.++
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3678999999999999887664

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=91.29  E-value=0.058  Score=43.59  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=19.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +.-|.++|.+|+|||||...+.++
T Consensus         4 ~~KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           4 LHKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCcCHHHHHHHHHhC
Confidence            345779999999999999987654

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {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: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.15  E-value=0.052  Score=44.22  Aligned_cols=21  Identities=19%  Similarity=0.373  Sum_probs=18.4

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||...+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999987653

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=91.15  E-value=0.049  Score=49.24  Aligned_cols=23  Identities=13%  Similarity=0.078  Sum_probs=19.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -.++.++|++|+|||.||+.+..
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~  145 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGE  145 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHH
T ss_pred             CceEEEECCCCccHHHHHHHHHH
Confidence            35566789999999999999988

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {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: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.12  E-value=0.053  Score=44.01  Aligned_cols=21  Identities=19%  Similarity=0.256  Sum_probs=18.1

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|.++|.+|+|||||++.+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            367899999999999998765

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.10  E-value=0.062  Score=43.47  Aligned_cols=21  Identities=14%  Similarity=0.458  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|..|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            567899999999999988764

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.08  E-value=0.053  Score=44.44  Aligned_cols=21  Identities=38%  Similarity=0.485  Sum_probs=18.5

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999987763

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.07  E-value=0.08  Score=45.37  Aligned_cols=25  Identities=16%  Similarity=0.118  Sum_probs=21.4

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.-+++-|.|.+|+||||||.++..
T Consensus        34 p~G~~~li~G~pGsGKT~~~lq~~~   58 (254)
T d1pzna2          34 ETQAITEVFGEFGSGKTQLAHTLAV   58 (254)
T ss_dssp             ESSEEEEEEESTTSSHHHHHHHHHH
T ss_pred             cCCEEEEEEcCCCCCHHHHHHHHHH
Confidence            3467999999999999999987754

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.06  E-value=0.052  Score=44.54  Aligned_cols=20  Identities=10%  Similarity=0.117  Sum_probs=17.3

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++|-+|+|||+|......
T Consensus         5 ivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            56899999999999988654

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=91.05  E-value=0.057  Score=46.36  Aligned_cols=22  Identities=9%  Similarity=-0.025  Sum_probs=20.2

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+|+|.|..|+||||+|+.+.+
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999998865

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.00  E-value=0.052  Score=44.85  Aligned_cols=18  Identities=17%  Similarity=0.331  Sum_probs=16.4

Q ss_pred             EEEEecCCCchHHHHHHh
Q 040913          193 VAILDSSGFDKTAFAADT  210 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v  210 (425)
                      |.++|.+|+|||||....
T Consensus         5 ivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            568999999999999887

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.93  E-value=0.068  Score=43.72  Aligned_cols=21  Identities=19%  Similarity=0.208  Sum_probs=18.3

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|..|+|||+|++.+.++
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568999999999999987764

>d1wmsa_ c.37.1.8 (A:) Rab9a {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: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.88  E-value=0.062  Score=43.56  Aligned_cols=22  Identities=23%  Similarity=0.354  Sum_probs=18.5

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|.+|+|||||...+.++
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3779999999999999877653

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {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: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.87  E-value=0.062  Score=45.67  Aligned_cols=21  Identities=24%  Similarity=0.420  Sum_probs=18.0

Q ss_pred             EEEEEE-ecCCCchHHHHHHhh
Q 040913          191 SVVAIL-DSSGFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~Iv-G~gGvGKTtLa~~v~  211 (425)
                      +||+|+ +-||+||||+|..+.
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA   24 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLS   24 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCcHHHHHHHHH
Confidence            689999 669999999987764

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G 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: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=90.87  E-value=0.061  Score=42.78  Aligned_cols=20  Identities=15%  Similarity=0.130  Sum_probs=18.0

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |+++|.+|+|||||..++..
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999988864

>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=90.86  E-value=0.079  Score=50.18  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=33.1

Q ss_pred             CCcccchhhHHHHHHHHhc-------C-----CCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          167 LDISEFERAREEWFDLLIE-------G-----PIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       167 ~~~vGr~~~~~~l~~~L~~-------~-----~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ..+||.++.+..+--.+..       +     +-..+=|.++|+.|+|||.||+.+..
T Consensus        14 ~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk   71 (443)
T d1g41a_          14 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   71 (443)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHH
Confidence            3578888888777554421       1     11244577899999999999999977

>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=90.85  E-value=0.089  Score=44.67  Aligned_cols=24  Identities=8%  Similarity=-0.004  Sum_probs=20.6

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-+++-|.|.+|+|||||+.++..
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~   56 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAV   56 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH
Confidence            457899999999999999987654

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {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: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=90.69  E-value=0.089  Score=42.26  Aligned_cols=25  Identities=16%  Similarity=0.139  Sum_probs=21.8

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhcC
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ..-+|.+.|.=|+||||+++.+.+.
T Consensus        32 ~g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          32 KAIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEecCCCccHHHHHHHHHhh
Confidence            3568999999999999999998863

>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=90.59  E-value=0.1  Score=44.54  Aligned_cols=25  Identities=8%  Similarity=0.057  Sum_probs=21.8

Q ss_pred             CCcEEEEEEecCCCchHHHHHHhhc
Q 040913          188 IGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       188 ~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.-+++-|.|.+|+|||++|.++..
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~   59 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCV   59 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999988764

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=90.54  E-value=0.064  Score=43.84  Aligned_cols=22  Identities=23%  Similarity=0.292  Sum_probs=19.2

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|+|+|..|+|||||...+.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            3789999999999999888764

>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=90.33  E-value=0.09  Score=44.63  Aligned_cols=24  Identities=21%  Similarity=0.129  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-.++.|.|.+|+|||++|.++..
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~   56 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCV   56 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHH
Confidence            457899999999999999988864

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G 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: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.31  E-value=0.069  Score=43.62  Aligned_cols=22  Identities=9%  Similarity=0.154  Sum_probs=18.7

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|.++|.+|+|||||...+.++
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3678999999999999987664

>d2ngra_ c.37.1.8 (A:) CDC42 {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: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.27  E-value=0.083  Score=43.56  Aligned_cols=21  Identities=14%  Similarity=0.222  Sum_probs=17.8

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |.++|.+|+|||+|...+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999887654

>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=90.19  E-value=0.068  Score=44.85  Aligned_cols=22  Identities=18%  Similarity=0.093  Sum_probs=19.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.|+|-|+-|+||||+++.+.+
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~   24 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVE   24 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4688999999999999998876

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.14  E-value=0.071  Score=45.14  Aligned_cols=23  Identities=17%  Similarity=0.052  Sum_probs=20.4

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+.|+|-|+-|+||||+++.+.+
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~   25 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYK   25 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHH
Confidence            35789999999999999998876

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.74  E-value=0.081  Score=43.46  Aligned_cols=20  Identities=15%  Similarity=0.213  Sum_probs=17.5

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++|.+|+|||+|...+..
T Consensus         5 iv~lG~~~vGKTsll~r~~~   24 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRI   24 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            56899999999999998755

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.64  E-value=0.14  Score=43.64  Aligned_cols=35  Identities=17%  Similarity=0.161  Sum_probs=26.9

Q ss_pred             hHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc
Q 040913          175 AREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN  214 (425)
Q Consensus       175 ~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~  214 (425)
                      .++.|.++|..     +...++|.+|+|||||...+..+.
T Consensus        85 g~~~L~~~l~~-----kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          85 GIEELKEYLKG-----KISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             THHHHHHHHSS-----SEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             hHhhHHHHhcC-----CeEEEECCCCCCHHHHHHhhcchh
Confidence            35777777742     356789999999999999987743

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.52  E-value=0.053  Score=44.00  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=8.2

Q ss_pred             EEEEecCCCchHHHHHHhhc
Q 040913          193 VAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~  212 (425)
                      |.++|.+|+|||||...+.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999987665

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal 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: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.28  E-value=0.2  Score=44.14  Aligned_cols=34  Identities=18%  Similarity=0.111  Sum_probs=28.0

Q ss_pred             HHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcC
Q 040913          180 FDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       180 ~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      ++.|..-+..+.||+|+|.-+.|||||...++..
T Consensus        22 l~~l~~~~~~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          22 LKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             HHHHHTCCSBEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             HHHHHcCCCCEEEEEEECCCCCCHHHHHHHHcCC
Confidence            4455555557999999999999999999998873

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

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: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=88.37  E-value=0.15  Score=45.06  Aligned_cols=34  Identities=24%  Similarity=0.064  Sum_probs=23.5

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.++.|..=-. -.-++|.|.+|+|||+|+..+.+
T Consensus        57 raID~l~pig~-GQr~~If~~~g~GKt~ll~~~~~   90 (285)
T d2jdia3          57 KAVDSLVPIGR-GQRELIIGDRQTGKTSIAIDTII   90 (285)
T ss_dssp             HHHHHHSCCBT-TCBCEEEESTTSSHHHHHHHHHH
T ss_pred             eEEecccCccC-CCEEEeecCCCCChHHHHHHHHH
Confidence            45666654221 23468899999999999876654

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=88.34  E-value=0.11  Score=44.03  Aligned_cols=22  Identities=9%  Similarity=0.078  Sum_probs=18.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-|.++|.+|+|||||......
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3467999999999999988754

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {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: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=88.24  E-value=0.13  Score=45.36  Aligned_cols=24  Identities=17%  Similarity=0.072  Sum_probs=21.1

Q ss_pred             CcEEEEEEecCCCchHHHHHHhhc
Q 040913          189 GLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +.+-|+|+|.+|.|||||+.++..
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHH
Confidence            477899999999999999988754

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.96  E-value=0.042  Score=43.72  Aligned_cols=21  Identities=14%  Similarity=0.281  Sum_probs=18.7

Q ss_pred             EEEEecCCCchHHHHHHhhcC
Q 040913          193 VAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~~~  213 (425)
                      |+++|.+|+|||||...+.+.
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999998753

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.95  E-value=0.13  Score=44.13  Aligned_cols=23  Identities=13%  Similarity=0.046  Sum_probs=19.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -+++.|.|+...||||+.+.+.-
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l   63 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTAL   63 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHH
Confidence            46788999999999999988754

>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=87.65  E-value=0.13  Score=43.27  Aligned_cols=22  Identities=23%  Similarity=0.131  Sum_probs=18.7

Q ss_pred             CcEEEEEEecCCCchHHHHHHh
Q 040913          189 GLSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       189 ~~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      .-.++-|.|.+|+|||+||.++
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~   46 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQF   46 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHH
Confidence            4568889999999999999664

>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=87.12  E-value=0.16  Score=44.14  Aligned_cols=22  Identities=23%  Similarity=0.283  Sum_probs=18.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..|+|.+|+|||||+.++.-
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            4667899999999999876543

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=87.02  E-value=0.15  Score=43.38  Aligned_cols=23  Identities=17%  Similarity=0.251  Sum_probs=20.0

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .++|+|+|..+.|||||+..+..
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHh
Confidence            35799999999999999988754

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=86.82  E-value=0.18  Score=44.08  Aligned_cols=22  Identities=23%  Similarity=0.383  Sum_probs=19.5

Q ss_pred             cEEEEEEecCCCchHHHHHHhh
Q 040913          190 LSVVAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~  211 (425)
                      .+-|+|+|..|.|||||+.++.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            4679999999999999998874

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=86.09  E-value=0.22  Score=41.38  Aligned_cols=21  Identities=10%  Similarity=0.026  Sum_probs=16.9

Q ss_pred             EEEEEEecC-CCchHHHHHHhh
Q 040913          191 SVVAILDSS-GFDKTAFAADTY  211 (425)
Q Consensus       191 ~vi~IvG~g-GvGKTtLa~~v~  211 (425)
                      +.+-|.|-| |+||||++-.+.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La   23 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALL   23 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHH
Confidence            457899998 999999876554

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {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: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=85.75  E-value=0.48  Score=40.11  Aligned_cols=111  Identities=15%  Similarity=0.086  Sum_probs=54.0

Q ss_pred             EEEEEEecCCCchHHHHHHhhcCcccc--ccccc--hHHH--HHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhc--CC
Q 040913          191 SVVAILDSSGFDKTAFAADTYNNNHVK--FYFDC--LAWI--LDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLT--NK  262 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~~~~~~--~~F~~--~~wv--~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~--~k  262 (425)
                      +++.|.|+...||||+.+.+.-..-..  ..|-+  .+.+  .+.|...+...... .........-...+...++  ++
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~-~~~~StF~~el~~~~~il~~~~~  114 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDL-AGGKSTFMVEMEEVALILKEATE  114 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC-------CCSHHHHHHHHHHHHHHHCCT
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccc-cCCccHHHHhHHHHHHHhccCCC
Confidence            367899999999999998875421000  00000  0000  11111111111110 0111222333344444443  68


Q ss_pred             eEEEEecccCCChh-------hHHHHHhhCCCCCCCcEEEEecCChhHHH
Q 040913          263 KYFIALDDVCHNIE-------IWDDLEEVLPDNQNGSRVLITVINPSLLT  305 (425)
Q Consensus       263 r~LlVLDdvw~~~~-------~~~~l~~~l~~~~~gskIivTTR~~~va~  305 (425)
                      +.|+++|.+....+       .|.-+ ..|.  ..++++++||...++..
T Consensus       115 ~sLvliDE~~~gT~~~eg~ala~ail-e~L~--~~~~~~i~tTH~~eL~~  161 (224)
T d1ewqa2         115 NSLVLLDEVGRGTSSLDGVAIATAVA-EALH--ERRAYTLFATHYFELTA  161 (224)
T ss_dssp             TEEEEEESTTTTSCHHHHHHHHHHHH-HHHH--HHTCEEEEECCCHHHHT
T ss_pred             CcEEeecccccCcchhhhcchHHHHH-HHHh--hcCcceEEeeechhhhh
Confidence            89999999963221       22222 2221  23678999999877654

>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=85.73  E-value=0.2  Score=45.13  Aligned_cols=98  Identities=16%  Similarity=0.106  Sum_probs=54.1

Q ss_pred             EEEEEecCCCchHHHHHHhhcCc----c---ccccccchHHHHHHHHHHhCCCCCCCccCCCCHHHHHHHHHHHhcCCeE
Q 040913          192 VVAILDSSGFDKTAFAADTYNNN----H---VKFYFDCLAWILDDIIRSLMPPSRVTVIIGEDYKLKKSILRDFLTNKKY  264 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~~----~---~~~~F~~~~wv~~~il~~l~~~~~~~~~~~~~~~~l~~~l~~~l~~kr~  264 (425)
                      -|.|.|..|+||||+.+.+.+..    +   +.+.++...          ..............-...+.++..|+...=
T Consensus       168 nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l----------~~~~~~~~~~~~~~~~~~~ll~~~lR~~pd  237 (323)
T d1g6oa_         168 NVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVF----------KHHKNYTQLFFGGNITSADCLKSCLRMRPD  237 (323)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCC----------SSCSSEEEEECBTTBCHHHHHHHHTTSCCS
T ss_pred             CEEEEeeccccchHHHHHHhhhcccccceeeccchhhhhc----------ccccccceeccccchhHHHHHHHHhccCCC
Confidence            37889999999999999887621    1   111111100          000000000001111344557778887777


Q ss_pred             EEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhH
Q 040913          265 FIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSL  303 (425)
Q Consensus       265 LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~v  303 (425)
                      -||+..+. +.+.|+-+.. ...+..|  ++.|....+.
T Consensus       238 ~iivgEiR-~~ea~~~l~a-~~tGh~g--~~tT~Ha~s~  272 (323)
T d1g6oa_         238 RIILGELR-SSEAYDFYNV-LCSGHKG--TLTTLHAGSS  272 (323)
T ss_dssp             EEEESCCC-STHHHHHHHH-HHTTCSC--EEEEECCSSH
T ss_pred             cccCCccC-chhHHHHHHH-HHhcCCc--EEEEECCCCH
Confidence            89999999 8888876554 3333334  4555544443

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=85.72  E-value=0.2  Score=40.86  Aligned_cols=22  Identities=27%  Similarity=0.211  Sum_probs=18.8

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-|.|.|.+|+||||||..+..
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            4578899999999999988665

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=85.58  E-value=0.21  Score=40.59  Aligned_cols=21  Identities=14%  Similarity=0.131  Sum_probs=19.1

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      -|+|+|..++|||||..++..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            489999999999999998875

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=85.40  E-value=0.22  Score=40.58  Aligned_cols=22  Identities=32%  Similarity=0.317  Sum_probs=18.6

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-|.|.|.+|+||||||..+..
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            4577899999999999988665

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=84.46  E-value=0.25  Score=39.98  Aligned_cols=22  Identities=27%  Similarity=0.249  Sum_probs=18.4

Q ss_pred             EEEEEEecCCCchHHHHHHhhc
Q 040913          191 SVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       191 ~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .-|.|.|.+|+||||||-....
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~   37 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIK   37 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEEeCCCCCHHHHHHHHHH
Confidence            4577999999999999977654

>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=83.13  E-value=0.38  Score=39.93  Aligned_cols=36  Identities=11%  Similarity=0.082  Sum_probs=27.4

Q ss_pred             HHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          176 REEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       176 ~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      ...+..+|. +.++-..+.++|+++.|||++|..+.+
T Consensus        40 l~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~   75 (205)
T d1tuea_          40 LGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIH   75 (205)
T ss_dssp             HHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHH
Confidence            455555663 445668899999999999999987765

>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=82.83  E-value=0.56  Score=40.82  Aligned_cols=35  Identities=9%  Similarity=0.005  Sum_probs=27.1

Q ss_pred             HHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhc
Q 040913          178 EWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       178 ~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .+..+|....+.-..+-++|+|+.|||+++..+.+
T Consensus        92 ~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~  126 (267)
T d1u0ja_          92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHH
Confidence            34455655545677888999999999999988776

>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=82.70  E-value=0.27  Score=44.97  Aligned_cols=21  Identities=24%  Similarity=0.207  Sum_probs=17.0

Q ss_pred             cEEEEEEecCCCchHHHHHHh
Q 040913          190 LSVVAILDSSGFDKTAFAADT  210 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v  210 (425)
                      .++..|.|++|.||||++..+
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~  183 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKL  183 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHH
Confidence            357888999999999987554

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

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: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=82.10  E-value=0.37  Score=43.51  Aligned_cols=24  Identities=8%  Similarity=0.034  Sum_probs=20.7

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +-.|.|=|.=|+||||+++.+.+.
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~   29 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASA   29 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHH
Confidence            456778899999999999999884

>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=81.71  E-value=0.12  Score=42.18  Aligned_cols=21  Identities=19%  Similarity=0.196  Sum_probs=17.4

Q ss_pred             EEEEEecCCCchHHHHHHhhc
Q 040913          192 VVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      +..|+|+.|+||||+..++.-
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~   46 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVT   46 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            445789999999999988763

>d1jala1 c.37.1.8 (A:1-278) YchF GTP-binding protein N-terminal 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: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=81.69  E-value=0.34  Score=42.40  Aligned_cols=22  Identities=9%  Similarity=0.083  Sum_probs=19.3

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      -|+|||++.+|||||-..+-+.
T Consensus         4 ~~GivG~Pn~GKSTlf~~lt~~   25 (278)
T d1jala1           4 KCGIVGLPNVGKSTLFNALTKA   25 (278)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHCC
Confidence            4899999999999999887754

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {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: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=81.59  E-value=0.36  Score=40.19  Aligned_cols=19  Identities=21%  Similarity=0.228  Sum_probs=17.5

Q ss_pred             EEEEecCCCchHHHHHHhh
Q 040913          193 VAILDSSGFDKTAFAADTY  211 (425)
Q Consensus       193 i~IvG~gGvGKTtLa~~v~  211 (425)
                      |+|+|..+.|||||+.++.
T Consensus         6 i~iiGhvd~GKSTL~~~Ll   24 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALT   24 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHH
Confidence            8899999999999998875

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=81.44  E-value=0.16  Score=43.43  Aligned_cols=22  Identities=14%  Similarity=0.194  Sum_probs=18.4

Q ss_pred             EEEEEecCCCchHHHHHHhhcC
Q 040913          192 VVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       192 vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..++|.+|+|||||...+..+
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             eEEEECCCCccHHHHHHhhccH
Confidence            3458899999999999998874

>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=81.18  E-value=0.99  Score=41.63  Aligned_cols=120  Identities=12%  Similarity=0.114  Sum_probs=66.8

Q ss_pred             ccchhhHHHHHHHHhcCCCCcEEEEEEecCCCchHHHHHHhhcCc-cccccccchHHHHHHHHHHhCCCCCCC-------
Q 040913          170 SEFERAREEWFDLLIEGPIGLSVVAILDSSGFDKTAFAADTYNNN-HVKFYFDCLAWILDDIIRSLMPPSRVT-------  241 (425)
Q Consensus       170 vGr~~~~~~l~~~L~~~~~~~~vi~IvG~gGvGKTtLa~~v~~~~-~~~~~F~~~~wv~~~il~~l~~~~~~~-------  241 (425)
                      .|.....-+.+..+....  .++|.|.|+.|+||||....+.+.- +-..++    .       .+-.+....       
T Consensus       140 LG~~~~~~~~l~~l~~~~--~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i----~-------tiEdPiE~~~~~~~q~  206 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKRP--HGIILVTGPTGSGKSTTLYAGLQELNSSERNI----L-------TVEDPIEFDIDGIGQT  206 (401)
T ss_dssp             SCCCHHHHHHHHHHHTSS--SEEEEEECSTTSCHHHHHHHHHHHHCCTTSCE----E-------EEESSCCSCCSSSEEE
T ss_pred             hcccHHHHHHHHHHHhhh--hceEEEEcCCCCCccHHHHHHhhhhcCCCceE----E-------EeccCcccccCCCCee
Confidence            465544433344444333  6899999999999999887776521 111111    0       000000000       


Q ss_pred             ccCCCCHHHHHHHHHHHhcCCeEEEEecccCCChhhHHHHHhhCCCCCCCcEEEEecCChhHHHH
Q 040913          242 VIIGEDYKLKKSILRDFLTNKKYFIALDDVCHNIEIWDDLEEVLPDNQNGSRVLITVINPSLLTS  306 (425)
Q Consensus       242 ~~~~~~~~~l~~~l~~~l~~kr~LlVLDdvw~~~~~~~~l~~~l~~~~~gskIivTTR~~~va~~  306 (425)
                      .....+.......++..|+...=.|++..+. +.+.-.....+   ...|-.|+-|-...+....
T Consensus       207 ~v~~~~~~~~~~~l~~~lR~dPDvi~igEiR-d~~ta~~a~~a---a~tGhlV~tTlHa~~a~~~  267 (401)
T d1p9ra_         207 QVNPRVDMTFARGLRAILRQDPDVVMVGEIR-DLETAQIAVQA---SLTGHLVMSTLHTNTAVGA  267 (401)
T ss_dssp             ECBGGGTBCHHHHHHHHGGGCCSEEEESCCC-SHHHHHHHHHH---HHTTCEEEEEECCSSSHHH
T ss_pred             eecCCcCCCHHHHHHHHHhhcCCEEEecCcC-ChHHHHHHHHH---HhcCCeEEEEeccCchHhh
Confidence            0111122345677888888888889999998 66544333222   2346677777666665544

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

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: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=80.85  E-value=0.4  Score=43.14  Aligned_cols=24  Identities=25%  Similarity=0.065  Sum_probs=20.2

Q ss_pred             cEEEEEEecCCCchHHHHHHhhcC
Q 040913          190 LSVVAILDSSGFDKTAFAADTYNN  213 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~~  213 (425)
                      +..|.|=|.=|+||||+++.+.+.
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHH
Confidence            445888999999999999999763

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.60  E-value=0.45  Score=44.06  Aligned_cols=23  Identities=22%  Similarity=0.289  Sum_probs=19.9

Q ss_pred             cEEEEEEecCCCchHHHHHHhhc
Q 040913          190 LSVVAILDSSGFDKTAFAADTYN  212 (425)
Q Consensus       190 ~~vi~IvG~gGvGKTtLa~~v~~  212 (425)
                      .--|+|+|.+|+|||||...+..
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            34589999999999999998874